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SSR analysis of introgression of drought tolerance from the genome of Hordeum spontaneum into cultivated barley (Hordeum vulgare ssp vulgare)

DOI:10.1007/s10681-012-0795-9
Authors:
Berhane Lakew at Ethiopian Institute of Agricultural Research
Berhane Lakew
Robert James Henry at The University of Queensland
Robert James Henry
J. Eglinton
J. Eglinton
J. Eglinton
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Michael Baum at International Center for Agricultural Research in the Dry Areas (ICARDA)
Michael Baum
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Wild barley (Hordeum vulgare ssp. spontaneum) and landraces are important sources of resistance to biotic and abiotic stresses since they possess wide genetic diversity that may be missing in current elite varieties. In this study, we evaluated a set of 57 barley introgression lines divided in groups depending on the expected levels of introgression (50, 25, and 12.5 %) from one Hordeum spontaneum accessions (Hsp 41-1) and on those (50 and 25 %) from a second (Hsp 41-5); in both cases the 25 % level was represented by two groups depending on the other parent. The two H. spontaneum accessions have been used as the best sources of drought tolerance in the ICARDA barley-breeding program. Graphical genotyping and genetic diversity analysis were used to examine the relative contribution of H. spontaneum and the extent of genetic differences among the 57 lines using 74 microsatellite markers that cover 941 cM of the barley genome. The average proportion of the genome containing H. spontaneum alleles in each group was of 44.5 %, group 1; 24.6 %, group 2; 21.6 %, group 3; 45.4 %, group 4; 19 %, group 5; 15.5 %, group 6 and 11.4 %, group 7. Introgression lines in group 1 and 4, with the highest observed introgression with Hsp 41-1 and Hsp 41-5, showed higher grain yield and better agronomic performance under field conditions in Breda and Khanaser, i.e., the two most stressed environments in which the groups were phenotyped, indicating the usefulness of using H. spontaneum as a source of chromosomal linkage blocks important for improved drought tolerance. However, more extensive genome coverage will be needed to identify the specific chromosomal regions associated with superior performance under extreme drought.
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Supplementary resource (1)

Supplementary material 1
Data
May 2013
Berhane Lakew · Robert James Henry · Salvatore Ceccarelli · Stefania Grando · Michael Baum
... Technical and financial challenges outweighed political/legal or ownership issues when it came respondents' ability to access and use crop wild relatives. While there are a number of success stories around the introduction of useful traits from the highly variable pools of crop wild relatives [41,[46][47][48][49][50], the transfer of alleles from wild populations tends to be slow, genetically tricky and expensive compared to when using advanced or elite lines [12,55,84]. Other limitations, such as the lack of genetic materials or information about them, only affected a minority of breeders working with wild relatives, a minority which seeks to mine an even greater variety of ex situ sources, including foreign ex situ institutions and collections from the private sector. ...
... While most of the surveyed breeders are continuing to pursue similar strategies working with genetic resources under increasing climate change awareness, our results offer some interesting insights from the minority of breeders who are diversifying their germplasm materials and sources. Overcoming the barriers they experience may encourage a broader diffusion of those diversity-based strategies that literature describes as essential in responding to climate change [36][37][38][39][40][41][42][43][44][45][46][47][48][49][50]91]. Though some argue this potential is overstated [92,93], introducing more advanced genomic/phenotyping tools into any breeding programme has the potential to improve the power and speed of exploring large pools of diversity [94,95]. ...
The Role of Genetic Resources in Breeding for Climate Change: The Case of Public Breeding Programmes in Eighteen Developing Countries
Article
Full-text available
  • Aug 2020
... Technical and financial challenges outweighed political/legal or ownership issues when it came respondents' ability to access and use crop wild relatives. While there are a number of success stories around the introduction of useful traits from the highly variable pools of crop wild relatives [41,[46][47][48][49][50], the transfer of alleles from wild populations tends to be slow, genetically tricky and expensive compared to when using advanced or elite lines [12,55,84]. Other limitations, such as the lack of genetic materials or information about them, only affected a minority of breeders working with wild relatives, a minority which seeks to mine an even greater variety of ex situ sources, including foreign ex situ institutions and collections from the private sector. ...
