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Malus sieversii: A Diverse Central Asian Apple Species in the USDA-ARS National Plant Germplasm System
Abstract
There are several Central Asian Malus species and varieties in the USDA-ARS National Plant Germplasm System (NPGS) apple collection. Malus sieversii is the most comprehensively collected species native to Central Asia. Other taxa such as M. sieversii var. kirghisorum, M. sieversii var. turkmenorum, M. pumila, and M. pumila var. niedzwetzkyana have primarily been donated to the collection by other institutions and arboreta. We sought to determine if genetic and/or phenotypic differences among the individuals that make up the gene pools of these taxa in the NPGS exhibit unique characteristics. Genetic data, based on microsatellite analyses, suggested that the diversity within each taxa is significantly greater than that among taxa. Trait data also revealed very few differences among taxa, the primary characteristic being the dark red fruit coloration and tinted flesh color of the accessions assigned to M. pumila var. niedzwetzkyana resulting from a known single-gene mutation in anthocyanin production. We found that M. sieversii is a highly diverse species with a range in genetic and phenotypic trait variation that includes the characteristics of the other Central Asian taxa of interest. We conclude that the gene pools that comprise the accessions within the NPGS Central Asian Malus collection are highly overlapping with respect to both phenotypic traits and genotypic characters.
... In China, M. sieversii forms wild apple forests from which fruit is collected, but it is not planted in orchards. It is recognized as an important source of germplasm (Volk et al., 2013;Cornille et al., 2014;Cui et al., 2019). Malus sieversii is likely a progenitor species of the domesticated apple, M. domestica (Velasco et al., 2010). ...
... Breeding material may be imported into collections/breeding programmes, in the form of seeds or budwood (e.g. M. sieversii and M. orientalis - Volk et al., 2013). France has a very active breeding programme for Malus, Pyrus, and Prunus and budwoods from China have been imported in the quarantine station (data from 2014-2017; Larguier et al., 2018). ...
... Malus sieversii is found only in the mountains of Central Asia, including southern Kazakhstan, eastern Uzbekistan, Kyrgyzstan, Tajikistan, Turkmenistan, and Xinjiang (China) (Fig 9.4;Volk et al., 2013). In Central Asia, wild apple and other wild fruit trees together form ancient forests (Tian et al., 2022). ...
... kirghisorum, M. sieversii var. turkmenorum, and M. sieversii f. niedzwetzkyana [41,44]. Over time, these subgroups have been placed in a wide range of botanical classes such as independent species, subspecies, varietals, and forms likely due to the distinct morphological differences from M. sieversii. ...
... For example, Dzhangaliev et al. [41] classified the red f leshed M. sieversii apples as M. niedzwetzkyana based on morphological observations. Volk et al. [44] with limited SSR marker data found evidence of highly overlapping gene pools between these red f leshed variants previously characterized as Malus pumila var. niedzwetzkyana and accessions labeled M. sieversii, M. sieversii var. ...
... kirghisorum, and M. pumila. More in-depth genetic analyses support that these groups are not discernable of outside of a common taxon of M. sieversii [35,[44][45][46]. Limited studies suggest that M. sieversii var. ...
Apples are one of the most valued tree fruit crops around the world. Currently, a few highly popular and economically successful apple cultivars dominate the commercial production and serve as main genetic contributors to the development of new apple cultivars. This limited level of genetic diversity grown as a clonally propagated monoculture renders the apple industry vulnerable to the wide range of weather events, pests, and pathogens. Wild apple species are an excellent source of beneficial alleles for the wide range of biotic and abiotic stressors challenging apple production. However, the biological barriers of breeding with small-fruited wild apples greatly limit their use. Using a closely related wild species of apple such as Malus sieversii can improve the efficiency of breeding efforts and broaden the base of available genetics. M. sieversii is the main progenitor of the domesticated apple, native to Central Asia. The similarity of fruit morphology to domesticated apples and resistances to abiotic and biotic stresses makes it appealing for apple breeding programs. However, this important species is under threat of extinction in its native range. Preserving the wild apple forests in Central Asia is vital for ensuring the sustainable protection of this important genetic resource. The insufficient awareness about the complete range of challenges and opportunities associated with M. sieversii hinders the maximization of its potential benefits. This review aims to provide comprehensive information on the cultural and historical context of M. sieversii, current genetic knowledge for breeding, and the conservation challenges of wild apple forests.
... It is located in Emin and Yumin Counties of Tacheng area, Xinyuan, Gongliu and Huocheng Counties of Ili area in Xinjiang Uygur Autonomous (XJUA) Region, China. It is rich in intraspecific variation and has strong resistance, high yield, dwarf and other characters, and is often used in rootstock grafting, cross breeding, and is also important for introduction, domestication and germplasm resources (Richards et al. 2009;Volk et al. 2013;Wang et al. 2018). It plays an irreplaceable role in the study of germplasm conservation and genetic development (Yan et al. 2008;Richards et al. 2009;Volk et al. 2013). ...
... It is rich in intraspecific variation and has strong resistance, high yield, dwarf and other characters, and is often used in rootstock grafting, cross breeding, and is also important for introduction, domestication and germplasm resources (Richards et al. 2009;Volk et al. 2013;Wang et al. 2018). It plays an irreplaceable role in the study of germplasm conservation and genetic development (Yan et al. 2008;Richards et al. 2009;Volk et al. 2013). This species has been listed in the index of China's endangered secondary pro-tected plants (Fu 1991). ...
... In recent years, M. sieversii is facing an unprecedented crisis of survival, mainly in terms of its shrinking area, reduction of biological species, single community structure, and destruction of population renewal (Volk et al. 2013). According to previous studies in the wild, it was found that the problem of pests and diseases of M. sieversii is very prominent (Li and Zhang 2018). ...
Apple tree canker is a serious disease caused by species of Cytospora. Xinjiang Uygur Autonomous Region is one of the most important apple-producing areas in China. However, losses due to apple Cytospora canker have seriously damaged the apple industry and affected the economic development of the apple growers in this region. In this study, we used morphological characteristics combined with multilocus phylogenetic analyses of the ITS, act, rpb2, tef1 and tub2 loci to identify isolates from apple (Malus domestica) and wild apple (M. sieversii). As a result, C. hippophaopsissp. nov. from M. sieversii and C. shawanensissp. nov. from M. domestica were discovered and proposed herein. Pathogenicity tests were further conducted on 13 varieties of apple and wild apple, which confirmed C. hippophaopsis and C. shawanensis as canker pathogens. Meanwhile, C. hippophaopsis is generally more aggressive than C. shawanensis on the tested varieties of apple and wild apple.
... Malus sieversii, a progenitor of the domesticated apple, represents a reservoir of genetic diversity [8,9]. Native to Central Asian montane forests, M. sieversii trees exhibit considerable phenotypic variability [10]. ...
... Therefore, it is considered to be an important reservoir of genetic diversity for many biotic and abiotic stress tolerance traits [10,44,45]. Some M. sieversiii genotypes have also been recognized for their fruit-quality traits [9,10]. Jurick et al. [46] identified postharvest disease resistance to both blue mold (Penicillium expansum) and Colletotrichum acumatum and Norelli et al. [6] used the GMAL4593 (PI 613981 × "Royal Gala") mapping population to identify a major QTL (contributed by the M. sieversii parent) for blue mold resistance. ...
... While some of these encoded proteins may also function as bark storage proteins (BSPs; [61]), a majority of the inserts were identified as biotic stress-related encode receptors for fungal and bacterial pathogens. M. sieversii is also noted for its disease resistance in its natural range and this was a key factor in prioritizing its collection [9,10]. ...
Malus sieversii is considered the progenitor of modern apple (Malus pumila) cultivars and to represent a valuable source of genetic diversity. Despite the importance of M. sieversii as a source of disease resistance, stress tolerance, and novel fruit traits, little is known about gene function and diversity in M. sieversii. Notably, a publicly annotated genome sequence for this species is not available. In the current study, the FOX (Full-length cDNA OvereXpressing) gene hunting system was used to construct a library of transgenic lines of Arabidopsis in which each transgenic line overexpresses a full-length gene obtained from a cDNA library of the PI619283 accession of M. sieversii. The cDNA library was constructed from mRNA obtained from bark tissues collected in late fall–early winter, a time at which many abiotic stress-adaptative genes are expressed. Over 4000 apple FOX Arabidopsis lines have been established from the pool of transgenic seeds and cDNA inserts corresponding to various Gene Ontology (GO) categories have been identified. A total of 160 inserts appear to be novel, with no or limited homology to M. pumila, Arabidopsis, or poplar. Over 1300 lines have also been screened for freezing resistance. The constructed library of transgenic lines provides a valuable genetic resource for exploring gene function and diversity in Malus sieversii. Notably, no such library of t-DNA lines currently exists for any Malus species.
... Many of these species around the world are now at risk of extinction due to a combination of escalating human activities and natural events [12,14,15]. Kazakhstan, with its rich tapestry of natural landscapes and unparalleled botanical diversity [16][17][18], is no exception to this alarming trend. Within its borders, 13 species of the Rosaceae family are considered endangered, earning them a place in the Red Book of Kazakhstan: Cotoneaster karatavicus Pojark. ...
... Rosaceae breeding programs require access to high-quality plant material, including that from wild species found in their native in situ locations, such as some areas in Kazakhstan [8,17,[21][22][23]. Traditionally, Rosaceae genebanks are maintained as living trees in field collections [18,[24][25][26]. The establishment of duplicate collections in a secondary field or other ex situ strategy is a commendable strategy to minimize the risk of loss from attacks by pests and diseases, ageing of the plants, and environmental diseases [27][28][29][30][31][32][33]. ...
The loss of plant species, especially endangered and endemic ones, poses a significant threat to global biodiversity. These species cannot easily be replaced when their populations decline or become extinct, which makes their loss particularly devastating. This study focuses on the geobotanical study of nine Rosaceae species (Cotoneaster karatavicus, Crataegus ambigua, Malus niedzwetzkyana, Malus sieversii, Prunus tenella, Prunus ulmifolia, Sibiraea laevigata, Sorbus persica, and Spiraeanthus schrenkianus) and the development of ex situ approaches for the conservation of Rosaceae species listed in the Red Book of Kazakhstan. The geobotanical study revealed an alarming trend of biodiversity loss in five regions of Kazakhstan. This loss is driven by threats from diseases and pests, as well as the aging of plants, small population sizes, weak in situ fruiting, and other factors, such as climate change. We have established an in vitro collection for the short- and medium-term conservation of seeds, embryos and shoots taken either directly from field-grown plants or from budwood cuttings forced indoors. We also use long-term sexual conservation methods, such as the cryopreservation of seed and embryonic axes, alongside conventional seed banking at −20 °C. Ex situ conservation efforts that use multiple propagules and storage methods for the same species are well-suited to a diverse genebank facility. These efforts enable future generations to use this valuable reservoir of genetic diversity for crop improvement and may also serve as a basis for propagating planting material to restore degraded populations.
... colonization of North America (Janick, 2007, pp. 29-31), producing an array of heirloom and commercial cultivars whose diverse origins from home gardens, orchards, and long-distance transmission can still be identified by linking the genetics to historical data (Gross et al., 2018), and it is the same exchange that goes on today between the germplasm repositories and crop breeding centers for domesticated apple (e.g., Volk et al., 2013). ...
... In our present context, the two systems of human-apple relations continue to coexist and are even further integrated in co-terminous spaces like the USDA-ARS National Plant Germplasm System Plant Genetic Resource Unit in Geneva, NY, where a diverse community of Malus sp. is maintained, cared for, and attentively selected in a reciprocal relationship between human and plant agencies (sensu Hartigan, 2017;Armstrong Oma, 2010), while being simultaneously duplicated in a backup system of cryogenic control that also extracts, systematizes, and freezes Malus sp. progeny for genetic manipulation (sensu Tsing, 2012, p. 144 andDidur, 2003;Volk et al., 2010Volk et al., , 2013. At the same time, the two systems create and maintain cartographies of difference at vast geographic scales; boundaries between core and margin where orchard production is distinguished in practice and experience from the upland foraging and roadside fruit stalls in the mountainous parts of Uzbekistan, Kyrgyzstan, and Kazakhstan (Juniper & Mabberley, 2006, pp. ...
