Fig 2 - uploaded by Paul L. Sanchez
Content may be subject to copyright.
2 The genus Oryza : 12 representative species  

2 The genus Oryza : 12 representative species  

Source publication
Book
Full-text available
The wild species of the genus Oryza serve as a virtually untapped reservoir of genetic diversity that can be used to improve the world's most important food crop—rice. The genus is com-posed of two domesticated (O . sativa and O . gla-berrima) and 22 wild species [ 68 ] and represents between 15 and 25 million years of evolutionary diversifi cation...

Similar publications

Article
Full-text available
During 2012–14, 737 sweetpotato, Ipomoea batatas (L.) Lam. (Convolvulaceae), plant introduction (PI) accessions from the U.S. Department of Agriculture, Agricultural Research Service (USDA, ARS) sweetpotato germplasm collection were evaluated for several phenotypic leaf and plant characteristics, and a photographic record of each accession was made...

Citations

... The domestication of O. glaberrima started ~3000 years ago in Africa with the cultivation of O. barthii along the delta of the Niger River and its later development into the modern African rice (Wang et al., 2014). In addition to the domesticated rice species, the Oryza genus contains 25 wild species distributed in the pan-tropics, which exhibit tremendous diversity in morphology, agronomic traits, and adaptations to different biotic and abiotic stress (Sanchez et al., 2013). The genus spans 15 million years (MYs) of evolutionary history, and includes species with different ploidy levels and genome architectures. ...
Article
Full-text available
The wild relatives of rice hold unexplored genetic diversity that can be employed to feed an estimated population of 10 billion by 2050. The Oryza Map Alignment Project (OMAP) initiated in 2003 has provided comprehensive genomic resources for comparative, evolutionary and functional characterization of the wild relatives of rice, facilitating the cloning of over 600 rice genes, including those for grain width (GW5) and submergence tolerance (SUB1A). Following the footsteps of the original project, the goal of “IOMAP: The Americas” is to investigate the present and historic genetic diversity of wild Oryza species endemic to the Americas through the sequencing of herbaria and in-situ specimens. The generation of a large diversity panel describing past and current genetic status and potential erosion of genetic variation in the populations will provide useful knowledge for the conservation of the biodiversity in these species. The wild relatives of rice in the Americas present a wide range of resistance traits useful for crop improvement and neodomestication approaches. In the race against time for a sustainable food future, the neodomestication of the first cereal species recently accomplished in O. alta opens the door to the potential neodomestication of the other wild Oryza species in Americas.
... These species are phenotypically inferior to cultivated rice. However, there is evidence of transgressive segregation for yield in crossbreeding between cultivated and wild species, which contain genes that can improve quantitative yield-related characteristics (Sánchez, 2013). ...
Article
Full-text available
La investigación se centra en las líneas avanzadas desarrolladas a través de cruces interespecíficos entre Oryza sativa L. ssp. japonica x Oryza rufipogon G., y la línea tipo japónica, cuya tolerancia a las sales bajo condiciones de invernadero y campo se sometieron a evaluación. En la primera fase en invernadero, se sembraron 24 líneas avanzadas de arroz F5, cinco líneas parentales y un cultivar comercial SFL-011 (control) en medio líquido con una concentración de 7,0 dS/m CE salinizado con NaCl y control con 0,2.dS/m CE de agua de riego. En la segunda fase en condiciones de campo se evaluaron líneas de arroz F6 en suelos salinos con 7.44 dS/m CE. Se midieron variables agronómicas y de rendimiento. En condiciones de invernadero se destacaron seis líneas: Puyón/JP003 P11-106716, Puyón/JP002 P8-30552, Puyón/JP003 P11-103115, Puyón/JP002 P8-294930, JP002/JP001 P × P 5P 1322 y JP001/JP003 P1 × 11P 413, con mayor tolerancia que el control en cuanto a vigor de planta, panículas por planta, granos por panícula, peso de 1000 granos y rendimiento (g/planta). En condiciones de campo, dos líneas, Puyón/JP003 P11-106716 y Puyón/JP003 P11-103115, se destacaron por tener mejores resultados agronómicos en cultivares y rendimiento. Los resultados mostraron la importancia del uso de cruces interespecíficos entre O. Sativa ssp. japonica x O. rufipogon, y la línea tipo japónica para mejorar la tolerancia a la salinidad del arroz y garantizar altos rendimientos potenciales en suelos salinizados; de ahí la importancia del cruce en términos de rendimientos agrícolas.