... While most of the surveyed breeders are continuing to pursue similar strategies working with genetic resources under increasing climate change awareness, our results offer some interesting insights from the minority of breeders who are diversifying their germplasm materials and sources. Overcoming the barriers they experience may encourage a broader diffusion of those diversity-based strategies that literature describes as essential in responding to climate change [36][37][38][39][40][41][42][43][44][45][46][47][48][49][50]91]. Though some argue this potential is overstated [92,93], introducing more advanced genomic/phenotyping tools into any breeding programme has the potential to improve the power and speed of exploring large pools of diversity [94,95]. ...
The Role of Genetic Resources in Breeding for Climate Change: The Case of Public Breeding Programmes in Eighteen Developing Countries
Article
Full-text available
  • Aug 2020
The role of plant breeding in adapting crops to climate changes that affect food production in developing countries is recognized as extremely important and urgent, alongside other agronomic, socio-economic and policy adaptation pathways. To enhance plant breeders’ capacity to respond to climate challenges, it is acknowledged that they need to be able to access and use as much genetic diversity as they can get. Through an analysis of data from a global survey, we explore if and how public breeders in selected developing countries are responding to climate challenges through a renewed or innovative use of plant genetic resources, particularly in terms of types of material incorporated into their breeding work as well as sources of such germplasm. It also looks at the possible limitations breeders encounter in their efforts towards exploring diversity for adaptation. Breeders are clearly considering climate challenges. In general, their efforts are aimed at intensifying their breeding work on traits that they were already working on before climate change was so widely discussed. Similarly, the kinds of germplasm they use, and the sources from which they obtain it, do not appear to have changed significantly over the course of recent years. The main challenges breeders faced in accessing germplasm were linked to administrative/legal factors, particularly related to obtaining genetic resources across national borders. They also underscore technical challenges such as a lack of appropriate technologies to exploit germplasm sets such as crop wild relatives and landraces. Addressing these limitations will be crucial to fully enhance the role of public sector breeders in helping to adapt vulnerable agricultural systems to the challenges of climate change.
... (hereafter referred to as H. spontaneum) is the wild progenitor of cultivated barley from which it differs for traits associated with the domestication process (Paterson et al. 1995). It is a valuable source of useful genes for crop improvement such as yield (von Korff et al. 2006), plant height under drought stress (Baum et al. 2003), drought and high temperature tolerance (Chen et al. 2008;Shakhatreh et al. 2010;Lakew et al. 2011Lakew et al. , 2013, leaf-scald, and leaf rust resistance Genger et al. 2003;von Korff et al. 2005;Repkova et al. 2006), seminal root characteristics (Grando and Ceccarelli 1995), and straw quality characteristics (Grando et al. 2005). The wild progenitor of barley is adapted to a broad range of eco-geographical conditions (Ivandic et al. 2002) despite its narrow geographical distribution that extends from 30°N to 40°N (Haas et al. 2019). ...
Phenotypic evolution of the wild progenitor of cultivated barley (Hordeum vulgare L. subsp. spontaneum (K. Koch) Thell.) across bioclimatic regions in Jordan
Article
Full-text available
Climate change affects the evolutionary potential and the survival of wild plant populations by acting on fitness traits. Resurrection approach was applied to investigate the phenotypic changes during the evolution of the wild progenitor of cultivated barley, Hordeum vulgare L. subsp. spontaneum (K. Koch.) Thell. in Jordan. We compared 40 Hordeum spontaneum populations collected in Jordan in 1991 with 40 Hordeum spontaneum populations collected from the same sites in 2014. In the comparison we included seven Hordeum vulgare checks (one local landrace and six improved varieties). The correlation analysis between the phenotypic and eco-geographical data based on Principal Component Analysis and Mantel test showed that the populations were aggregated according to their ecological geographical pattern in two groups with a significant (p < 0.0001) correlation between groups. Four heritable traits, namely plant height, biological yield, number of tillers, and awn length, determined the phenotypic structure of the populations. The two populations collected at 23 years distance, diverged in two distinctive phenotypic structure categories; a conserved structure and an evolved structure with a reduction in the phenotypic trait diversity in the population collected in 2014. These results reveal the value of combining phenotypic and environmental data to understand the evolution and adaptation of the population to climate change over a long period and the consequences on the wild progenitor of cultivated barley collection to avoid loss of genetic materials.