The study of agricultural origins has been revolutionized by genomic science. Whole genome sequencing of plant domesticates opens a door to multiple new approaches by which the timing, nature, and geography of human selective pressures on the evolution of domesticated species might be detected. These new scientific pathways greatly enhance understandings of domestication as an evolutionary process, but they also renew long-standing questions for archaeologists about whether and how to perceive human agency in the ancient past of human–plant interspecies relations. Due to its importance as a global commercial crop, the apple (Malus x domestica Borkh.) was the tenth plant genome to be successfully sequenced in 2010. The genomic record of the apple reveals a deep history of human–plant co-evolution by unconscious selection, domestication through hybridization, and a phylogeographic origin in Central Asia. The first two of these insights document a domesticate that has evolved from protracted and unconscious processes, but the third—the identification of the progenitor Malus sieversii (Ledeb.) M. Roem. in Central Asia, and the necessary corollary that its hybridization arose along the ‘Silk Road’—invites further discussion about the roles of human agency and intentionality in the initial stages of plant domestication. This paper presents a review of apple domestication studies in archaeology and genetics and considers the problematic of Central Asia and the Silk Road in the current paradigm shift of agricultural origins research.
... kirghisorum, and M. sieversii var. turkmenorum [23]. Recent studies highlighted the prevalent crop-to-wild gene flow of apples in Kazakhstan, posing an accelerated risk of genetic swamping [24,25]. ...
The modern apple is a result of hybridization between wild apples and various landraces, with the genetic composition of Malus domestica being primarily shaped by the hybridization of wild species M. sieversii, M. baccata, M. orientalis, and M. sylvestris. The genetic purity of wild apple populations before and after domestication is a concern. Malus sieversii is the primary progenitor of modern apples, with 46% of the M. domestica genome originating from this species. Despite facing harsh environmental conditions, the species has continuously adapted, developing genetic resistance to both abiotic and biotic factors. This resilience makes it a valuable source for breeding purposes. The population analysis of M. sieversii in Kazakhstan indicates substantial genetic variety; yet there is a notable prevalence of gene flow from cultivated to wild apple populations. This hybridization process is likely intensifying the extinction risk faced by wild progenitors of apples, posing a threat to biodiversity preservation and hindering efforts to improve apple varieties, including enhancing resistance to abiotic stress and optimizing production capabilities.
... By 2002, A. mali had infested 35% of wild apple trees in Gongliu County, Xinjiang [9], and, subsequently, killed tens of thousands of wild apple trees and infested over 80% of the total area of wild apple forests in the Yili River Valley in Xinjiang [4]. This particular wild apple species, Malus sieversii, is only found in the mountains of Central Asia, including southern Kazakhstan, eastern Uzbekistan, Kyrgyzstan, Tajikistan, Turkmenistan, and China (Xinjiang) [10,11]. It is considered the key ancestor of cultivated apples [12]. ...
Simple Summary
The apple buprestid beetle Agrilus mali is a pest that can cause serious harm to various domestic apples and many species of Malus. Currently, it is distributed in 17 provinces of China. After spreading from Shandong province to Xinjiang Uygur Autonomous Region, it has caused great damage to the local wild apple resources. China is a major producer of apples; once this pest spreads, it will seriously affect China’s apple industry. We used the MaxEnt model to analyze the changes in the distribution area of A. mali under future climate change scenarios in China. The forecasted suitable regions for A. mali in China will expand northward in the 2050s and 2070s. The forecasted highly suitable regions were 1.11–1.34 times larger than they are currently, and their central distributions were 61.57–167.59 km further north. These findings suggest that monitoring and management measures should be implemented urgently to protect the commercial apple industry and wild apple resources alike.
Abstract
The apple jewel beetle (AJB), Agrilus mali Matsumura (Coleoptera: Buprestidae), is a dangerous pest of commercial apple orchards across China, the largest apple production country in the world, and has recently become invasive in the Xinjiang Uygur Autonomous Region (XUAR) of northwestern China, where wild apple forests also occur. This pest poses a serious threat to apple production and wild apple forests throughout the world. Global warming is expected to change the geographical distribution of A. mali in China, but the extent of this is unknown. Based on empirical data from 1951 to 2000, a MaxEnt model was used to forecast the ecological distribution of A. mali under three different climate scenarios projected in the fifth report of the Intergovernmental Panel on Climate Change. The results showed that the most important variables were the maximum temperature of November, precipitation in January, and minimum temperatures in April. Under all climate scenarios, the forecasted suitable regions for A. mali in China will expand northward in the 2050s and 2070s. The forecasted highly suitable regions will be 1.11–1.34 times larger than they are currently, and their central distributions will be 61.57–167.59 km further north. These findings suggest that the range and damage caused by A. mali in China will increase dramatically in the future. Monitoring and management measures should be implemented urgently to protect both the commercial apple industry and wild apple resources.
... ansu (Maxim.) Yü et Lu), and wild hawthorns (Crataegus songorica K. Koch.) are found only in the mountainous regions of Central Asia, including southern Kazakhstan, eastern Uzbekistan, Kyrgyzstan, Tajikistan, Turkmenistan, and the Xinjiang Uygur Autonomous Region of China [4]. Among them, the Xinjiang wild apple (Malus sieversii) is included in China's list of priority protected species and is a nationally protected plant. ...
As an important ecosystem, the wild fruit forest in the Tianshan Mountains is one of the origins of many fruit trees in the world. The wild fruit forest in Emin County, Xinjiang, China, was taken as the research area, the spatial and temporal distribution of the wild fruit forest was inverted using random forest and PLUS models, and the 2027 distribution pattern of the wild fruit forest was simulated and predicted. From 2007 to 2013, damage to the wild fruit forest from tourism and overgrazing was very serious, and the area occupied by the wild fruit forest decreased rapidly from 9.59 km² to 7.66 km². From 2013 to 2020, suitable temperatures and reasonable tourism management provided strong conditions for the rejuvenation of wild fruit forests. The distance of the center of gravity of the wild fruit forest increased, and the density of distribution of the wild fruit forest in the northwest direction of the study area also increased. It is predicted that the wild fruit forest in the study area will show a steady and slowly increasing trend in places far away from tourist areas and with more complex terrain. It is suggested that non-permanent fences be set up as buffer zones between wild fruit forests, ensuring basic maintenance of wild fruit forests, limiting human disturbance such as overgrazing, and reducing the risk of soil erosion.
... Cоврeмeнныe гeнeтичecкиe иccлeдовaния примeрно 2500 cоврeмeнных cортов яблонь покaзaли, что яблоня Cивeрca являeтcя прaродитeльницeй прaктичecки вceх cортов домaшнeй яблони [6][7][8]. К cожaлeнию, зa поcлeдниe полвeкa площaдь диких популяций яблони Cивeрca рeзко cокрaтилacь, поэтому вaжноcть cохрaнeния этих яблонeвых лecов диктуeт трeбовaния по уcилeнию их охрaны и рaзрaботки cиcтeмы мeр по зaщитe от рaзнообрaзных угроз [9][10][11][12]. ...
В cтaтьe привeдeны cвeдeния по поврeждeнию яблони Cивeрca розaнной лиcтовeрткой нa тeрритории Илeйcкого и Жeтыcуйcкого Aлaтaу. По рeзультaтaм рaботы рaзрaботaны кaрты рacпроcтрaнeния и влияния pοзaннοй лиcтοвepтки Archіps rosana L. нa тeрритории Илe-Aлaтaуcкого и Жонгaр-Aлaтaуcкого ГНПП. Cтoит oтмeтить o нeoбхoдимocти изучeния рacпрocтрaнeния и влияниe pοзaннοй лиcтοвepтки Archіps rosana L., тaк кaк дaнный вид нaнocит знaчитeльный врeд яблoнe Cивeрca нa дaнных тeрритoриях. Ocнoвнoй цeлью иccлeдoвaния являeтcя выявлeниe cтeпeни пoврeждaeмocти pοзaннοй лиcтοвepтки Archіps rosana L. для примeнeния cвoeврeмeннoй мeры бoрьбы c дaнным врeдитeлeм яблoни Cивeрca. В Илeйcком Aлaтaу, a имeнно, в Aкcaйcком и Тaлгaрcком филиaлaх, имeeт мecто болee cильнaя поврeждaeмоcть, чeм в филиaлaх Жeтыcуйcкого Aлaтaу. Выявлeнο, чтο pοзaннaя лиcтοвepткa имeeт cильную cтeпeнь врeдоcноcти в Aкcaйcком лecничecтвe Aкcaйcкого филиaлa, Cолдaтcaйcком лecничecтвe Тaлгaрcкого филиaлa и Иccыкcком лecничecтвe Тургeнcкого филиaлa, однaко eё врeдоноcноcть в гeнeтичecком рeзeрвaтe «Кузнeцово ущeльe» Тургeнcкого филиaлa зaмeтнο нижe. Aктуaльноcть иccлeдовaния зaключaeтcя в том, что зa поcлeдниe нecколько дecятилeтий aрeaл этого видa знaчитeльно cокрaтилcя, это объяcняeтcя гоcудaрcтвeнными и экономичecкими потрeбноcтями, гeнeтичecким и экологичecким зaгрязнeниeм диких популяций, a тaкжe рaзвитиeм опacных врeдитeлeй вокруг рaйонa.
... Мы выбрали их потому, что они представляют основные лесные экосистемы региона, содержат большие площади произрастания и охватывают наиболее значительные популяции этих видов деревьев. (van Nocker et al., 2012;Volk et al., 2013). Этот вопрос требует дополнительных генетических исследований для уточнения видовой принадлежности, а также общего понимания «видовых границ» (Mace, 2004 (Cornille et al., 2014). ...
Понимание фенологии лесов имеет важное значение для мониторинга глобального баланса углерода и управления растительными ресурсами в условиях меняющегося климата. На юге Кыргызстана произрастают леса, где доминирующими видами являются грецкий орех и дикая яблоня. Эти леса содержат уникальное генетическое разнообразие и открывают потенциал для выведения климатически устойчивых сортов сельскохозяйственных культур. Они также являются источником дохода для местного населения, предоставляя природные ресурсы для выпаса скота, сбора дров и фруктов. Однако такая практика представляет угрозу естественному возобновлению лесов. Изменение климата усугубляет эти проблемы, изменяя экологические условия в местах произрастания этих видов. Несмотря на это, лишь немногие исследования посвящены изучению фенологии лесов и её связи с климатом в Кыргызстане. Чтобы восполнить этот пробел, мы собрали экологические данные с лесных участков в трёх охраняемых природных территориях и одном лесничестве. Сюда вошли координаты деревьев, их виды и данные о ландшафте. Временные ряды индексов растительности (EVI), температуры поверхности земли и осадков были получены на основе данных дистанционного зондирования. Регрессионный анализ показал, что температурные тренды имели ограниченную предсказательную силу для растительности, в то время как сезонные колебания температуры оказывали положительное влияние на растительность до тех пор, пока температура не превышала определённого предела, что имело отрицательный эффект. Среднегодовые тренды осадков и их сезонные колебания оказали наиболее существенное воздействие на растительность с запаздывающим эффектом. Были разработаны регрессионные модели для Juglans regia L. (R2 = 0,8) и Malus spp. (R2 = 0,75) для прогнозирования индекса растительности на основе данных о температуре и осадках с высокой точностью. На небольшой территории была отмечена пространственная неоднородность реакции древесных видов на климатические факторы. В исследовании подчеркивается влияние ландшафтного и климатического разнообразия на динамику лесов и важность сезонности климатических факторов по сравнению со среднегодовыми трендами.