... From these evaluations, seven accessions that exhibited ShB resistance were identified. Three of the accessions were classified as O. nivara (Brar and Singh 2011;Sanchez et al. 2013), thus less likely to have problems with sterility in crosses with cultivated rice. ...
Article
Full-text available
Oryza nivara is considered one of the wild progenitors of cultivated Asian rice (O. sativa). An O. nivara (IRGC104443) accession, previously identified as being moderately resistant to rice sheath blight disease, was used as the donor parent to develop an advanced backcross population with the U.S. rice (O. sativa) cultivar, LaGrue, as the recurrent parent. The population was genotyped with 210 DNA markers and a linkage map constructed that spanned 1488.9 cM. Sheath blight (ShB) disease was evaluated in both greenhouse and field conditions. Days to heading (DTHD), plant height (PTHT) and culm (angle) habit (CULMHAB) were recorded because they can confound sheath blight disease ratings under field conditions. Multiple interval mapping identified qShB9 as the ShB-QTL being the source of resistance and the resistance was attributed to the O. nivara allele. The single CULMHAB QTL, qCULMHAB9, was also located in this region but had a different peak suggesting the more open tillering was most likely due to the TILLER ANGLE CONTROL-1 gene which was fine-mapped near the chromosome 9 ShB resistance in other O. sativa populations. The ShB QTL, qShB3-2-mc, identified in the greenhouse study was not verified in the field studies. None of the three DTHD QTL were colocalized with ShB QTL, while the single PTHT QTL was mapped to the region of the semi-dwarf-1 gene for short stature on chromosome 1. Further studies will be undertaken to fine map the qShB9 region and identify linked markers for use in cultivar development.
... India accounts for the production of 117 million tons and consumption of 108 million tons by -21 (Susan Reidy, 2020. Rice belongs to the genus Oryza, comprising 25 species including two cultivated species; Oryza sativa (Asian rice) and O. glaberimma (African rice) (Sanchez et al., 2014). The rice crop is host to numerous pests and diseases including plant parasitic nematodes. ...
Article
Full-text available
Rice (Oryza sativa) is an important cereal crop and staple food for more than half of the world population. The sedentary endoparasitic nematode Meloidogyne graminicola is one of the major biotic stress factors that limit rice production globally irrespective of the agro-ecosystem. To tackle this, the host plant resistance is given prime importance due to global awareness towards ecologically stable and environmentally safe management options. However, the availability of resistant source within O. sativa against M. graminicola is limited and hence the search was extended to its wild relatives globally. In line with that, about 24 germplasms of different Oryza species collected from the gene bank of NRRI, Cuttack were evaluated against M. graminicola under artificial inoculation condition. Among them O. eichingeri and O. grandiglumis belonging to O. officinalis species complex and O. brachyantha were found to be resistant to M. graminicola with the lowest gall index (2.0-2.3 galls /root system). Oyza rufipogon, O. officinalis and O. alta were found tolerant to the nematode while all other species exhibited susceptible to highly susceptible reaction to the nematode. A more comprehensive study is necessary to shed light on the consistency of resistance within each Oryza species and also suggest the utilization of molecular tools to decipher the resistance mechanism govern in the reported accessions against rice root-knot nematode.
... However, this is clearly supported by previous works that reported that photosynthesis in wild rice species was superior to O. sativa, although there were a few variations between wild rice species [18,28,[33][34][35][36]. Tsutsumi et al. [35] explained that a higher photosynthetic rate in O. latifolia was due to bigger mesophyll cells and greater Rubisco activity, and the photosynthetic rate showed a positive correlation with leaf width [35,37]. Water use efficiency (WUE, photosynthetic rate, P n /transpiration rate, E) is often defined as an indicator of drought resistance, and some wild rice species, O. meridionalis, O. officinalis, and O. punctata, were known as drought-resistant species [38]. In this study, O. minuta, shade-to semi-shade-grown, exhibited significantly higher WUE, and our finding suggests that O. minuta could be a useful source of germplasm to enhance WUE against climate change [39]. ...