... This germplasm has not been evaluated extensively for yield performance. Furthermore, molecular markers and agronomic traits associated with drought tolerance were reported for the derived germplasm (Baum et al., 2007;Hajjar & Hodgkin, 2007;Lakew et al., 2013;Schmalenbach, Léon, & Pillen, 2009). ...
Traits discovery in Hordeum vulgare sbsp. spontaneum accessions and in lines derived from interspecific crosses with wild Hordeum species for enhancing barley breeding efforts
Article
Full-text available
  • Oct 2020
Barley is a crop of global significance with multiple uses (feed, food and beverages), but its productivity worldwide is limited by several abiotic and biotic stresses. Crop wild relatives, exclusively, Hordeum vulgare ssp. spontaneum and H. bulbosum, are important genetic resources needed to develop new adapted varieties. A total of 117 accessions of H. spontaneum from different origins and 145 lines derived from crosses between barley and H. bulbosum supplied by NordGen were evaluated for field reactions to four major diseases. In addition, a set of 45 lines derived from interspecific crosses with H. spontaneum and H. bulbosum along with 10 checks were evaluated for agronomic traits and yield performance under four different environmental conditions and for quality attributes. The results showed that 37.7%, 71.6%, 15.1%, and 79.5% of H. spontaneum accessions were resistant to moderately resistant to net form net blotch, scald, leaf rust and powdery mildew, respectively, while the respective percentages in case of H. bulbosum derivatives were 31%, 20.4%, 17.9% and 70.6%. Only three accessions of H. spontaneum showed high resistance levels to the four diseases while 23 other accessions and 16 Bulbosum derived lines showed resistance to a combination of two to four diseases. When H. bulbosum and H. spontaneum derived lines were evaluated under different environments, none of them gave higher grain yield and higher thousand kernel weight than the best checks. However, a few H. bulbosum derived lines showed higher straw yield, and lines combining tall stature, and lodging resistance were identified. Pre‐breeding efforts need to be strengthened further by evaluating more wild Hordeum accessions, their crossing with the best available parents and selection of elite germplasm to be made available to barley breeding programs for the development of new adapted and high yielding varieties. Trait discovery in Hordeum vulgare sbsp. spontaneum Trait discovery in lines derived from interspecific crosses Disease resistance in wild barley No data available. No data available. This article is protected by copyright. All rights reserved
... spontaneum, the wild relative of cultivated barley (spp. vulgare) which has been used routinely in the barley breeding program at the International Center for Agricultural Research in Dry Areas (ICARDA) (Ceccarelli and Grando, 1987;Grando and Ceccarelli, 1991) as a donor of tolerance to drought (Lakew et al., 2011(Lakew et al., , 2013. In general, introgression of useful genes from wild relatives, even from those of the primary gene pool, may require repeated backcrossing to break undesirable genes. ...