... sieversii), also called "Xinjiang wild apple", is considered the ancestor of the modern cultivated apple (Malus pumila), and mainly distributed in the Yili river valley in Xinjiang province, northwest China [1,2]. As a reservoir of genetic diversity, M. sieversii is of high economic value for apple tolerance breeding and is usually used as a popular rootstock for its cold-tolerance trait in north-western China [3][4][5][6]. M. sieversii in different habitats of Xinjiang has been exposed to cold environments for a long time. Through natural selection and genetic variation, different abilities to tolerate a cold environment have been formed [7]. ...
Malus sieversii is considered the ancestor of the modern cultivated apple, with a high value for apple tolerance breeding. Despite studies on the temperature adaptability of M. sieversii carried out at a physiological response and the genome level, information on the proteome changes of M. sieversii during dormancy is limited, especially about the M. sieversii subtypes. In this study, a DIA-based approach was employed to screen and identify differential proteins involved in three overwintering periods of flower buds in two M. sieversii subtypes (Malus sieversii f. luteolus, GL; Malus sieversii f. aromaticus, HC) with different overwintering adaptabilities. The proteomic analysis revealed that the number of the down-regulated differential expression proteins (DEPs) was obviously higher than that of the up-regulated DEPs in the HC vs. GL groups, especially at the dormancy stage and dormancy-release stage. Through functional classification of those DEPs, the majority of the DEPs in the HC vs. GL groups were associated with protein processing in the endoplasmic reticulum, oxidative phosphorylation, starch and sucrose metabolism and ribosomes. Through WGCNA analysis, tricarboxylic acid cycle and pyruvate metabolism were highly correlated with the overwintering stages; oxidative phosphorylation and starch and sucrose metabolism were highly correlated with the Malus sieversii subtypes. This result suggests that the down-regulation of DEPs, which are predominantly enriched in these pathways, could potentially contribute to the lower cold tolerance observed in HC during overwintering stage.
... We selected them because they represent the main forest ecosystems in the region, contain large areas of habitat for the chosen species, and encompass the most significant population of these tree species. van Nocker et al., 2012;Volk et al., 2013). This issue requires additional genetic research to clarify species assignment, as well as a common understanding of species 'boundaries' (Mace, 2004 (Cornille et al., 2014). ...
Understanding forest phenology is essential for monitoring global carbon budgets and managing vegetation resources in a changing climate. In southern Kyrgyzstan, walnut and wild apple trees dominate the forest landscape. These forests contain unique genetic diversity and offer potential for the development of climate-resilient crop varieties. They also support local communities through activities such as grazing, firewood collection, and fruit harvesting. However, these practices pose a threat to natural regeneration. Climate change exacerbates these challenges by altering their ecological niche. Despite this, few studies have examined forest phenology and its relationship to climate in Kyrgyzstan. To address this gap, we collected ecological data from forest plots in several protected areas and one forestry unit. This included tree species coordinates and landscape. Time series of vegetation indices, land surface temperature and precipitation were generated from remote sensing data. Regression analyses showed that temperature trends had limited predictive power for vegetation, while seasonal temperature variations had a positive effect on vegetation until excessive heat was reached, which had a negative effect. Precipitation trends and seasons had the most significant effects on vegetation, with lagged effects. Regression models were developed for Juglans regia L. (R2=0.8) and Malus spp. (R2=0.75) to predict vegetation index from temperature and precipitation data with high accuracy. Spatial heterogeneity in species response to climatic factors was evident within a small area. The study highlights the influence of landscape and climatic diversity on forest dynamics and emphasizes the importance of seasonal climate patterns over interannual trends.
... M.Roem. is the main ancestor of many domesticated apple varieties (M. domestica), mainly in Central Asia and Xinjiang, China [1,2]. Malus sieversii (Ledeb.) ...
Malus sieversii (Ledeb.) M.Roem. is the ancestor of cultivated apples, and is an excellent germplasm resource with high resistance to cold. Artificial refrigerators were used to simulate the low temperature of −3 °C to treat Malus sieversii (Ledeb.) M.Roem. histoculture seedlings. Observations were performed to find the effects of freezing stress on the status of open or closed stomata, photosystems, and detection of metabolomic products in leaves of Malus sieversii (Ledeb.) M.Roem. histoculture seedlings. The percentage of closed stomata in the Malus sieversii (Ledeb.) M.Roem. histoculture seedlings increased, the maximum fluorescence (Fm’) excited by a strong light (saturating pulse) was weakened relative to the real-time fluorescence in its vicinity, and the quantum yield of unregulated energy dissipation was increased in PSII under freezing stress. The metabolites in the leaves of the Malus sieversii (Ledeb. M.Roem.) histoculture seedlings were analyzed by ultra-performance liquid chromatography–tandem mass spectrometry using CK, T12h, T36 h, and HF24h. Results demonstrated that cold stress in the Malus sieversii (Ledeb.) M.Roem. histoculture seedlings led to wilting, leaf stomatal closure, and photosystem damage. There were 1020 metabolites identified as lipids (10.2%), nucleotides and their derivatives (5.2%), phenolic acids (19.12%), flavonoids (24.51%), amino acids and their derivatives (7.75%), alkaloids (5.39%), terpenoids (8.24%), lignans (3.04%), organic acids (5.88%), and tannins (0.88%). There were 110 differential metabolites at CKvsT12h, 113 differential metabolites at CKvsT36h, 87 differential metabolites at T12hvsT36h, 128 differential metabolites at CKvsHF24h, 121 differential metabolites at T12hvsHF24h, and 152 differential metabolites at T36hvsHF24h. The differential metabolites in the leaves of the Malus sieversii (Ledeb.) M.Roem. seedlings grown under low-temperature stress mainly involved glycolysis, amino acid metabolism, lipid metabolism, pyrimidine metabolism, purine metabolism, and secondary metabolite metabolism. The Malus sieversii (Ledeb.) M.Roem. seedlings responded to the freezing stress by coordinating with each other through these metabolic pathways. The metabolic network of the leaves of the Malus sieversii (Ledeb.) M.Roem. histoculture seedlings under low temperature stress was also proposed based on the above pathways to deepen understanding of the response of metabolites of Malus sieversii (Ledeb.) M.Roem. to low-temperature stress and to lay a theoretical foundation for the development and utilization of Malus sieversii (Ledeb.) M.Roem. cultivation resources.
... Kom., Malus baccata (L.) Borkh and Malus sieboldii (Regel) Rehder complex may have ascended with hybridization with native species toward China. On the other hand, hybridization with other local cultivars of Malus orientalis Uglitzk and M. sylvestris into the west is still speculated (Nikiforova et al., 2013;Volk et al., 2013). ...
... Kom., Malus baccata (L.) Borkh and Malus sieboldii (Regel) Rehder complex may have ascended with hybridization with native species toward China. On the other hand, hybridization with other local cultivars of Malus orientalis Uglitzk and M. sylvestris into the west is still speculated (Nikiforova et al., 2013;Volk et al., 2013). ...
... Kom., Malus baccata (L.) Borkh and Malus sieboldii (Regel) Rehder complex may have ascended with hybridization with native species toward China. On the other hand, hybridization with other local cultivars of Malus orientalis Uglitzk and M. sylvestris into the west is still speculated (Nikiforova et al., 2013;Volk et al., 2013). ...
Owing to polymorphism, apple has extraordinary diversity. Depending on varieties, apple fruits can differ in colors and shades, and size. There are more than 10000 varieties of apple, which vary in taste, shape, juiciness, texture, color, firmness and other qualities. For this reason, apple has been diversely studied from time to time and many improvements have been made like that of introduction of high density cropping; rootstock breeding; or varietal development etc. Therefore it is important to understand and document the production ways and methods implemented over times for harvesting the maximum possible benefits of the crop. Apples: Preharvest & Postharvest Technology has documented all the production practice that are taken in practice with detailed illustration on varieties, rootstocks, important cultural practices and post harvest management. This book will therefore serve as a complete guide for apple production from farm to fork and will help students, scholars, researchers and scientists working in this domain. The book will benefit pomologists, horticulturalist, agricultural Scientists, food technologists, university scholars, researchers and college students.
... However, the area of wild populations of the apple tree species has significantly decreased over the past 100 years due to large scale clearance and land use in recent business activities (Dzhangaliev et al., 2003). At present, according to experts, the situation is close to critical, as the unique intraspecific diversity of the Kazakhstan populations of wild apple trees is currently being intensively reduced, leading to impoverishment of their gene pool value (Dzhangaliev, 2007;Volk et al., 2013). The same situation is applied to neighbouring areas of China, Kyrgyzstan, Uzbekistan, Tajikistan and Turkmenistan. ...
... The 'modern' apple was domesticated in Central Asia from Malus sieversii (Velasco et al., 2010;Cornille et al., 2012;Volk et al., 2005Volk et al., , 2013 and was brought to Europe through human migrations between 6000 and 3000 years ago (Janick, 2005;Ross-Ibarra et al., 2007;Cornille et al., 2012). Humans have been exploiting, selecting, and transporting apples for centuries, and several thousand apple cultivars have been historically documented (Ross-Ibarra et al., 2007;Cornille et al., 2014). ...
A molecular characterization on the ancient variety ‘Rosa Romana’ was carried out to improve biodiversity knowledge and preserve these trees from extinction risks.
In this work, 47 accessions were collected throughout an investigation in the Emilia-Romagna region (Italy) and particularly in the mountain area of the Bologna province (19 collection sites). The analysis at molecular level by using 15 SSR (microsatellites) identified two main genotype groups and ascertained their relationship with several phenotypic traits. This two clusters contained most of the collected accessions, while remaining genotypes differ clearly, according with the phenotypic diversity on the behavior of the trees or fruits.
This study also revealed the highest quality traits of ‘Rosa Romana’ apple grown in the Apennines mountain around Bologna (in a range between 400 and 1000 m.a.s.l.) if compared to each main clone produced at the lowland corresponding to the Bologna University Agricultural Experimental Station (30 m.a.s.l). Therefore, the apple quality as color, appearance, taste (flesh firmness and texture, sweetness, acidity, aroma, polyphenol soreness), were improved in the higher altitudes. In conclusion, the results of this environmental and genetic investigation on the residual cultivation of ‘Rosa Romana’ apple provided a genomic validation of its best identified clones (correspondent to the main two clusters), which now can be recovered and promoted as new planting, with a own brand ‘Rosa Romana’ produced in the Apennines mountain of north Italy.
... Genetic diversity is expected to be well maintained due to the potential hybrid events. Genetic studies often found an escalated infra-specific genetic diversity pattern in M. sieversii, possibly in association with closely related, M. kirghisorum and M. niedzwetzkyana [20,24,28,29]. Accordingly, we included Malus niedzwetzkyana Diek, an endangered congener that is closely related, in our analysis to assess the influence of the related taxa (M. ...
There is growing attention given to gene flow between crops and the wild relatives as global landscapes have been rapidly converted into agricultural farm fields over the past century. Crop-to-wild introgression may advance the extinction risks of rare plants through demographic swamping and/or genetic swamping. Malus sieversii, the progenitor of the apple, is exclusively distributed along the Tien Shan mountains. Habitat fragmentation and hybridization between M. sieversii and the cultivated apples have been proposed to be the causal mechanism of the accelerated extinction risk. We examined the genetic diversity pattern of eleven wild and domesticated apple populations and assessed the gene flow between M. sieversii and the cultivated apples in Kazakhstan using thirteen nuclear microsatellite loci. On average, apple populations harbored fairly high within-population diversity, whereas population divergences were very low suggesting likely influence of human-mediated dispersal. Assignment results showed a split pattern between the cultivated and wild apples and frequent admixture among the apple populations. Coupled with the inflated contemporary migration rates, the admixture pattern might be the signature of increased human intervention within the recent past. Our study highlighted the prevalent crop to wild gene flow of apples occurring in Kazakhstan, proposing an accelerated risk of genetic swamping.