Article
Full-text available
The ever-increasing human population alongside environmental deterioration has presented a pressing demand for increased food production per unit area. As a consequence, considerable research effort is currently being expended in assessing approaches to enhance crop yields. One such approach is to harness the allelic variation lost in domestication. This is of particular importance since crop wild relatives often exhibit better tolerance to abiotic stresses. Here, we wanted to address the question as to why wild rice species have decreased grain production despite being characterized by enhanced rates of photosynthesis. In order to do so, we selected ten rice species on the basis of the presence of genome information, life span, the prominence of distribution, and habitat type and evaluated the expression of genes in photosynthesis, photorespiration, sucrose and starch synthesis, sucrose transport, and primary and secondary cell walls. We additionally measured the levels of a range of primary metabolites via gas chromatography–mass spectrometry. The results revealed that the wild rice species exhibited not only higher photosynthesis but also superior CO2 recovery by photorespiration; showed greater production of photosynthates such as soluble sugars and starch and quick transportation to the sink organs with a possibility of transporting forms such as RFOs, revealing the preferential consumption of soluble sugars to develop both primary and secondary cell walls; and, finally, displayed high glutamine/glutamic acid ratios, indicating that they likely exhibited high N-use efficiency. The findings from the current study thus identify directions for future rice improvement through breeding.
... Compounding the problem is the current practice of crossing elite lines, which is expected to reduce genetic variability in the working germplasm, thus, preventing the discovery of novel traits to improve yield. Undoubtedly, plant breeders have witnessed a substantial increase in yield over the years with adoption of new cultivars and better management practices (Sanchez et al. 2013). But, in order to solve the envisioned 9 billion people question (Jacquemin et al. 2013), the rate of rice production must increase on the currently available land. ...
... The Asian cultivated rice, O. sativa, belongs to genus Oryza that includes another cultivated African rice species, O. glabberima (2n = 24, AA) and 22 wild species (2n = 24, 48) representing the AA, BB, CC, BBCC, CCDD, EE, FF, GG, KKLL, and HHJJ genome types (Sanchez et al. 2013). It has been envisioned that utilizing the useful novel variability present in wild relatives of rice could be a promising approach to increase the genetic variability in a breeder's pool. ...
Article
Full-text available
Being one of the most important staple dietary constituents globally, genetic enhancement of cultivated rice for yield, agronomically important traits is of substantial importance. Even though the climatic factors and crop manage- ment practices impact complex traits like yield immensely, the contribution of variation by underlying genetic factors surpasses them all. Previous studies have highlighted the importance of utilizing exotic germplasm, landraces in enhancing the diversity of gene pool, leading to better selections and thus superior cultivars. Thus, to fully exploit the potential of progenitor of Asian cultivated rice for productivity related traits, genome wide association study (GWAS) for seven agronomically important traits was conducted on a panel of 346 O. rufipogon accessions using a set of 15,083 high-quality single nucleotide polymorphic markers. The phenotypic data analysis indicated large continuous variation for all the traits under study, with a significant negative correlation observed between grain parameters and agronomic parameters like plant height, culm thickness. The presence of 74.28% admixtures in the panel as revealed by investigating population structure indicated the panel to be very poorly genetically differentiated, with rapid LD decay. The genome-wide association analyses revealed a total of 47 strong MTAs with 19 SNPs located in/close to previously reported QTL/genic regions providing a positive analytic proof for our studies. The allelic differences of significant MTAs were found to be statistically significant at 34 genomic regions. A total of 51 O. rufipogon accessions harboured combination of superior alleles and thus serve as potential candidates for accelerating rice breeding pro- grams. The present study identified 27 novel SNPs to be significantly associated with different traits. Allelic differences between cultivated and wild rice at significant MTAs determined superior alleles to be absent at 12 positions imply- ing substantial scope of improvement by their targeted introgression into cultivars. Introgression of novel significant genomic regions into breeder’s pool would broaden the genetic base of cultivated rice, thus making the crop more resilient.
