GWAS of a soybean breeding collection from South East and South Kazakhstan for resistance to fungal diseases

Soybean (Glycine max (L.) Merr) is an essential food, feed, and technical culture. In Kazakhstan the area under soybean is increasing every year, helping to solve the problem of protein deficiency in human nutrition and animal feeding. One of the main problems of soybean production is fungal diseases causing yields losses of up to 30 %. Modern genomic studies can be applied to facilitate efficient breeding research for improvement of soybean fungal disease tolerance. Therefore, the objective of this genome-wide association study (GWAS) was analysis of a soybean collection consisting of 182 accessions in relation to fungal diseases in the conditions of South East and South Kazakh­stan. Field evaluation of the soybean collection suggested that Fusarium spp. and Cercospora sojina affected plants in the South region (RIBSP), and Septoria glycines – in the South East region (KRIAPP). The major objective of the study was identification of QTL associated with resistance to fusarium root rot (FUS), frogeye leaf spot (FLS), and brown spot (BS). GWAS using 4 442 SNP (single nucleotide polymorphism) markers of Illumina iSelect array allowed for identification of fifteen marker trait associations (MTA) resistant to the three diseases at two different stages of growth. Two QTL both for FUS (chromosomes 13 and 17) and BS (chromosomes 14 and 17) were genetically mapped, including one presumably novel QTL for BS (chromo­some 17). Also, five presumably novel QTL for FLS were genetically mapped on chromosomes 2, 7, and 15. The results can be used for improvement of the local breeding projects based on marker-assisted selection approach

A study of the genetic diversity in the world soybean collection using microsatellite markers associated with fungal disease resistance

Background. Soybean (Glycine max (L.) Merr.) gradually becomes one of the leading legume crops in Kazakhstan. The area under soybeans in the country has been increasing annually and requires the development of adapted cultivars with a higher yield, improved quality characters, and resistance to emerging fungal diseases. The enlargement of the crop’s gene pool also suggests the need to study and document local soybean accessions to meet the standards of the available world soybean collection by using reliable and informative types of DNA markers.Materials and methods. In this study, the soybean collection consisting of 288 accessions from different countries, including 36 cultivars and promising lines from Kazakhstan, was studied. The molecular genetic analysis was performed using nine polymorphic SSR (simple sequence repeats) markers, seven of which (Satt244, Satt565, Satt038, Satt309, Satt371, Satt570 and Sat_308) were associated with resistance to three main fungal diseases of soybean – frogeye leaf spot, fusarium root rot, and purple seed stain.Results. The average PIC (polymorphism information content) value of the analyzed SSR markers constituted 0.66 ± 0.07, confirming their highlevel polymorphism. The principal coordinate analysis suggested that the local accessions were genetically most close to the accessions from East Asia. As the collection showed a robust resistance to three studied fungal diseases in Almaty Region during 2018–2019, the distribution of the studied SSR markers in the population was not significantly associated with resistance to the analyzed diseases under field conditions.Conclusion. SSR genotyping of the soybean collection helped to identify accessions that potentially possess resistance-associated alleles of fungal disease resistance genes. The data obtained can be further used for the development of DNA documentation and the breeding the promising cultivars and lines of soybean

Exploiting the Genetic Diversity of Wild Ancestors and Relatives of Wheat for its Improvement

Wheat is the third most staple food worldwide but current 1% annual improvement in the wheat production is insufficient to meet the growing demands in future. The narrow genetic base of wheat limits continuous improvement in wheat productivity and tolerance to biotic and abiotic stresses under changing climate. Wild ancestors and relatives of wheat hold a potential in widening the genetic pool of wheat and enhance its resilience to biotic and abiotic stresses. This study was focused towards characterizing the genetic diversity in wild relatives of wheat for disease resistance and efficient association with diazotrophs. In the first study, we evaluated a mini core set of Triticum turgidum subsp. (tetraploid wheat, AABB) for resistance to Fusarium head blight (FHB), leaf rust and tan spot. Three, six, and nine accessions showed resistance response to Fusarium head blight (FHB), leaf rust and tan spot respectively. These germplasm resources could be further exploited in wheat breeding. In the second study, in addition to tetraploid wheat, diploid and hexaploid germplasm of both wild and adapted species were evaluated for efficient association with diazotrophic bacteria by analyzing the N content. We observed significant differences for 15N content among different species, represented as average σ15N. Lower σ15N indicates a higher possibility of biologically fixed nitrogen (BNF). Wild accessions both in diploid (T. boeticum, AmAm, σ15N = 20.85) and tetraploid species (T. turgidum subsp. dicoccoides, AABB, σ15N = 16.44) showed significantly better associations with diazotrophs as compared to domesticated species (T. monococcum, AmAm, σ15N = 26.67) and modern hexaploid varieties (T. aestivum, AABBDD, σ15N =31.74). Our study shows that the wild species hold a promise in identification and characterization of efficient association with diazotrophic bacteria and this interaction can be recovered in modern cultivars of wheat to enhance the performance of wheat in marginal soils. In the final study, we analyzed the genetic diversity in the global collection (178 accessions) of rye using 4,037 high-quality SNPs and developed of a mini core set of 32 accessions of rye that represents more than 95 % of the allelic diversity (PIC = 0.25) of our collection (PIC = 0.26). Genome-wide association study (GWAS) was performed on 160 accessions (Secale cereale subsp. cereale) with 4,037 high-quality SNPs to identify genomic regions conferring tan spot resistance. Nearly 32%, 27%, 24%, and 17% accessions showed resistant, moderately resistant, moderately susceptible and susceptible reaction to Pyrenophora tritici-repentis race 5 (PTR race 5) respectively. Two QTLs conferring resistance to tan spot (PTR race 5) were identified (p= \u3c 0.001) using mixed linear model (GAPIT) on chromosomes 5R and 2R. The QTLs QTs-sdsu-5R and QTs-sdsu-2R explained 13.11% and 11.62 % of the variation. In conclusion, wild relatives and ancestors of wheat hold a potential for wheat improvement especially for tolerance to abiotic and biotic factors