... However, the area of wild populations of the apple tree species has significantly decreased over the past 100 years due to large scale clearance and land use in recent business activities (Dzhangaliev et al., 2003). At present, according to experts, the situation is close to critical, as the unique intraspecific diversity of the Kazakhstan populations of wild apple trees is currently being intensively reduced, leading to impoverishment of their gene pool value (Dzhangaliev, 2007;Volk et al., 2013). The same situation is applied to neighbouring areas of China, Kyrgyzstan, Uzbekistan, Tajikistan and Turkmenistan. ...
... Malus sieversii (Ledeb.) M. Roem., a native of Western China and Central Asia (Kazakhstan, Kyrgyzstan, Tajikistan, Uzbekistan), is the primary relative of the domesticated apple based on nuclear and chloroplast-DNA analyses (Gharghani et al., 2009;Richards et al., 2009;Gross et al., 2012a;Nikiforova et al., 2013;Volk et al., 2013). Hybridization with the European crabapple M. sylvestris (L.) Mill. ...
This book covers the biotechnology of all the major perennial fruit and nut species, including Actinidia spp., Anacardium occidentale , Mangifera indica , Pistacia vera , Annona spp., Cocos nucifera , Elaeis guineensis , Phoenix dactylifera , Ananas comosus , Carica papaya , Garcinia mangostana , Diospyros kaki , Vaccinium spp., Castanea spp., Carya illinoinensis , Juglans regia , Persea americana , Theobroma cacao , Musa spp., Psidium guajava , Olea europaea , Averrhoa carambola , Passiflora spp., Eriobotrya japonica , Fragaria × ananassa , Malus × domestica , Prunus persica , Prunus armeniaca , Prunus domestica , Prunus spp., Prunus dulcis , Pyrus spp., Cydonia spp., Rubus spp., Citrus spp., Dimocarpus longan , Litchi chinensis , and Vitis spp. This book also covers biotechnologies and also traditional ones, such as regeneration pathways, protoplast culture, in vitro mutagenesis, and ploidy manipulation that have been applied to many of these species. The species are organized by plant family to facilitate comparisons among related ones. Each species is discussed in relation to its family and its related wild forms, and most are accompanied by full colour illustrations. This book is a vital resource for those working on the improvement of perennial fruit, nut and plantation crops.
... Wild apple populations, also known as 'crab apples', are native throughout the Northern hemisphere in temperate areas (Luby, 2003). They are mainly found on the edge of woods and areas of scrub, in moist or coastal regions (e.g., Routson et al., 2012 (Richards et al., 2008;Gharghani et al., 2009;Gross et al., 2012;Nikiforova et al., 2013;Volk et al., 2013), but has become a rare and threatened plant in People's Republic of China (Yan et al., 2008;IUCN, 2019). ...
This OECD Consensus Document on the Biology of APPLE (Malus domestica Borkh.) has recently been published. It is also available on the OECD BioTrack public website. Apple is a major fruit crop of temperate regions. It is traded and consumed worldwide as fresh fruit, juice and many other food products. The primary purpose of such a document is for use in biosafety assessment, for example, with transgenic varieties. But it should be of interest to a wider audience.
http://www.oecd.org/officialdocuments/publicdisplaydocumentpdf/?cote=ENV-JM-MONO(2019)30%20&doclanguage=en
... mandshurica. Interestingly, M. sieversii did not group with the cultivated apple cultivar Golden Delicious, which might be due to the high genetic diversity within the Malus sieversii population (Volk et al. 2013). ...
The genetic diversity and population structure studies on 32 wild Malus species were conducted using the nine inter simple sequence repeat (ISSR) markers. The average value of diversity indices, viz. resolving power (Rp), polymorphic information content (PIC), effective multiplex ratio (EMR) and marker index (MI) of ISSR markers were 2.389, 0.388, 16.429 and 6.228, respectively, while the Jaccard's similarity coefficient ranged from 0.46 to 0.97. The cluster analysis divided the selected Malus species into two major clusters and principal coordinate analysis (PCoA) further reconfirmed the result of the cluster analysis. The first three axes of PCoA explained 43.49% variation and analysis of molecular variance (AMOVA) explained 16% variation between the indigenous and exotic Malus populations. The studied Malus species were genetically differentiated into four distinct populations which were revealed through the model based population structure analysis. Thus, the present investigation revealed substantial genetic diversity among the studied wild Malus species and existing genetic diversity could be valuable genetic resources for future apple improvement programme.
... Golden Delicious and hence clustered in separate clade. This might be due to the high genetic diversity within the M. sieversii variants (Volk et al. 2013). Furthermore, M. esseltine and M. hilleiri showed close genetic relationship with M. 9 domestica cv. ...
The inadequate information on genetic diversity and population structure of wild Malus genotypes including indigenous Himalayan crabapples [M. baccata (L.) Borkh. and M. sikkimensis (Wenzig) Koehne ex C. Schneider] collected and maintained at different field gene banks of apple necessitated this study. A set of 31 SSR loci covering all the linkage groups of apple genome was successfully used in this study. The average number of alleles at per locus, major allelic frequency, expected heterozygosity, observed heterozygosity and PIC values were 3.29, 0.592, 0.506, 0.271 and 0.438, respectively among the studied SSR loci. The set of SSR loci yielded 8 unique and 11 rare alleles among the wild Malus genotypes. These wild Malus genotypes were grouped into seven distinct clades, where the indigenous Himalayan M. baccata (L.) Borkh. ecotypes were grouped in separate clades confirming them to be genetically distinct. Furthermore, model based population structure differentiated the wild apple genotypes into three populations of which one was indigenous Himalayan M. baccata (L.) Borkh. ecotypes. The high allele-frequency divergence among populations revealed high genetic differences between them. The AMOVA revealed high genetic diversity between populations of wild Malus genotypes; and within; and among the individuals of the populations. The PCoA validated and reconfirmed the three groups of the population as differentiated by model based population structure. The genetic uniqueness of indigenous Himalayan M. baccata (L.) Borkh. ecotypes can further add the new genes in the global gene pool of apple. This study could serve as base information for future exploration and collection of more accessions of indigenous Himalayan crabapples from the region extending to about 7000 km in the Indian Himalayan region. The existing high degree of genetic diversity among the studied wild apple genotypes could be the valuable genetic resource for the apple improvement programmes.
... This particular wild apple species is found only in the mountains of Central Asia, including southern Kazakhstan, eastern Uzbekistan, Kyrgyzstan, Tajikistan, Turkmenistan and Xinjiang province, China Correspondence: Zhao-Zhi Lu. e-mail: zhaozhi@ms.xjb.ac.cn 1 These authors contributed equally to this work. (Volk et al. 2013). This important germplasm resource (Chen et al. 2007;Richards et al. 2009) has been severely impacted by overgrazing, pest insects, diseases, timber industries and climate change (Liu et al. 2014b). ...
• Wild apple Malus sieversii (Ledeb.) M. Roem. (Rosales: Rosaceae), the ancestor of cultivated apples, is widely distributed in Central Asia and is recognized as an important germplasm bank. Recently, the invasive pest Agrilus mali Matsumura (Coleoptera: Buprestidae), originally distributed in eastern Asia, has damaged endemic apple forests in the Yili River valley, Xinjiang, China, and has spread rapidly, infesting more than 80% of wild apple trees in this region.
• We investigated the life‐history traits and native natural enemies in the recently invaded range during 2016 and 2017. Agrilus mali has a univoltine life cycle and overwinters as young larvae in galleries in the cambium. Adults emerged from early June to mid‐August and their density peaked in mid‐July.
• Several native natural enemies were identified from Agrilus mali larvae, including Atanycolus denigrator (L.) (Hymenoptera: Braconidae), the mite Pyemotes moseri Yu et Liang (Acari: Pyemotidae) and fungal entomopathogens.
• Combined, these natural enemies were responsible for mortality rates ranging from 20% to 80% during the summer and autumn. The most abundant and important natural enemy was A. denigrator, which was responsible for up to 15% mortality of A. mali.
• The results of the present study suggest that augmentation and conservation of A. denigrator and P. moseri should be considered with respect to biological control against this devastating pest.
... Golden Delicious and hence clustered in separate clade. This might be due to the high genetic diversity within the M. sieversii variants (Volk et al. 2013). Furthermore, M. esseltine and M. hilleiri showed close genetic relationship with M. 9 domestica cv. ...
The wild apples (Malus sp.) are important genetic resources for apple improvement programmes. In the present investigation, 32 Malus genotypes including indigenous Himalayan crab apples and exotic wild apples collected and maintained in the field gene banks at different ICAR institutes, were selected for genetic diversity and population structure analysis using the RAPD markers. The mean diversity indices, viz., Rp, PIC, EMR and MI of 18 RAPD markers were 5.829, 0.326, 8.432 and 2.851, respectively among the wild Malus genotypes. The cluster analysis segregated the wild Malus genotypes into two major clusters and the Jaccard’s similarity coefficient ranged from 0.66 to 0.90. The first three axes of PCoA explained 40.26% variation and AMOVA explained 2% between the indigenous and exotic wild apple genotypes. The model based population structure studies revealed three major populations in the present set of genotypes. It could be concluded that there was substantial level of genetic diversity and population differentiation among the wild apple genotypes maintained at different research stations. Thus, the available diversity among the present set of wild apples could be explored for the scion as well as for rootstock breeding.
... Isutsa and Merwin, 2000;St. Laurent et al., 2010;Robinson et al., 2012;Volk et al., 2013). In addition, an improved strategy for defense responses of plant roots by modulating cellular signals such as the oscillation of Ca 2+ concentration, reactive oxygen species burst or protein kinase activity (Emmett et al., 2014) is under debate. ...
After replanting apple (Malus domestica Borkh.) on the same site severe growth suppressions, and a decline in yield and fruit quality are observed in all apple producing areas worldwide. The causes of this complex phenomenon, called apple replant disease (ARD), are only poorly understood up to now which is in part due to inconsistencies in terms and methodologies. Therefore we suggest the following definition for ARD: ARD describes a harmfully disturbed physiological and morphological reaction of apple plants to soils that faced alterations in their (micro-) biome due to the previous apple cultures. The underlying interactions likely have multiple causes that extend beyond common analytical tools in microbial ecology. They are influenced by soil properties, faunal vectors, and trophic cascades, with genotype-specific effects on plant secondary metabolism, particularly phytoalexin biosynthesis. Yet, emerging tools allow to unravel the soil and rhizosphere (micro-) biome, to characterize alterations of habitat quality, and to decipher the plant reactions. Thereby, deep insights into the reactions taking place at the root rhizosphere interface will be gained. Counteractions are suggested, taking into account that culture management should emphasize on improving soil microbial and faunal diversity as well as habitat quality rather than focus on soil disinfection.
... Isutsa and Merwin, 2000;St. Laurent et al., 2010;Robinson et al., 2012;Volk et al., 2013). In addition, an improved strategy for defense responses of plant roots by modulating cellular signals such as the oscillation of Ca 2+ concentration, reactive oxygen species burst or protein kinase activity (Emmett et al., 2014) is under debate. ...
... The fifth cluster (V) with four Djangaliev clones was at the maximum distance from all the others. It is obvious that the location of clusters with clones at considerable distances from each other and from cultivars is due to significant genetic/phenotypic differences within the taxa of wild apple [36]. ...