... Moreover, there are 22 wild relatives of Oryza (2n ¼ 24 or 48) with a broad geographic range (Khush 1997;Vaughan 1989). They represent ten genome types (Sanchez et al. 2013) (Table 21.1). O. sativa is grown and consumed as a staple food in most Asian countries. ...
Chapter
Breeders need access to unique genetic variability to meet the growing demand for food while maintaining sustainable agricultural production with the impacts of climate change for generating high-quality nutritional food. Changes in climate and anthropogenic activities and a multitude of environmental influences pose severe threats to food supply and preservation of natural diversity. For example, unpredictable droughts, elevated temperature, and new diseases and pests threaten crop production. Thus, breeding with crop wild relatives (CWR) gives significant resilience to modern agricultural systems and the ability to help sustainably boosting agricultural productivity. As a result, numerous genotype screenings are necessary for broad adaptability, producing a segregating material through fast breeding or rapid generation to shorten the breeding cycle and improving genetic gain. In addition, CWR genomics generates data that support CWR’s usage to boost agricultural genetic diversity. QTL mapping, identifying of candidate genes by next-generation sequencing, gene-based marker development, or significant candidate gene pyramiding of stress-responsive loci in popular cultivar are required to maintain the sustainability of crop production. Thus, genomic data is useful for identifying and isolating novel and dominant alleles of genes from crop gene pools that are agronomically important, which can be used to generate improved crop cultivars. Hence, the natural allelic difference in candidate genes that influences major agronomic characteristics and crop development initiatives is being investigated via allele mining. Among the CWRs of economically important crops, the wild species of rice is essential to improve modern rice cultivars. The awareness of novel genetic and genomic approaches of rice genetic resources for efficient utilization is crucial. Further, their conservation status and availability have not been quantified globally. As a result, a joint effort is required to improve the conservation and accessibility of crop wild relatives for rice breeding. Keywords: Genomics of CWR, Crop improvement, Rice genetic resources
... Moreover, there are 22 wild relatives of Oryza (2n ¼ 24 or 48) with a broad geographic range (Khush 1997;Vaughan 1989). They represent ten genome types (Sanchez et al. 2013) (Table 21.1). O. sativa is grown and consumed as a staple food in most Asian countries. ...
Chapter
Permaculture has been known to intentionally integrate diversity into the design of farms and mimic natural landscapes. This approach is in contrast to the mainstream monocropping system in conventional agriculture. The objectives of the study were to identify what plant species are commonly cultivated in permaculture farms and determine its uses as narrated by farmers and practitioners. The researchers conducted a crop inventory in 12 permaculture sites in the Philippines from August to November in 2018. To survey a 1 ha sampling area, a modified belt transect method with alternating 20 m2 plots was employed for full enumeration of plant species in each plot. To determine uses, key informant interviews and focus group discussions were conducted among farm staff. A total of 215 plant species were identified with an average species richness of 46 per farm. A comparison of crop inventories revealed that Colocasia esculenta and Capsicum frutescens were the most commonly cultivated crops found in ten sites (83%). It is followed by Annona muricata (nine sites) and Bambusoideae (eight). Results revealed that the majority of crops found were cultivated for household consumption.
... Moreover, there are 22 wild relatives of Oryza (2n ¼ 24 or 48) with a broad geographic range (Khush 1997;Vaughan 1989). They represent ten genome types (Sanchez et al. 2013) (Table 21.1). O. sativa is grown and consumed as a staple food in most Asian countries. ...