Identification of QTL for resistance against two fungal pathogens, Pyrenophora teres f. teres and Bipolaris sorokiniana, in a barley (Hordeum vulgare L.) diversity set

Barley is worldwide the fourth most important cereal crop and is cultivated in near desert to sub-arctic conditions. The majority of production, around 70 %, is used for animal feed, 20 % are used for malting and the rest for human consumption, with regional differences.Pests and diseases constantly result in high yield losses. Two worldwide important fungal foliar diseases of barley are Pyrenophora teres f. teres (Ptt) and Bipolaris sorokiniana (Bs), the causal agents of net blotch and spot blotch, respectively. Yield losses are on average around 40 % and can amount to over 70 % in years with epidemics. Both pathogens are highly variable and the occurrence of new pathogenic strains demands for breeding of resistant cultivars.In order to identify new resistance sources, a diverse barley set comprising 449 accessions originating from over 50 different regions all over the world, expressing different levels of resistance against both pathogens, was screened. Seedling resistance was tested under controlled greenhouse conditions with three isolates of each pathogen. Adult plant resistance was tested in field trials at three and two locations for Ptt and Bs, respectively. Phenotypic results showed a wide range of the level of resistance and significant differences between accessions were observed in all trials. The set was genotyped using the Illumina iSelect 50k barley SNP chip. After filtering for quality control parameters, i.e. failure rates < 10%, heterozygous calls < 12.5% and minor allele frequency > 5%, 33,318 polymorphic, mapped SNPs were left for further genome-wide association studies (GWAS). Markers were mapped against the barley reference sequence. GWAS was conducted using a compressed mixed linear model (CMLM) including population structure and kinship matrix. GWAS for Ptt revealed 254 significant marker-trait associations (MTAs) located on chromosomes 3H, 4H, 5H, 6H, and 7H and corresponding to 15 quantitative trait loci (QTL). Four of these loci are putatively new and were not previously described. In nine out of the 15 regions, 63 high-confidence genes that are directly involved in pathogen defence are located and represent putative candidate genes. GWAS for Bs revealed 38 significant MTAs corresponding to two major QTL on chromosomes 1H and 7H and a putative new minor QTL on chromosome 7H. In the major QTL regions, 10 and 14 high-confidence genes were identified, respectively. Based on haplotypes and phenotypic reactions it was possible to identify accessions with enhanced resistance against Ptt and Bs.Barley is worldwide the fourth most important cereal crop and is cultivated in near desert to sub-arctic conditions. The majority of production, around 70 %, is used for animal feed, 20 % are used for malting and the rest for human consumption, with regional differences.Pests and diseases constantly result in high yield losses. Two worldwide important fungal foliar diseases of barley are Pyrenophora teres f. teres (Ptt) and Bipolaris sorokiniana (Bs), the causal agents of net blotch and spot blotch, respectively. Yield losses are on average around 40 % and can amount to over 70 % in years with epidemics. Both pathogens are highly variable and the occurrence of new pathogenic strains demands for breeding of resistant cultivars.In order to identify new resistance sources, a diverse barley set comprising 449 accessions originating from over 50 different regions all over the world, expressing different levels of resistance against both pathogens, was screened. Seedling resistance was tested under controlled greenhouse conditions with three isolates of each pathogen. Adult plant resistance was tested in field trials at three and two locations for Ptt and Bs, respectively. Phenotypic results showed a wide range of the level of resistance and significant differences between accessions were observed in all trials. The set was genotyped using the Illumina iSelect 50k barley SNP chip. After filtering for quality control parameters, i.e. failure rates < 10%, heterozygous calls < 12.5% and minor allele frequency > 5%, 33,318 polymorphic, mapped SNPs were left for further genome-wide association studies (GWAS). Markers were mapped against the barley reference sequence. GWAS was conducted using a compressed mixed linear model (CMLM) including population structure and kinship matrix. GWAS for Ptt revealed 254 significant marker-trait associations (MTAs) located on chromosomes 3H, 4H, 5H, 6H, and 7H and corresponding to 15 quantitative trait loci (QTL). Four of these loci are putatively new and were not previously described. In nine out of the 15 regions, 63 high-confidence genes that are directly involved in pathogen defence are located and represent putative candidate genes. GWAS for Bs revealed 38 significant MTAs corresponding to two major QTL on chromosomes 1H and 7H and a putative new minor QTL on chromosome 7H. In the major QTL regions, 10 and 14 high-confidence genes were identified, respectively. Based on haplotypes and phenotypic reactions it was possible to identify accessions with enhanced resistance against Ptt and Bs