Advanced analytics, phenomics and biotechnology approaches to enhance genetic gains in plant breeding
Chapter
Agriculture production is a major driver of destabilization of the earth's planetary boundaries within which humanity can safely operate. Producing enough food that is safe and nutritious is the biggest challenge in 21st century agriculture. Yield gains through genetic enhancement have either slowed down or not rising to the level needed to meet the ever-growing demand for nutritious food. A continuous supply of high-quality crop germplasm is the key to developing climate-resilient, resource-use efficient, nutritious and productive cultivars. Global efforts are underway to develop pre-breeding populations, by exploiting exotic germplasm including wild and weedy relatives with required characteristics to support breeding programs. Comprehensive profiling of germplasm/breeding lines (relative to uncharacterized lines) and adopting a strategy based on physiological characterization of parental lines have the potential to facilitate the accumulation of favorable alleles to enhance genetic gain in plant breeding. Advances in genomics, phenomics and bioinformatic resources have led to the deployment of several knowledge-intensive approaches to accelerate genetic gains in diverse food crops. Enhanced capability in data storage, retrieval and analysis has greatly facilitated the development of genotype-phenotype models to predict phenotypes, thus enhancing selection efficiency. Genomic-aided breeding has been successful in enhancing genetic gain relative to pedigree-based phenotypic selection. Genes controlling “recombination hotspots” and targeted recombination may provide breeders opportunity to significantly increase genetic gains. Combining genomic selection with doubled haploid technology, speed breeding and high-throughput phenomics with genotype-by-sequencing profiling allows the fast transfer of increased genetic gains per unit time. An open source software system has the potential to increase breeding efficiency through data and code sharing, while open source seed systems should allow for continued seed saving, breeding, and seed exchange without restriction. Taken together, these approaches should provide breeders with the opportunity to make genetic gains through new technologies and through the infusion of useful genetic variation in crop breeding.
... Previous studies showed that only some 40% of the alleles found in wild barley are present in cultivars and wild barley is thus a rich source of genetic variations for various breeding programmes (Ellis et al., 2000;Horns and Hood, 2012;Tombuloglu et al., 2015). A wide range of traits in wild barley have been assessed, and they include resistance and tolerance to different biotic (Abbott et al., 1991;Biselli et al., 2010;Chen et al., 2013;Friedt et al., 2011;Schmalenbach et al., 2008) and abiotic (Kalladan et al., 2013;Lakew et al., 2013;Newton et al., 2011;Pakniyat and Namayandeh, 2007;Russell et al., 2014;Shavrukov et al., 2010;Wang et al., 2018) stresses, as well as variations for grain quality (Batchu and Zimmermann, 2006;Ellis et al., 1993;Erkkil€ a et al., 1998;Jun et al., 2011;Li et al., 2010). The existence of genetic variation is the foundation for crop improvement. ...
The draft genome of a wild barley genotype reveals its enrichment in genes related to biotic and abiotic stresses compared to cultivated barley
Article
Full-text available
  • Jul 2019
Wild barley (Hordeum spontaneum) is the progenitor of cultivated barley (H. vulgare) and provides a rich source of genetic variations for barley improvement. Currently, the genome sequences of wild barley and its differences with cultivated barley remain unclear. In this study, we report a high‐quality draft assembly of wild barley accession (AWCS276; henceforth named as WB1), which consists of 4.28 Gb genome and 36,395 high‐confidence protein coding genes. BUSCO analysis revealed that the assembly included full lengths of 95.3% of the 956 single‐copy plant genes, illustrating that the gene‐containing regions have been well‐assembled. By comparing with the genome of the cultivated genotype Morex, it is inferred that the WB1 genome contains more genes involved in resistance and tolerance to biotic and abiotic stresses. The presence of the numerous WB1‐specific genes indicates that, in addition to enhance allele diversity for genes already existing in the cultigen, exploiting the wild barley taxon in breeding should also allow the incorporation of novel genes. Furthermore, high levels of genetic variation in the pericentomeric regions were detected in chromosome 3H and 5H between the wild and cultivated genotypes, which may be the results of domestication. This H. spontaneum draft genome assembly will help to accelerate wild barley research and be an invaluable resource for barley improvement and comparative genomics research. This article is protected by copyright. All rights reserved.
... spontaneum (K. Koch) Thell., the wild progenitor of cultivated barley (hereafter ''Spontaneum'') represents an important genetic resource for disease resistance traits such as powdery mildew, leaf scald or leaf rust resistance (Fischbeck et al. 1976;Ivandic et al. 1998;Backes et al. 2003;Dreiseitl and Bockelman 2003;Genger et al. 2003;von Korff et al. 2005;Repkova et al. 2006), drought and temperature tolerance (Chen et al. 2008;Lakew et al. 2013), yield (von Korff et al. 2006) and malting quality (Erkkila et al. 1998;von Korff et al. 2008) or research on the genetics of flowering time and root traits (Naz et al. 2014;Maurer et al. 2015). Maxted and Kell (2009) suggested that, although Spontaneum is widespread and locally common (von Bothmer et al. 1995), individual populations might contain important adaptive traits, thus populations should be actively conserved throughout the geographical range. ...