Chapter
Full-text available
Integrating greeneries into the indoor dwelling environment boosts work performance and relieves stress to add to the overall psychological well-being especially in deserted urban settings. In addition to mental soothing, thermal regulation, air purification, aesthetics, public health, and comfort, the addition of plants to indoor settings may also contribute to the conservation of dwindling floral biodiversity. Despite authorities’ pledge for sustainable urban management, the status of indoor gardening has hitherto remained unexplored in the emerging megapolis of Bangladesh—Chattogram—the second largest urban center of the country. In addressing that gap, this study aims to explore the composition, diversity, and management of indoor plants in urban dwellings at Halishahar of Chattogram based on interviews on 48 households selected through multistage random sampling. Data from all selected households were collected by using a semi-structured questionnaire through physically visiting the households. Almost half of the households (48%) living at Halishahar had indoor plants in their dwellings. The study recorded a handsome 120 indoor plant species belonging to 108 genera from 60 families. While the diversity was in no way comparable to the tropical ecosystem of the country, in consideration of the strict set of requirements for plants to be suitable for an indoor setting, the diversity seemed excellent as evident from four diversity indices. Soil mixed with compost, sand, and surki at different ratios is used as potting media. Pests were identified as the major challenge in managing the indoor plants. Application of domestic manure with the potting media was common as a means to maintain the nutrient flow. Bruised tea leaf is the most frequently added nutrient supplement. Apart from the aesthetic values, urban dwellers from Halishahar reported the immense potential of indoor gardening in supplementing daily nutrition and in mitigating the impacts of climate change. The lessons from this study can be used in informed policymaking for the promotion of biodiversity conservation and other benefits from indoor greening among urban dwellers in Bangladesh.
... The genus Oryza is composed of 2 domesticated (O. sativa and O. glaberrima) and 22 wild species (Sanchez et al., 2013). All of six AA-genome wild species and 5 distantly related species with CC, BBCC, CCDD, EE, and FF genomes have been successfully used to construct ILs (Ali et al., 2010;Sanchez et al., 2013;Zhang et al., 2022). ...
... sativa and O. glaberrima) and 22 wild species (Sanchez et al., 2013). All of six AA-genome wild species and 5 distantly related species with CC, BBCC, CCDD, EE, and FF genomes have been successfully used to construct ILs (Ali et al., 2010;Sanchez et al., 2013;Zhang et al., 2022). To date, more than twenty sets of ILs derived from crosses between wild relatives and cultivated rice have been developed (Ali et al., 2010;Balakrishnan et al., 2019), and some public resource platforms, such as CSSLs created with introgression from four wild rice into the japonica rice variety Taichung 65 and ILs developed from crosses between two varieties (IR64 and Cybonnet) and three wild accessions , have been initially established. ...
... Accessions from these subpopulations were rarely used in the past, but are encouraged used as donors for constructing ILs in the future because more new QTLs might be detected using this kind of ILs. Many ILs have been constructed using AA-genome wild species as donors, but there are few successful cases of constructing ILs using other wild Oryza species as donors due to the strong incompatibility barriers (Sanchez et al., 2013). These wild species not only have strong biotic and abiotic stress resistance, but also have unique and excellent traits, such as the early morning flowering trait in CC-genome wild rice Oryza officinalis and the high biomass production in CCDD-genome wild species (Sanchez et al., 2013;Hirabayashi et al., 2015). ...
Article
Full-text available
The narrow base of genetic diversity of modern rice varieties is mainly attributed to the overuse of the common backbone parents that leads to the lack of varied favorable alleles in the process of breeding new varieties. Introgression lines (ILs) developed by a backcross strategy combined with marker-assisted selection (MAS) are powerful prebreeding tools for broadening the genetic base of existing cultivars. They have high power for mapping quantitative trait loci (QTLs) either with major or minor effects, and are used for precisely evaluating the genetic effects of QTLs and detecting the gene-by-gene or gene-by-environment interactions due to their low genetic background noise. ILs developed from multiple donors in a fixed background can be used as an IL platform to identify the best alleles or allele combinations for breeding by design. In the present paper, we reviewed the recent achievements from ILs in rice functional genomics research and breeding, including the genetic dissection of complex traits, identification of elite alleles and background-independent and epistatic QTLs, analysis of genetic interaction, and genetic improvement of single and multiple target traits. We also discussed how to develop ILs for further identification of new elite alleles, and how to utilize IL platforms for rice genetic improvement.