Identification of the varieties is the primary requirement for characterization of the gene pool in agricultural production and implementation of breeding programs. In the present work, a set of six SSR markers was used for identification of cultural material collected on various horticultural farms in Kazakhstan: 30 varieties of Kazakhstani selection, 40 foreign varieties, and 16 Dzhangaliev’s apple clones selected in wild apple populations. Values of expected (He) and observed (Ho) heterozygosity in groups of all analyzed varieties were high: from 0.735 to 0.812 and from 0.661 to 0.721 respectively. Cluster analysis and analysis of genetic distances (STRUCTURE, UPGMA) showed a distribution of all samples into four major groups with a set of small subgroups caused by origin diversity. The first group included Kazakhstani varieties originating from Reneitte Burchardt, the second group included varieties with Aporta in parentage, the third group was represented by subclusters with a majority of foreign varieties, and the last group was composed of Dzhangaliev’s apple clones and Kazakhstani varieties with wild apple as their ancestor. Genotyping revealed inconsistencies in individual samples (and/or parentage) with claimed names. Analysis by markers of the Md-ACS1 and Md-ACO1 genes responsible for ethylene levels in fruits, which according to the literature correlates with fruit hardness and storability, did not reveal among Kazakhstani varieties any ACS1-2/2 homozygotes, the genotype with the highest expression of these traits. A quarter of Kazakhstani varieties and about a half of foreign varieties were heterozygous in ACS1, an indication of medium hardness and relatively long period of fruit storage. In two Kazakhstani and two foreign varieties heterozygous in ACS1, an improvement of the traits is possible owing to homozygosity in ACO1-1/1.
... Golden Delicious was the outliers and accordingly separated into two different clusters. This might be due to high level of phenotypic and genotypic diversity within the M. sieversii (Volk et al., 2013). The cluster and scatter plot analysis revealed that the no separate group or cluster was formed either by among exotic Malus species or by indigenous Himalayan wild apples, which decipher high level of morphological and biochemical diversity among them. ...
In the present investigation, 32 Malus species including 12 indigenous Himalayan wild apples were evaluated
during 2014–2015, for their morphological (14 No.) and biochemical (14 No.) variabilities based on 28 parameters.
The leaf related attributes like leaf shape, leaf apex shape, leaf base shape, leaf blade margin and tree
attributes like tree habit, suckering tendency, burrknot tendency and presence of lenticels on shoot exhibited
considerable variation. The maximum coefficient of variation value was recorded for foliar peroxidase activity
(98.18%) followed by catechin (91.32%) content. Principal component analysis (PCA) revealed that the first five
principal components (PC1, PC2, PC3, PC4 and PC5) together accounted for more than 50% variation of the total
observed variations. The PC1 strongly integrated with the traits like tree habit, leaf blade length, leaf blade
width, rutin, phloridzin, chlorophyll a, chlorophyll b, − chlorophyll a:b, total chlorophyll and total phenolics
content, which were found to be effective parameters for explaining the natural variability among the studied
Malus species. The dendrogram generated based on unweighted Neighbhor-joining method clustered all the
Malus species including the indigenous wild apples into three distinct clusters. Scatter plot based on PC1 and PC2
suggested high morphological and biochemical diversity among the Malus species including the indigenous wild
apples. The cluster analysis and scatter plot revealed that the indigenous wild apples were quite diverse as
observed for the exotic Malus species; though there were no separate groups detected. The higher diversity for
endogenous biochemical compounds indicates differential physiological behaviour of Malus species under the
prevailing environmental conditions. These findings revealed that there were several biochemical constituents,
which could serve as effective indices for indirect selection of potential biotic and abiotic stresses resistance/
tolerance Malus species for their potential use in genetic improvement programmes. Similarly, knowledge on
graft compatibility with respect to wild Malus could help in exploiting them as new rootstock genotypes. These
parameters are known to influence the expression of different traits in scion genotypes upon grafting and thus
could help in sustaining the apple production in Indian Himalayan region under changing climate situations The
potential genotypes based on their morphological and biochemical parameters identified like M. baccata (Khrot),
M. baccata (Kinnaur), M. baccata (Pangi), M. baccata (Rohru), M. baccata (Shillong), M. hilleiri, M. micromalus, M.
prunifolia (Maruba), M. prunifolia (Ringo-Assami), M. sieversii and M. spectabilis suggested them to be quite diverse.
Besides, some indigenous Himalayan crab apples were also identified, which have inherent potential to
serve as valuable genetic resources for rootstock improvement programmes.
... Between 1989 and 1996, American scientists collected M. sieversii at eight sites located Table 3 Genetic distance analysis using Nei's (1972) Nei's (1972) genetic distances, b with group membership defined accordingly to mountain ranges using principal coordinate analysis in six different regions in Kazakhstan (Tarbagatay, Dzhungarskiy Alatay, Ketmen, Zailisky Alatau, Talas Alatau, and Karatau). Seeds of mother trees were brought to different international apple research institutions, where seedlings were planted and evaluated on their genetic variability among others (Richards et al. 2009b;Volk et al. 2005Volk et al. , 2013Gross et al. 2013). ...
Kazakhstan belongs to the center of origin of apple. Malus sieversii (Ledeb.) M. Roem., the ancestral progenitor of the cultivated apple is native to this region. Pressure on the natural habitats of this wild apple has been intensified due to agriculture, grazing, and urbanization in the last century. For decades, M. sieversii in Kazakhstan has been subjected to the “Red Book of the Kazakh SSR” and today, this species is threatened with extinction. Wild apple undergoes exceptional losses in habitats, and the risk for losing the genetic integrity becomes worse due to increasing cultivation of cultivated apples and frequently occurring crosspollination events. The present study was focused on the current state of M. sieversii in Kazakhstan, the level of its diversity, its genetic integrity, and the identification of regions where future activities for conservation will have a good chance of success. A total of 311 M. sieversii samples of 12 populations collected in the wild, 16 previously selected wild apple genotypes, and 50 grown cultivars were studied using 16 simple sequence repeat (SSR) markers for genetic analysis. The results suggest that the level of genetic diversity is high. The differentiation between the populations was low, although the within-population heterozygosity was relatively high. A significant number of hybrids (8–95%) between M. sieversii and cultivated apples were found suggesting frequent crop-to-wild gene flow. The percentage of pure wild apple genotypes was highest in Krutoe truct and Tauturgen. These sites should be taken into account for future in situ long-term preservation activities.
... Collaborative efforts between the United States Department of Agriculture, Agricultural Research Service (USDA-ARS), U.S. scientists, and Central Asian counterparts resulted in several successful expeditions between 1989 and 1996 to collect M. sieversii in Kazakhstan, Tajikistan, and Uzbekistan. These expeditions produced an extensive collection of over 130,000 seeds and vegetative materials collected from 44 elite accessions with phenotypes of interest [15,[18][19][20]. Several of these seed and elite accessions of M. sieversii were later found to be resistant to P. expansum [21][22], including USDA-ARS National Plant Germplasm System plant introduction (PI)613981 [23]. ...
Blue mold caused by Penicillium expansum is the most important postharvest disease of apple worldwide and results in significant financial losses. There are no defined sources of resistance to blue mold in domesticated apple. However, resistance has been described in wild Malus sieversii accessions, including plant introduction (PI)613981. The objective of the present study was to identify the genetic loci controlling resistance to blue mold in this accession. We describe the first quantitative trait loci (QTL) reported in the Rosaceae tribe Maleae conditioning resistance to P. expansum on genetic linkage group 3 (qM-Pe3.1) and linkage group 10 (qM-Pe10.1). These loci were identified in a M.× domestica ‘Royal Gala’ X M. sieversii PI613981 family (GMAL4593) based on blue mold lesion diameter seven days post-inoculation in mature, wounded apple fruit inoculated with P. expansum. Phenotypic analyses were conducted in 169 progeny over a four year period. PI613981 was the source of the resistance allele for qM-Pe3.1, a QTL with a major effect on blue mold resistance, accounting for 27.5% of the experimental variability. The QTL mapped from 67.3 to 74 cM on linkage group 3 of the GMAL4593 genetic linkage map. qM-Pe10.1 mapped from 73.6 to 81.8 cM on linkage group 10. It had less of an effect on resistance, accounting for 14% of the experimental variation. ‘Royal Gala’ was the primary contributor to the resistance effect of this QTL. However, resistance-associated alleles in both parents appeared to contribute to the least square mean blue mold lesion diameter in an additive manner at qM-Pe10.1. A GMAL4593 genetic linkage map composed of simple sequence repeats and ‘Golden Delicious’ single nucleotide polymorphism markers was able to detect qM-Pe10.1, but failed to detect qM-Pe3.1. The subsequent addition of genotyping-by-sequencing markers to the linkage map provided better coverage of the PI613981 genome on linkage group 3 and facilitated discovery of qM-Pe3.1. A DNA test for qM-Pe3.1 has been developed and is currently being evaluated for its ability to predict blue mold resistance in progeny segregating for qM-Pe3.1. Due to the long juvenility of apple, the availability of a DNA test to screen for the presence of qM-Pe3.1 at the seedling stage will greatly improve efficiency of breeding apple for blue mold resistance.
... Between 1 and 36 individuals represented each species. Th e nine individuals that are listed as M. pumila Mill. in the Genetic Resources Information Network (GRIN; U. S. Department of Agriculture, 2014 ) were designated as M. sieversii in our analyses, because of the high degree of similarity among the accessions associated with these two species names ( Volk et al., 2013 ;Kumar et al., 2014). A Sorbus aucuparia L. individual (PI 635088) from the U. S. National Arboretum, Washington, D.C., was selected for use as an outgroup for phylogenetic and network analyses ( Potter et al., 2007 ). ...
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The genus Malus represents a unique and complex evolutionary context in which to study domestication. Several Malus species have provided novel alleles and traits to the cultivars. The extent of admixture among wild Malus species has not been well described, due in part to limited sampling of individuals within a taxon.•
Four chloroplast regions (1681 bp total) were sequenced and aligned for 412 Malus individuals from 30 species. Phylogenetic relationships were reconstructed using maximum parsimony. The distribution of chloroplast haplotypes among species was examined using statistical parsimony, phylogenetic trees, and a median-joining network.•
Chloroplast haplotypes are shared among species within Malus. Three major haplotype-sharing networks were identified. One includes species native to China, Western North America, as well as Malus domestica Borkh, and its four primary progenitor species: M. sieversii (Ledeb.) M. Roem., M. orientalis Uglitzk., M. sylvestris (L.) Mill., and M. prunifolia (Willd.) Borkh; another includes five Chinese Malus species, and a third includes the three Malus species native to Eastern North America.•
Chloroplast haplotypes found in M. domestica belong to a single, highly admixed network. Haplotypes shared between the domesticated apple and its progenitors may reflect historical introgression or the retention of ancestral polymorphisms. Multiple individuals should be sampled within Malus species to reveal haplotype heterogeneity, if complex maternal contributions to named species are to be recognized.
© 2015 Botanical Society of America, Inc.
This document reports on research conducted within “Conservation and Research of Wild Fruit Species in Western Tian Shan, Kyrgyz Republic” (CEPF-110679) project kindly supported by the Critical Ecosystem Partnership Fund, however, data collected within this project will be further analyzed and more publications are being developed with proper acknowledgements; authors declare no conflict of interests.
Chitinases are responsible for catalyzing the hydrolysis of chitin and contribute to plant defense against fungal pathogens by degrading fungal chitin. In this study, genome-wide identification of the chitinase gene family of wild apple (Malus sieversii) and domesticated apple (Malus domestica) was conducted, and the expression profile was analyzed in response to Valsa mali infection. A total of 36 and 47 chitinase genes belonging to the glycosyl hydrolase 18 (GH18) and 19 (GH19) families were identified in the genomes of M. sieversii and M. domestica, respectively. These genes were classified into five classes based on their phylogenetic relationships and conserved catalytic domains. The genes were randomly distributed on the chromosomes and exhibited expansion by tandem and segmental duplication. Eight of the 36 MsChi genes and 17 of the 47 MdChi genes were differentially expressed in response to V. mali inoculation. In particular, MsChi35 and its ortholog MdChi41, a class IV chitinase, were constitutively expressed at high levels in M. sieversii and domesticated apple, respectively, and may play a crucial role in the defense response against V. mali. These results improve knowledge of the chitinase gene family in apple species and provide a foundation for further studies of fungal disease prevention in apple.
A historical analysis of apple nomenclature leads to the conclusion that the legitimate epithet for the cultivated apple is Malus Xdomestica Borkh.