Genotypic and phenotypic changes in wild barley (Hordeum vulgare subsp. spontaneum) during a period of climate change in Jordan
Article
Full-text available
Climate change and other anthropogenic disturbances can lead to the loss of genetic variation and thereby affect evolutionary potential and survival of plant populations in the wild. We examined these predictions in the primary wild relative of barley, Hordeum vulgare L. subsp. spontaneum (K. Koch) Thell., within its center of diversity, in Jordan. Changes in genotypic and phenotypic diversity were assessed using seed samples collected in 1981 and 2012 from the same 18 sites across Jordan. The overall population structure was conserved, but we observed an increase of within population genetic diversity and a reduction in population differentiation. Phenotypic variation differed among years and sites but the magnitude and direction of change variated among sites. While the sampled region became significantly hotter and drier during this period, simple correlation models did not support association between measures of climate change and the observed genetic and phenotypic changes. Agricultural activities that promote disturbance and demographic fluctuations may affect crop wild relatives that grow in agricultural landscapes, in unexpected ways. The observed increase in genetic diversity within populations might be explained by increased migration or by an advantage of increased genetic variation in the face of variable environmental conditions. This study provides a new perspective on the range of possible responses of crop wild relatives to environmental pressures.
Phenotypic Evolution of The Wild Progenitor of Cultivated Barley (Hordeum Vulgare Subsp. Spontaneum (C. Koch) Thell.) Across Bioclimatic Regions In Jordan
Preprint
Full-text available
  • Aug 2021
Climate change affects the evolutionary potential and the survival of wild plant populations by acting on fitness traits. Resurrection approach was applied to investigate the phenotypic changes during the evolution of the wild progenitor of cultivated barley, Hordeum spontaneum K. Koch in Jordan. We compared 40 Hordeum spontaneum K. Koch populations collected in Jordan in 1991 with 40 Hordeum spontaneum K. Koch populations collected from the same sites in 2014. In the comparison we included seven Hordeum vulgare checks (one local landrace and six improved varieties). The analysis of the phenotypic data showed that the populations were aggregated according to their ecological geographical pattern in two groups with a significant (p < 0.0001) correlation between groups. Four heritable traits, namely plant height, biological yield, number of tillers, and awn length, determined the phenotypic structure of the populations. The two populations collected at 23 years distance, diverged in two distinctive phenotypic structure categories; a conserved structure and an evolved structure with a reduction in the phenotypic trait diversity in the population collected in 2014. These results reveal the value of combining phenotypic and environmental data to understand the evolution and adaptation of the population to climate change over a long period and the consequences on the wild progenitor of cultivated barley collection to avoid loss of genetic materials.
Salvatore Ceccarelli
Chapter
  • Nov 2020
Salvatore Ceccarelli is a geneticist, plant breeder, innovator, mentor, and farmers’ friend with over 50 years of dedicated work to agricultural research for development. His major contributions have been in the development of breeding methodologies for barley and other important crops for the livelihoods of resource poor farming community in marginal environments. After a career in academia in Italy, in 1980 Salvatore moved to ICARDA, based in Aleppo, Syria, initially as a forage breeder and later as a barley breeder and manager of the barley improvement program until he left the center over 30 years later. It was while at ICARDA that he developed and adopted a new breeding strategy, based on decentralized selection for specific adaptation, a drastic departure from the dominant philosophy in plant breeding based on wide adaptation. A further development of this strategy was the idea of PPB, initially implemented in Syria and later extended to other Middle East countries, North Africa, Horn of Africa, and more recently to Italy, accompanied by a continuous refinement in experimental techniques and statistical analysis. When Salvatore recognized the limitation of PPB to ensure a continuous flow of new material to farmers, he proposed the use of EPPB to adapt crops to their specific environment and to climate change, while providing diversity for farmers to manage. His breeding program distributed new barley material to farmers worldwide and to numerous research institutions for basic and applied research, and generated information and methodologies to establish breeding programs for difficult and stressful environments. He has published over 270 scientific articles and been invited to countless national and international events. He has collaborated with researchers and mentored breeders and technicians from around the world, helped establishing participatory breeding programs in several countries, supervised 25 MSc and PhD students, and conducted courses on participatory and evolutionary plant breeding in numerous countries. In 2017, he returned to Italy and continued to work as a consultant in national and international projects, which brings that decision‐making process and seed ownership back in the hands of farmers. He is currently involved in projects in Bhutan, Ethiopia, Iran, Jordan, Nepal, Uganda, and Europe.
Enhancing genetic gain in the era of molecular breeding
Article
Full-text available
  • May 2017
As one of the important concepts in conventional quantitative genetics and breeding, genetic gain can be defined as the amount of increase in performance that is achieved annually through artificial selection. To develop pro ducts that meet the increasing demand of mankind, especially for food and feed, in addition to various industrial uses, breeders are challenged to enhance the potential of genetic gain continuously, at ever higher rates, while they close the gaps that remain between the yield potential in breeders' demonstration trials and the actual yield in farmers' fields. Factors affecting genetic gain include genetic variation available in breeding materials, heritability for traits of interest, selection intensity, and the time required to complete a breeding cycle. Genetic gain can be improved through enhancing the potential and closing the gaps, which has been evolving and complemented with modern breeding techniques and platforms, mainly driven by molecular and genomic tools, combined with improved agronomic practice. Several key strategies are reviewed in this article. Favorable genetic variation can be unlocked and created through molecular and genomic approaches including mutation, gene mapping and discovery, and transgene and genome editing. Estimation of heritability can be improved by refining field experiments through well-controlled and precisely assayed environmental factors or envirotyping, particularly for understanding and controlling spatial heterogeneity at the field level. Selection intensity can be significantly heightened through improvements in the scale and precision of genotyping and phenotyping. The breeding cycle time can be shortened by accelerating breeding procedures through integrated breeding approaches such as marker-assisted selection and doubled haploid development. All the strategies can be integrated with other widely used conventional approaches in breeding programs to enhance genetic gain. More transdisciplinary approaches, team breeding, will be required to address the challenge of maintaining a plentiful and safe food supply for future generations. New opportunities for enhancing genetic gain, a high efficiency breeding pipeline, and broad-sense genetic gain are also discussed prospectively. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved.
Barley landraces from the Fertile Crescent: A lesson for plant breeders
Article
Full-text available
  • Nov 1999
Diversity for morphological and agronomic characters in Hordeum vulgare ssp. spontaneum C
Article
Full-text available
  • Jan 1987
Genotype and phenotype associations with drought tolerance in barley tested in North Africa
Article
Full-text available
A review is presented of genetic strategies deployed in a 3-yr project on drought tolerance in barley. Data were collected on genetic, physiological and agronomic traits in non-irrigated and irrigated field trials in Egypt, Morocco and Tunisia. A wide range of barley germplasm (developed from African and European cultivars, adapted landraces and wild barleys) was tested, and positive traits were found in each gene pool. The contrasting environments of the three North African countries had major effects on plant/genotype performance. Genetic effects were also detected, as were genotype × environment interactions.