Reduced availability of water for agricultural use has been forecast for much of the planet as a result of global warming and greater urban demand for water in large metropolitan areas. Strategic improvement of water use efficiency (WUE) and drought tolerance in perennial crops, like fruit trees, could reduce water use without compromising yield or quality. We studied water use in apple trees using 'Royal Gala', a relatively water use-efficient cultivar, as a standard. To examine whether genes useful for improving WUE are represented in a wild relative genetically close to M. ×domestica, we surveyed Malus sieversii for traits associated with WUE and drought resistance using material collected from xeric sites in Kazakhstan. This collection has been maintained in Geneva, NY, and surveyed for various phenotypes and has been genetically characterized using simple sequence repeats (SSRs). These data suggest that most of the diversity in this population is contained within a subpopulation of 34 individuals. Analysis of this subpopulation for morphological traits traditionally associated with WUE or drought resistance, e.g., leaf size and stomata size and arrangement, indicated that these traits were not substantially different. These results imply that some of the genetic diversity may be associated with changes in the biochemistry, uptake, and/or transport of water, carbon, or oxygen that have allowed these trees to survive in water-limited environments. Furthermore, genes responding to drought treatment were isolated from 'Royal Gala' and categorized according to the biological processes with which they are associated. A large fraction of upregulated genes from roots were identified as stress-responsive, whereas genes from leaves were for the most part associated with photosynthesis. We plan to examine expression of these genes in the M. sieversii population during water deficit in future studies to compare their patterns of expression with 'Royal Gala'.
Seeds and scionwood of Malus sieversii Lebed. have been collected from wild populations of apple trees in Kazakhstan. Seedlings and grafted trees were planted in the orchards at the U.S. Dept. of Agriculture Plant Genetic Resources Unit in Geneva, N.Y. We developed core collections to capture the genetic and phenotypic diversity represented in the trees from each of two of the Kazakhstan collection sites. These core collections capture more than 90% of the genetic diversity of the original populations, as determined using seven unlinked simple sequence repeat markers and 19 quantitative traits. Since phenotypic evaluations of these materials have been completed, the 35 trees within each population will be used as parents in crosses so that the genetic diversity in the orchard populations can be captured as seed for long-term ex situ conservation. This strategy of storing seeds, rather than maintaining costly field collections, could be applied to other collections of wild plant materials in the National Plant Germplasm System.
Incidence and severity of fire blight [Erwinia amylovora (Burr.) Winslow, Broadhurst, Buchanan, Krumwiede, Rogers, and Smith] following field infection were recorded using families resulting primarily from open-pollination of Malus sylvestris (L.) Mill. var.domestica (Borkh.) Mansf. cultivars and a few other Malus Mill. sp. The families were structured as three sublines, planted in three successive years (1992 to 1994), of a diverse population of apple germplasm established at HortResearch, Hawkes Bay, New Zealand. The incidence of fire blight varied among the sublines with the oldest planting exhibiting more fire blight. Flowering trees were more likely to be infected than nonflowering trees, in terms of both incidence and severity. Furthermore, the level of fire blight was related to flowering date, with later flowering trees having higher levels. Thus, family means and narrow-sense heritability estimates were computed after first adjusting the fire blight score for flowering date by fitting a linear model. Provenance of origin of the maternal parent explained little variation except that M. sieversii Lebed. families were more resistant than M. sylvestris var. domestica families in one subline. Family means computed using all trees, and those from only flowering trees were highly correlated. Families from open-pollination of M. honanensis Rehder and M. xhartwiggii Koehne females were among the more susceptible. Those from several European M. sylvestris var. domestica cultivars as well as from M. baccata (L.) Borkh. and M. toringoides (Rehder) Hughes females were among the more resistant families. Narrow-sense heritability estimates ranged from 0.05 to 0.85 depending on the subline, with most estimates between 0.12 and 0.36. They were higher in the two older sublines that consisted primarily of open-pollinated families from M. sylvestris var. domestica, and lower in the younger subline that consisted primarily of M. sieversii, due to lower incidence and severity in the latter subline. Breeders who consider potential complications of juvenility, tree size, and flowering date in relation to infection periods should be able to exploit field epidemics to perform effective selection. 1996; Fischer et al., 1983b; Gardner et al., 1980b; Korban et al., 1988; Lespinasse and Paulin, 1990;) or older juvenile seedlings in a nursery (Moore, 1946). Researchers have observed quantita-tive inheritance in most crosses suggesting polygenic control (Fischer et al., 1983b; Gardner et al., 1980b; Korban et al., 1988; Lespinasse and Paulin, 1990; Moore, 1946;). Dominance of resistance has been observed in some crosses (Gardner et al., 1980b; Korban et al., 1988). At the Horticulture and Food Research Institute of New Zealand, Ltd. (HortResearch), a large apple breeding population has been established to maintain biodiversity for cultivar devel-opment (Noiton and Alspach, 1996), as well as to study genetic aspects of important traits (Currie et al., 2000; Noiton and Shelbourne, 1992; Noiton et al., 1999; Oraguzie et al., 2001). The population could potentially provide novel sources of mono-and polygenic resistances to a range of pests and diseases for applica-tion in a long-term breeding strategy based on recurrent selection. This paper reports evaluation of part of the aforementioned population for fire blight damage following natural infection. Due to warm spring weather and abundant inoculum from the previous season, fire blight was common and widespread in the 1998–99 season in the Hawkes Bay production region of New Zealand, including the HortResearch orchards in Havelock North. We were able to 1) assess variation for resistance in this popula-tion, 2) identify families and their female parents that were especially resistant or susceptible, and 3) estimate heritability of Received for publication 28 Mar. 2001. Accepted for publication 12 Nov. 2001. The authors gratefully acknowledge support from the University of Minnesota and the New Zealand Foundation for Research, Science, and Technology. Madelein Hofstee and Mirco Stefanati assisted with data collection. Dominique Noiton was instrumental in establishing the apple breeding populations. Aimak Djangaliev arranged and assisted in collection of germplasm in Kazakstan.
One of the primary progenitors of the cultivated apple is Malus sieversii L., a species native to the forested regions of central Asia. Despite the horticultural importance of M. sieversii, little is known about genetic variation in this species. In this study, allozyme diversity at 18 loci was determined for 259 seedlings belonging to 31 sib families, each consisting of the set of offspring from a different open-pollinated maternal (seed) parent. Maternal parents belonged to 14 populations from four geographic regions. Genetic diversity statistics were computed from the resulting allele and phenotype frequencies. Cluster analysis of sib families showed that there was some grouping based on geographic region, but 16 of the sib families were most closely related to sib families from other regions. Analysis of molecular variance (AMOVA) indicated that 85% of the enzyme variability was due to differences among sib families within populations and 15% was due to differences among regions. No variability could be assigned to differences among populations within regions. In addition, no alleles were found that were fixed in a region and unique to that region. These results suggest that plants belonging to M. sieversii effectively form a panmictic population. Consequently, a thorough sampling of a few large populations will efficiently capture most of the genetic diversity present in wild M. sieversii.
Some debated issues of the genus Malus (apple) taxonomy were examined using a variety of species from the collection of the Maikop Experimental Station, Vavilon Research Institute of Plant Industry (Krasnodar krai). Phylogenetic relationships among these species were studied using traditional analysis of morphological traits, RAPD, and complete sequencing of the 5"- internal transcribed spacer (ITS1), 5.8S rRNA, 3"- internal transcribed spacer (ITS2) (constituting a cluster of the rRNA genes), and the terminal fragment of the matK gene encoding chloroplast maturase. The results showed that the Sorbomalus section was polyphyletic; the American apple M. fusca was closely related to the species contributing to the East Asian center of the genus origin, and the American species M. angustifolia, M. coronaria, and M. ioensis were closely related to the M. trilobata relict species, whose assignment to the genus Malus is debated by some authors. Molecular analysis of the species relationships showed that the Middle Asian apple M. sieversii is the species from which apple domestication started.
A checklist of the economically and ecologically important subfamily Maloideae (Rosaceae) is presented. One thousand one hundred and ten species are recognised in 23 genera, as well as 33 species in 13 intergeneric hybrid genera. An alphabetic arrangement is used within each taxonomic rank. The larger genera are subdivided into infrageneric groupings to represent structure. Several new infrageneric taxa were created to reconcile different sources. This checklist is believed to be complete to 1986 and represents the compilation and synthesis of over 170 publications. The following new names are published: Crataegus series Henryanae Phipps, ser.nov. et stat.nov.; Crataegus section Hupehensis Phipps, sect.nov.; Crataegus series Hupehenses Phipps, ser.nov.; Crataegus section Lacrimatae Phipps, sect, et stat.nov.; Malacomeles paniculata (Rehder) Phipps, comb.nov.; Sorbus subgen. Micromeles (Decne.) Phipps, Robertson & Spongberg, subgen. et stat.nov.; Sorbus section Albo-carmesini H.A. McAllister, sect.nov.
Anthocyanin accumulation is coordinated in plants by a number of conserved transcription factors. In apple (Malus x domestica, Borkh.) a R2R3 MYB transcription factor has been shown to control fruit flesh and foliage anthocyanin pigmentation (MYB10), and fruit skin colour (MYB1). However, the pattern of expression and allelic variation at these loci does not explain all anthocyanin-related apple phenotypes. One such example is an open-pollinated seedling of 'Sangrado' that has green foliage and develops red flesh in the fruit cortex late in maturity. We used methods that combine plant breeding, molecular biology and genomics to identify duplicated MYB transcription factors that could control this phenotype. We then demonstrated that the red flesh cortex phenotype is associated with enhanced expression of MYB110a, a paralogue of MYB10. Functional characterisation of MYB110a showed that it was able to up-regulate anthocyanin biosynthesis in tobacco. The chromosomal location of MYB110a is consistent with a whole genome duplication event that occurred during evolution of apple within the Maloideae family. Both MYB10 and MYB110a have conserved function in some cultivars but they differ in their expression pattern and response to fruit maturity.
Acidity levels greatly affect the taste and flavor of fruit, and consequently its market value. In mature apple fruit, malic acid is the predominant organic acid. Several studies have confirmed that the major quantitative trait locus Ma largely controls the variation of fruit acidity levels. The Ma locus has recently been defined in a region of 150 kb that contains 44 predicted genes on chromosome 16 in the Golden Delicious genome. In this study, we identified two aluminum-activated malate transporter-like genes, designated Ma1 and Ma2, as strong candidates of Ma by narrowing down the Ma locus to 65–82 kb containing 12–19 predicted genes depending on the haplotypes. The Ma haplotypes were determined by sequencing two bacterial artificial chromosome clones from G.41 (an apple rootstock of genotype Mama) that cover the two distinct haplotypes at the Ma locus. Gene expression profiling in 18 apple germplasm accessions suggested that Ma1 is the major determinant at the Ma locus controlling fruit acidity as Ma1 is expressed at a much higher level than Ma2 and the Ma1 expression is significantly correlated with fruit titratable acidity (R
2 = 0.4543, P = 0.0021). In the coding sequences of low acidity alleles of Ma1 and Ma2, sequence variations at the amino acid level between Golden Delicious and G.41 were not detected. But the alleles for high acidity vary considerably between the two genotypes. The low acidity allele of Ma1, Ma1-1455A, is mainly characterized by a mutation at base 1455 in the open reading frame. The mutation leads to a premature stop codon that truncates the carboxyl terminus of Ma1-1455A by 84 amino acids compared with Ma1-1455G. A survey of 29 apple germplasm accessions using marker CAPS1455 that targets the SNP1455 in Ma1 showed that the CAPS1455A allele was associated completely with high pH and highly with low titratable acidity, suggesting that the natural mutation-led truncation is most likely responsible for the abolished function of Ma for low pH or high acidity in apple.