The potential contribution of wild barley (Hordeum vulgare ssp. spontaneum) germplasm to drought tolerance of cultivated barley (H. vulgare ssp. vulgare)
Data
Full-text available
  • Feb 2011
Improving drought tolerance has always been an important objective in many crop improvement programs and is becoming more important as one way of adapting crops to climate changes. However, due to its complexity, the genetic mechanisms underlying the expression of drought tolerance in plants are poorly understood and this trait is difficult to characterize and quantify. This study assessed the importance of the wild progenitor of cultivated barley, Hordeum spontaneum C. Koch, in contributing developmental and yield-related traits associated with drought tolerance and therefore its usefulness in breeding for improved adaptation to drought stress conditions. Fifty-seven fixed barley lines derived from crosses with two H. spontaneum lines (41-1 and 41-5) were evaluated in Mediterranean low rainfall environments with 10 improved varieties and three landraces for grain yield, developmental and agronomic traits. The study was conducted for three years (2004–2006) in a total of nine environments (location–year combinations), eight in Syria and one in Jordan, which were eventually reduced to seven due to a large error variance in two of them. There was significant genetic variation among the genotypes for most of the traits measured, as well as differential responses of genotypes across environments. Traits such as peduncle length, peduncle extrusion and plant height were positively correlated with grain yield in the dry environments. Differences in phenology were small and not significantly correlated with differences in grain yield under stress. Performances at the three highest yielding environments were much more closely correlated than those at the four stress environments. The GGE biplot analysis allowed identification of genotypes consistently best adapted to the lowest yielding environments and confirmed the existence of unique environments for identifying better adapted genotypes in the low rainfall environments of Syria. The top yielding lines in the driest of the seven environments derived mostly from crosses with H. spontaneum 41-1, while most of the improved varieties showed a positive genotype by environment (GE) interaction with the highest yielding environments. The results of the field experiments indicated that there was variation for grain yield under drought stress among barley genotypes, and that some of the lines derived from H. spontaneum had consistently superior specific adaptation to the range of severe stress conditions used in this study. The usefulness of H. spontaneum in breeding programs for stress conditions is likely to increase in view of the predicted increase in the occurrence of high temperatures and droughts
Genetic diversity of barley: use of locally adapted germplasm to enhance yield and yield stability of barley in dry areas.
Chapter
  • Jan 2001
This book focuses on the previously neglected interface between the conservation of plant genetic resources and their utilization. Only through utilization can the potential value of conserved genetic resources be realized. However, as this book shows, much conserved germplasm has to be subjected to long-term pre-breeding and genetic enhancement before it can be used in plant breeding programmes. The authors explore the rationale and approaches for such pre-breeding efforts as the basis for broadening the genetic base of crop production. Examples from a range of major food crops (pearl millet, maize, potatoes, cassava and Musa ) are presented and issues analysed by leading authorities from around the world. Twenty-seven papers are presented in 4 sections: general principles (7 papers), crop case studies (5 papers), population management (8 papers), and other approaches to broadening the genetic base of crops (7 papers). The book is aimed at plant breeders, genetic resource conservation scientists and research managers in agriculture and biodiversity.
A consensus map of barley integrating SSR, RFLP, and AFLP markers
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A consensus map of barley combining simple sequence repeat (SSR), restriction fragment length polymorphism (RFLP), and amplified fragment length polymorphism (AFLP) markers has been developed by combining 5 Australian barley linkage maps, Galleon x Haruna Nijo, Chebec x Harrington, Clipper x Sahara, Alexis x Sloop, and Amaji Nijo x WI2585, using the software package JOINMAP 2.0. The new consensus map consists of 700 markers, with 136 being SSRs, and has a total genetic distance of 933 cM. The consensus map order appears to be in good agreement with the Australian barley linkage maps, with the exception of a small inversion located close to the centromere of chromosome 5H. Similarly, the SSR map orders are in good agreement with SSR markers integrated into the doubled haploid linkage map of Lina x Hordeum spontaneum, Canada Park. The new consensus map provides a framework to cross examine and align partial and complete barley linkage maps using markers common to many barley maps. This map will allow researchers to rapidly and accurately select SSR markers for chromosome regions of interest for barley genetic and plant breeding studies.
Restriction fragment length polymorphism maps and the concept of graphical genotypes
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With the advent of high density restriction fragment length polymorphism (RFLP) maps, it has become possible to determine the genotype of an individual at many genetic loci simultaneously. Often, such RFLP data are expressed as long strings of numbers or letters indicating the genotype for each locus analyzed. In this form, RFLP data can be difficult to interpret or utilize without complex statistical analysis. By contrast, numerical genotype data can also be expressed in a more useful, graphical form, known as a "graphical genotype", which is described in detail in this paper. Ideally, a graphical genotype portrays the parental origin and allelic composition throughout the entire genome, yet is simple to comprehend and utilize. In order to demonstrate the usefulness of this concept, graphical genotypes for individuals from backcross and F2 populations in tomato are described. The concept can also be utilized in more complex mating schemes involving two or more parents. A model that predicts the accuracy of graphical genotypes is presented for hypothetical RFLP maps of varying marker spacing. This model indicates that graphical genotypes can be more than 99% correct in describing a genome of total size, 1000 cM, with RFLP markers located every 10 cM. In order to facilitate the application of graphical genotypes to genetics and breeding, we have developed computer software that generates and manipulates graphical genotypes. The concept of graphical genotypes should be useful in whole genome selection for polygenic traits in plant and animal breeding programs and in the diagnosis of heterogenously based genetic diseases in humans.
Liu Z-W, Biyashev RM, Saghai Maroof MA. Development of simple sequence repeat DNA markers and their integration into a barley linkage map. Theor Appl Genet 93: 869-876
Article
  • Oct 1996
Simple sequence repeats (SSRs), or microsatellites, are a new class of PCR-based DNA markers for genetic mapping. The objectives of the present study were to develop SSR markers for barley and to integrate them into an existing barley linkage map. DNA sequences containing SSRs were isolated from a barley genomic library and from public databases. It is estimated that the barley genome contains one (GA)n repeat every 330 kb and one (CA)n repeat every 620 kb. A total of 45 SSRs were identified and mapped to seven barley chromosomes using doubled-haploid lines and/or wheat-barley addition-line assays. Segregation analysis for 39 of these SSRs identified 40 loci. These 40 markers were placed on a barley linkage map with respect to 160 restriction fragment length polymorphism (RFLP) and other markers. The results of this study demonstrate the value of SSRs as markers in genetic studies and breeding research in barley.
Mapping physiological traits in barley
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summaryAmplified fragment length polymorphisms (AFLPs) offer a reproducible, multiplex DNA assay by which to genotype mapping populations. We have evaluated physiological traits in barley seedlings grown in an hydroponic system and given a salt treatment. Multiple regression was used to show associations between AFLPs and quantitative traits. Effects at different loci were detected in stress treatments in comparison to the control implying that either novel gene action was induced by salt stress or that normal activity was reduced to a low level where alternate gene action is revealed. The QTLs occurred on all chromosomes but there appeared to be clusters of loci on chromosomes 1 (7H), 4 (4H), 5 (1H) and 6 (6H). The significance of our results is discussed in the context of studies to explore the barley genome and the application of the results of these genetical analyses to barley breeding.
GGEbiplot—A Windows Application for Graphical Analysis of Multienvironment Trial Data and Other Types of Two-Way Data
Article
Plant breeding trials produce quantities of data and finding the useful information within that data has historically been a major challenge of plant breeding. A recently developed graphical data summary, called GGEbiplot, can aid in data exploration. GGEbiplot is a Windows application that performs biplot analysis of two-way data that assume an entry X tester structure. GGEbiplot analyzes the data and outputs the results as an image, and it also produces an interactive show of the data. It allows interactive visualization of the biplot from various perspectives. A multienvironment trial data set, in which cultivars are entries and environments are testers, was used to demonstrate the functions of GGEbiplot. These include but are not limited to: (i) ranking the cultivars based on their performance in any given environment, (ii) ranking the environments based on the relative performance of any given cultivar, (iii) comparing the performance of any pair of cultivars in different environments, (iv) identifying the best cultivar in each environment, (v) grouping the environments based on the best cultivars, (vi) evaluating the cultivars based on both average yield and stability, (vii) evaluating the environments based on both discriminating ability and representativeness, and (viii) visualizing all of these aspects for a subset of the data by removing some of the cultivars or environments. GGEbiplot has been applied to visual analysis of genotype X environment data, genotype X trait data, genotype X marker data, and diallel cross data.