A collection of 66 Malus×domestica Borkh. accessions from the USDA-ARS Plant Genetic Resources Unit’s core collection was screened with a set of eight SSR (simple
sequence repeat) primers developed at the PGRU in order to determine genetic identities, estimate genetic diversity, and to
identify genetic relationships among these accessions. All eight primer pairs generated multiple fragments when used in amplification
reactions with DNA from these accessions. High levels of variation were detected with a mean of 12.1 alleles per locus and
a mean heterozygosity across all eight loci of 0.693. The eight primer pairs utilized in this study unambiguously differentiated
all but seven pairs of accessions in this collection of 66 M.×domestica Borkh. genotypes. The probability of matching any two genotypes at all eight loci in this study was approximately 1 in 1
billion. The markers detected two misnamed accessions in the collection. Genetic-identity data produced a genetic-relatedness
phenogram which was concordant with geographic origins and/or known pedigree information. These SSR markers show great promise
as tools for managing Malus ex situ germplasm collections as well as for collection and preservation strategies concerning wild Malus populations in situ.
Knowledge about the sequence-based genetic diversity of a crop species is important in order to develop highly informative
genotyping assays, which will eventually positively impact breeding practice. Diversity data were obtained from two pools
of 185 and 75 accessions each, representing most of the species belonging to the genus Malus, by re-sequencing 27 gene-specific amplicons and by screening 237 Malus × domestica SNPs using the multiplex genotyping technology SNPlex™. Nucleotide diversity and insertion/deletion rates in M. × domestica were estimated as π = 0.0037 and 1/333bp, respectively. The SNP frequency was estimated as 0.0194 (1 SNP/52bp) while within a single apple
cultivar an average of one SNP in every 455bp was found. We also investigated transferability (T
SNP) of the heterozygous state of SNPs across the species M. × domestica and the genus Malus. Raw re-sequencing showed that 12–15% of M. × domestica SNPs are transferable to a second M. × domestica cultivar, however T
SNP rose to ∼41% with SNPs selected for high minor allele frequency. T
SNP of chosen SNPs averaged ∼27% in the two M. × domestica-related species, Malus sieversii and Malus sylvestris, but was much lower in more distantly related species. On the basis of T
SNP, simulations, and empirical results, we calculated that a close-design, multiplexed genotyping array with at least 2,000
SNPs is required for building a highly saturated linkage maps within any M. × domestica cross. The same array would gradually lose informativeness in increasingly phylogenetically distant Malus species.
KeywordsApple–High-throughput genotyping–SNP
Malus sieversii (Lebed.) M. Roem. is a wild progenitor species of the domesticated apple. It is found across a mountainous region of central
Asia and has been the focus of several collection expeditions by the USDA-ARS-National Plant Germplasm System. This study
used microsatellite variation at seven loci to estimate diversity and differentiation within M. sieversii using several complimentary approaches. Multilocus genotypes were amplified from 949 individuals representing seedling trees
from 88 half-sib families from eight M. sieversii populations collected in Kazakhstan. Apportioning of genetic variation was estimated at both the family and site level. Analyses
using a hierarchical model to estimate F
st showed that differentiation among individual families is more than three times greater than differentiation among sites.
In addition, average gene diversity and allelic richness varied significantly among sites. A rendering of a genetic network
among all sites showed that differentiation is largely congruent with geographical location. In addition, nonhierarchical
Bayesian assignment methods were used to infer genetic clusters across the collection area. We detected four genetic clusters
in the data set. The quality of these assignments was evaluated over multiple Markov Chain Monte Carlo runs using both posterior
likelihood and stability of the assignments. The spatial pattern of genetic assignments among the eight collection sites shows
two broadly distributed and two narrowly distributed clusters. These data indicate that the southwestern collection sites
are more admixed and more diverse than the northern sites.
The apple is the most common and culturally important fruit crop of temperate areas. The elucidation of its origin and domestication history is therefore of great interest. The wild Central Asian species Malus sieversii has previously been identified as the main contributor to the genome of the cultivated apple (Malus domestica), on the basis of morphological, molecular, and historical evidence. The possible contribution of other wild species present along the Silk Route running from Asia to Western Europe remains a matter of debate, particularly with respect to the contribution of the European wild apple. We used microsatellite markers and an unprecedented large sampling of five Malus species throughout Eurasia (839 accessions from China to Spain) to show that multiple species have contributed to the genetic makeup of domesticated apples. The wild European crabapple M. sylvestris, in particular, was a major secondary contributor. Bidirectional gene flow between the domesticated apple and the European crabapple resulted in the current M. domestica being genetically more closely related to this species than to its Central Asian progenitor, M. sieversii. We found no evidence of a domestication bottleneck or clonal population structure in apples, despite the use of vegetative propagation by grafting. We show that the evolution of domesticated apples occurred over a long time period and involved more than one wild species. Our results support the view that self-incompatibility, a long lifespan, and cultural practices such as selection from open-pollinated seeds have facilitated introgression from wild relatives and the maintenance of genetic variation during domestication. This combination of processes may account for the diversification of several long-lived perennial crops, yielding domestication patterns different from those observed for annual species.
We report a high-quality draft genome sequence of the domesticated apple (Malus × domestica). We show that a relatively recent (>50 million years ago) genome-wide duplication (GWD) has resulted in the transition from nine ancestral chromosomes to 17 chromosomes in the Pyreae. Traces of older GWDs partly support the monophyly of the ancestral paleohexaploidy of eudicots. Phylogenetic reconstruction of Pyreae and the genus Malus, relative to major Rosaceae taxa, identified the progenitor of the cultivated apple as M. sieversii. Expansion of gene families reported to be involved in fruit development may explain formation of the pome, a Pyreae-specific false fruit that develops by proliferation of the basal part of the sepals, the receptacle. In apple, a subclade of MADS-box genes, normally involved in flower and fruit development, is expanded to include 15 members, as are other gene families involved in Rosaceae-specific metabolism, such as transport and assimilation of sorbitol.
We estimate the minimum core size necessary to maximally represent a portion of the U.S. Department of Agriculture's National Plant Germplasm System apple (Malus) collection. We have identified a subset of Malus sieversii individuals that complements the previously published core subsets for two collection sites within Kazakhstan. We compared the size and composition of this complementary subset with a core set composed without restrictions. Because the genetic structure of this species has been previously determined, we were able to identify the origin of individuals within this core set with respect to their geographic location and genetic lineage. In addition, this core set is structured in a way that samples all of the major genetic lineages identified in this collection. The resulting panel of genotypes captures a broad range of phenotypic and molecular variation throughout Kazakhstan. These samples will provide a manageable entry point into the larger collection and will be critical in developing a long-term strategy for ex situ wild Malus conservation.
Malus sieversii, a wild apple species native to Central Asia, has been recognized as the major progenitor of the domestic apple. Collection trips to Central Asia have verified that M. sieversii is very diverse and has all the qualities present in M. × domestica. Nearly 130,000 seeds from 950 wild M. sieversii trees were collected in eight distinct sites, mostly in Kazakhstan, on four collection trips from 1989 to 1996. The investigation of 1480 seedlings from these diverse sites is summarized. All seedlings were screened as young seedlings for resistance to Venturia inaequalis (apple scab) and planted as own-rooted seedlings in a high-density orchard in Geneva, New York. Resistance was recorded in 41% of the seedlings (7%-66% among sites). Natural infection by Erwinia amylovora (fire blight) was also recorded, with 45% exhibiting no infection (26%-75% among sites). Seedlings with no fire blight symptoms were grafted, and replicates were inoculated in the greenhouse and 60% of that group was resistant. Resistance to V. inaequalis was re-assessed on those grafted plants. Those with original reactions similar to the Vr gene showed 100% agreement and those similar to Vf, 50% agreement. A large subset was also screened as young seedlings for resistance to Gymnosporangium juniperi-virginianae (cedar apple rust), with 55% showing resistance. We are in the process of evaluating the heritability of resistance to Phytophthora, Rhizoctonia and other components of apple replant disease in these accessions. In another collaborative project, fruit from a subset of the collection are being screened for resistance to the post harvest disease, blue mold (Penicillium expansum) with some indication of resistance. Seven of the scab resistant elite accessions were crossed with the susceptible cultivar Royal Gala. By screening >200 seedlings/population with V. inaequalis, 10% to 67% of each population were observed to be resistant. Correlation of the markers with phenotype indicated some M. sieversii parents likely had known resistance genes but, in some cases, exhibited patterns suggesting they also contained novel resistance loci. Seven highly diverse microsatellite markers were selected to assess the genetic relationships among the trees in the field collections that represent the populations and the collection sites. We characterized trees and fruit for horticultural traits using multiple descriptors on 746 seedlings. Among the many descriptors measured, individual fruit sizes (17 g-158 g) were quite variable among the trees and sites. We anticipate this germplasm will offer useful genetic diversity for crop improvement.
We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci—e.g., seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/~pritch/home.html.
China is one of the major germplasm centers of Malus species and is the origin of more than 25 species. Northwest China includes the three provinces of Shaanxi, Gansu and Qinghai and the two autonomous regions of Ningxia Huis and Xinjiang Uighur. It contains an unusually high diversity of wild apple germplasm resources comprising 16 Malus species. The species and ecotypes in the Qinling Mountains are richest, accounting for 80% of those in the Northwest China (65% of those of all China). Among the 16 species, the ecotypes of are most abundant and they are mainly found in humid conditions. M. sieversii is mostly distributed in the valleys of the Tianshan Mountains with its central distribution area being the counties of Yili, Gongliu and Xinyuan in Xinjiang, covering 14,000 ha. The wild Malus species of China are differentiated and adapted to local climates. Chinese wild Malus has been used for rootstocks for a long time in China. Among them, the seedlings of are widely used for rootstocks. However, it is important to make an additional effort to incorporate the desirable genes of this germplasm into dwarfing apple rootstocks.
Malus sieversii, a wild apple species native to Central Asia has been recognized as the major progenitor of the domestic apple. Recent collection trips to Central Asia have verified that M. sieversii is very diverse and has all the qualities present in M. × domestica. Nearly 100,000 seeds from 700 wild M. sieversii trees were collected in seven distinct areas of Kazakhstan over two collection trips (1995/96). Nearly 20,000 of these seeds have been distributed to scientists worldwide who are evaluating seedlings for multiple traits under different environments. This investigation features a subset of 6-yr-old seedlings originating from two areas in Kazakhstan: the northernmost (site 9); and southernmost (site 6). Seedlings were screened for resistance to Venturia inaequalis (apple scab) at the young seedling stage and planted as own-rooted seedlings in a high density orchard in Geneva, New York. Included are 14 elite populations (204 seedlings) out of the 85 seed lots collected at site 6, and 29 elite populations (388 seedlings) out of the 207 seed lots from site 9, as well as 12 grafted elite clones (mothers of some of the 388 seedlings) from site 9. Scab resistance of plants grown in Geneva was found in 40% of seedlings from site 6 and 47% of those from site 9. Natural infection with Erwinia amylovora (fire blight) was recorded, with those from site 9 showing significantly higher levels than those from site 6. In the 6th leaf, we characterized fruit using multiple descriptors on 55% of seedlings from site 6 and 28% from site 9. Among the many descriptors measured, individual fruit size was quite variable among the many trees, but generally much larger from site 9 than site 6. The range of fruit weight from different trees was: 17-72 g (site 6); 20-102 g (site 9); and 74-158 g (site-9 clones). We anticipate this germplasm, along with that from the broad M. sieversii evaluation project, will offer useful genetic diversity for crop improvement.
Subfam. Maloideae (x = 17) has been held to be tetraploid since 1931 while later, Sax elaborated by Stebbins, specifically implicated subfam. Spiraeoideae (x = 9) and Amygdaloideae (x = 8) in an allotetraploid ancestry. The allotetraploid theory has gained considerable credibility with many workers on Rosaceae but, although support for it is not unanimous, and it is sometimes ignored, there has never been any attempt at refutation. To date, the theory has depended mainly on chromosome constitution, and, in a rather general way, on the morphological characteristics of the respective taxa. In this paper we review the allotetraploid hypothesis and generally verify it by an extensive character analysis of the Maloideae, Amygdaloideae, and Spiraeoideae. Since no specifically rosoid or quillajoid characters exist in the Maloideae, no candidate near-ancestral genera in subfam. Rosoideae or tribe Quillajeae can be pinpointed. The autapomorphic fruit of the Maloideae-the pome-is derivable from spiraeoid or proto-amygdaloid characters. In a parsimony analysis of a 96 taxa x 36 variable data matrix the phenetic genera were, for the most part, returned as clades, but their placement was to a significant extent, peculiar. The consistency index was extremely low. Furthermore, the addition of only three OTUs resulted in major relocations of some of the genera. We concluded that, in this type of situation, parsimony analysis is not robust, and sought other explanations for the relationships suggested. We favour the idea that several clades of Maloideae originated independently in a highly reticulate system existing shortly after the original allotetraploid cross. This notion of polychotomous early evolution alone, we feel, makes sense of the general correspondence of phenetic genera to cladistic genera, remarkably low consistency index, great instability of the cladogram with respect to changing only a few OTU's, and the manifestly great ability of most maloidean genera to hybridize. Thus, the precise phylogeny of the Maloideae must remain quite unknown until a very different kind of investigation has been successfully conducted.
Potential interspecific hybrids are usually identified in natural populations by their proximity to interbreeding species or their intermediate phenotypes; hybridization can then be confirmed by comparing the genetic makeup of putative hybrids to pure species. In contrast, detecting interspecific hybridization and misclassifications in ex situ collections can be difficult because fine-scale geographic locations and species-specific phenotypic data are generally unavailable. Thus, there is little a priori information available to suggest which individuals might be hybrids. Instead, hybrids or misclassified individuals must be identified based on molecular data via population assignment and admixture detection programs. We have applied a variety of population assignment and admixture detection programs to over 400 samples of four closely related Malus species held in the US Department of Agriculture–Agricultural Research Service National Plant Germplasm System that were genotyped at 19 simple sequence repeat loci. Our findings indicate that over 10 % of the samples of the wild species Malus sieversii and Malus orientalis and nearly 20 % of the samples of the wild species Malus sylvestris may be admixed or misclassified. The percentage of admixed or misclassified samples of the domesticated species, Malus × domestica, was much lower, at <5 %. These findings provide an illustration of how to detect hybridization and misclassification in ex situ collections using molecular data and, ultimately, should help to maximize the utility of the collections. In addition, the presence of wild-collected samples that show admixture with domesticated apple suggests that gene flow may be occurring from the crop into natural populations of the wild species.
Anthocyanins are flavonoid pigments imparting red, blue, or purple pigmentation to fruits, flowers and foliage. These compounds are powerful antioxidants in vitro, and are widely believed to contribute to human health. The fruit of the domestic apple (Malus x domestica) is a popular and important source of nutrients, and is considered one of the top ‘functional foods’—those foods that have inherent health-promoting benefits beyond basic nutritional value. The pigmentation of typical red apple fruits results from accumulation of anthocyanin in the skin. However, numerous genotypes of Malus are known that synthesize anthocyanin in additional fruit tissues including the core and cortex (flesh). Red-fleshed apple genotypes are an attractive starting point for development of novel varieties for consumption and nutraceutical use through traditional breeding and biotechnology. However, cultivar development is limited by lack of characterization of the diversity of genetic backgrounds showing this trait. We identified and cataloged red-fleshed apple genotypes from four Malus diversity collections representing over 3,000 accessions including domestic cultivars, wild species, and named hybrids. We found a striking range of flesh color intensity and pattern among accessions, including those carrying the MYB10
R
6
allele conferring ectopic expression of a key transcriptional regulator of anthocyanin biosynthesis. Although MYB10
R
6
was strongly associated with red-fleshed fruit among genotypes, this allele was neither sufficient nor required for this trait in all genotypes. Nearly all red-fleshed accessions tested could be traced back to ‘Niedzwetzkyana’, a presumed natural form of M. sieversii native to central Asia.
Introduction Historical Review The Role of Wild Apple in the Vegetative Cover of Mountain Regions in Kazakhstan The Influence of Wild Apples on the Structure of the Environment Characteristics of Wild Apple Growth and Development Intraspecific Polymorphism of Wild Apple Utility and Biochemical Characterization of Wild Apple Fruit Preservation of Wild Apples Conclusion Literature Cited
Introduction Germplasm Acquisition Central Asian Collections Maintenance Distribution Characterization and Evalution Utilization Conclusion Literature Cited
Thirteen polymorphic microsatellite loci were developed in the Japanese pear (Pyrus pyrifolia Nakai) by using an enriched genomic library. The obtained microsatellite loci showed a high degree of polymorphism in the Japanese pear with 3–6 alleles per locus. The average values of observed and expected heterozygosities among these 13 loci were 0.69 and 0.71, respectively. Ten microsatellites could successfully amplify loci in the European pear (Pyrus communis L.), which were highly polymorphic as well.
The phylogenetic relationship of cultivated apple and its closely related species is still not clear in the taxonomy of genus Malus. To try to find new evidence for the origin and evolution of the cultivated apple, random amplified polymorphic DNA (RAPD) markers of 14 taxa of Malus, among which a reference species (M. toringoides) and six presumably ancestral species of cultivated apple in the genus were investigated. The RAPD data obtained were used to construct both unrooted and rooted trees using TREECON software package. The result showed in our rooted tree that M. sieversii from the Xinjiang Autonomous Region of China is the species which is most closely related to the cultivated apple, M. domesticacv. `Golden Delicious'. The phylogenetic relationships among the species studied are discussed.
China is the centre of origin of the genus Malus Mill. About 80% of all species of the genus have areas in this country – among them 8 newly described ones. All species are encountered, their distribution within the provinces is listed and completed by characteristics and uses.
Screening of an apple genomic library with (GA)15 and (GT)15 probes demonstrated that these repeats are abundant, occurring
about every 120 and 190 kb, respectively. Microsatellites isolated from a small insert library enriched for (GA) repeats contained
numbers of repeats ranging from 7 to 39. Primers to these microsatellite loci were able to direct the amplification of the
repeats in 21 different cultivars. The majority of markers were highly polymorphic, diploid, and showed simple Mendelian inheritance,
although about 25% of markers generated complex banding patterns consistent with the amplification of more than one locus.
As few as three microsatellite markers were sufficient to differentiate between all 21 cultivars.
Malus sieversii (Ledeb.) Roem. is a wild apple species which is distributed in the western mountains in Xinjiang, P.R. China, as well as
in Central Asia, including Kazakhstan, Kyrgyzstan, Tajikistan, Uzbekistan and Turkmenistan. M. sieversii germplasm is valuable for plant breeders for drought, cold and disease resistance. Genetic polymorphisms of 20 populations
of M. sieversii and 2 populations of M. niedzwetzkyana in Xinjiang, China were analyzed using RAPD markers. We present geographical distribution data as well as the discovery of
a rare king old tree. Different types of pollen grain morphology were analyzed.
Twenty-nine Malus species, 12 M. domestica cultivars and representative outgroup taxa were chosen for sequence analysis of the internal transcribed spacer of nuclear
ribosomal DNA and the matK region of the chloroplast genome, in order to develop an explicit phylogenetic hypothesis for the genus and identify potential
germplasm donors to the domesticated apple, M. domestica. Maximum parsimony analysis generated nuclear and chloroplast cladograms that provide reasonable resolution of sub-generic
groups, as recognised in classifications. All of the close relatives of M. domestica occur in a poorly resolved series Malus clade. Two matK duplications were found, one in series Malus and the other in most M. domestica cultivars and one Central Asian M. sieversii accession.
The availability of suitable genetic markers is essential to efficiently select and breed apple varieties of high quality and with multiple disease resistances. Microsatellites (simple sequence repeats, SSR) are very useful in this respect since they are codominant, highly polymorphic, abundant and reliably reproducible. Over 140 new SSR markers have been developed in apple and tested on a panel of 7 cultivars and 1 breeding selection. Their high level of polymorphism is expressed with an average of 6.1 alleles per locus and an average heterozygosity (H) of 0.74. Of all SSR markers, 115 have been positioned on a genetic linkage map of the cross Fiesta × Discovery. As a result, all 17 linkage groups, corresponding to the 17 chromosomes of apple, were identified. Each chromosome carries at least two SSR markers, allowing the alignment of any apple molecular marker map both with regard to identification as well as to orientation of the linkage groups. To test the degree of conservation of the SSR flanking regions and the transferability of the SSR markers to other Rosaceae species, 15 primer pairs were tested on a series of Maloideae and Amygdaloideae species. The usefulness of the newly developed microsatellites in genetic mapping is demonstrated by means of the genetic linkage map. The possibility of constructing a global apple linkage map and the impact of such a number of microsatellite markers on gene and QTL mapping is discussed
We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci-e.g. , seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/ approximately pritch/home. html.
Molecular genetic markers complement archaeological, breeding and geographical investigations of the origins, history and domestication of plants. With increasing access to wild apples from Central Asia, along with the use of molecular genetic markers capable of distinguishing between species, and explicit methods of phylogeny reconstruction, it is now possible to test hypotheses about the origin of the domesticated apple. Analyses of nuclear rDNA and chloroplast DNA (cpDNA) sequences indicate that the domesticated apple is most closely related to series Malus species. Moreover, the occurrence of a shared 18-bp duplication in the cpDNAs of wild and cultivated apple supports the close relationship between them. Hypotheses about the hybridization and the origin of the domesticated apple cannot be rejected completely until more variable, phylogenetically informative markers are found.
Some debated issues of the genus Malus (apple) taxonomy were examined using a variety of species from the collection of the Maikop Experimental Station, Vavilon Research Institute of Plant Industry (Krasnodar krai). Phylogenetic relationships among these species were studied using traditional analysis of morphological traits, RAPD, and complete sequencing of the 5'-internal transcribed spacer (ITS1), 5.8S rRNA, 3'-internal transcribed spacer (ITS2) (constituting a cluster of the rRNA genes), and the terminal fragment of the matK gene encoding chloroplast maturase. The results showed that the Sorbomalus section was polyphyletic; the American apple M. fusca was closely related to the species contributing to the East Asian center of the genus origin, and the American species M. angustifolia, M. coronaria, and M. ioensis were closely related to the M. trilobata relict species, whose assignment to the genus Malus is debated by some authors. Molecular analysis of the species relationships showed that the Middle Asian apple M. sieversii is the species from which apple domestication started.
To unravel the relationship between the European wild apple, Malus sylvestris (L.) Mill., and its domesticated relative M. domestica Borkh., we studied chloroplast DNA variation in 634 wild and 422 domesticated accessions originating from different regions. Hybridization between M. sylvestris and M. domestica was checked using 10 nuclear microsatellites and a Bayesian assignment approach. This allowed us to identify hybrids and feral plants escaped from cultivation. Sixty-eight genotypes belonging to 12 other wild Malus species, including 20 M. sieversii (Ledeb.) Roem. accessions were also included in the analysis of chloroplast diversity. Marker techniques were developed to type a formerly described duplication and a newly detected transversion in the matK gene. Chloroplast DNA variation was further investigated using PCR-RFLP (Polymerase Chain Reaction-Random Fragment Length Polymorphism), and haplotypes were constructed based on all mutational combinations. A closer relationship than presently accepted between M. sylvestris and M. domestica was established at the cytoplasmic level, with the detection of eight chloroplast haplotypes shared by both species. Hybridization between M. sylvestris and M. domestica was also apparent at the local level with sharing of rare haplotypes among local cultivars and sympatric wild trees. Indications of the use of wild Malus genotypes in the (local) cultivation process of M. domestica and cytoplasmic introgression of chloroplast haplotypes into M. sylvestris from the domesticated apple were found. Only one of the M. sieversii trees studied displayed one of the three main chloroplast haplotypes shared by M. sylvestris and M. domestica. This is surprising as M. sieversii has formerly been described as the main maternal progenitor of the domesticated apple. This study hereby reopens the exciting discussion on the origin of M. domestica.
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