Studies on Genetic Characterization of Agronomic Traits and Disease Resistance in Bread Wheat

A steady increase in wheat yield is vital to feed the continuously rising world population. Systematic exploitation of wheat germplasm and a better understanding of the underlying genetic control could be pivotal in accelerating the genetic gain for yield and disease management. Various modern techniques such as genome-wide association study (GWAS), genomic selection (GS), fine mapping, and cloning can expedite wheat improvement and broaden our understanding of the complex wheat genome. In the first objective of this study, we evaluated the Watkins core set of 121 landrace cultivars (LCs) to identify novel sources of resistance against the tan spot, Stagonospora nodorum blotch (SNB), and Fusarium Head Blight (FHB). The phenotypic evaluation identified 13 LCs with multiple resistance to tan spot and SNB, while five other LCs were found to be a potential source for FHB resistance. A total of 30 significant marker-trait associations (MTAs) were identified in a GWAS for response to tan spot and SNB. In the second objective, we performed GWAS in a panel of 297 hard red winter wheat lines from the US Great Plains region to identify QTLs for various spike and kernel-related traits and evaluated the prediction accuracy (PA) of GS models for these traits. Most of the MTAs (47) were identified for spike-related traits, where 16, 15, 11, and 5 MTAs were identified for spike length, spikelet per spike, spike density, and kernel per spike, respectively, while only 6 MTAs were identified for three kernel-related traits (kernel weight, kernel area, and thousand kernel weight). Fourteen MTAs were identified at two or more individual environments were considered stable QTLs. Univariate genomic selection (GS) models like genomic best linear unbiased prediction (GBLUP) were compared with multivariate models like Bayesian multi-trait multi-environment (BMTME) and we found that the multi-trait model (BMTME) outperformed the singletrait model (GBLUP) in terms of PA. In the last objective, we developed a fine map of a grain yield QTL on chromosome 7DS introgressed into bread wheat from Aegilops tauschii (D-Genome donor of wheat). Heterogeneous inbred families (HIFs) were developed. Eleven high-quality SNP markers were developed and mapped to the target region (3-17 Mb) on chromosome 7DS using recombination breakpoints (recombinants). A total of 29 homozygous recombinants (7 haplotype groups) were identified and evaluated in the greenhouse and field. KASP markers spanning to the QTL region can be used for marker-assisted selection of 7DS yield QTL. Overall, the finding of this study can be used for genetic improvement of wheat and accelerate the genetic gain

Pre-breeding - fishing in the gene pool

This Book of Abstracts “Pre-breeding – fishing in the gene pool” includes the summary for each of the invited keynotes, volunteer talks and posters presented at the EUCARPIA Genetic Resources Section Meeting held at the campus of the Swedish University of Agricultural Sciences (SLU) in Alnarp from 10 to 13 June 2013. This meeting gathers various members of the gene bank community of practice as well as users of the genetic resources from all around Europe and the World. The selected overall theme for the meeting is “Pre-Breeding - fishing in the gene pool” because we want to discuss how we better can use our genetic resources to cope with the issues being faced today by humankind. Germplasm enhancement or pre-breeding refers to the transfer or introgression of genes and gene combinations from non-adapted sources into breeding materials. It should therefore be understood as an early component of sustainable plant breeding that deals with identifying a useful character, capturing its genetic diversity, and putting genes into usable forms that will be further used in population improvement or line development. During this gathering we will address the role of genomics for adding value to genebank holdings and facilitating their management, the conservation and use of crop wild relatives in germplasm enhancement, how plant genetic resources serve multifunctional agriculture and what traits gene banks can offer to address climate change. We will also learn more about the role of gene banks for ensuring food and feed, and how genetic diversity contributes to human health and nutrition. Last but not least we will assess how genetic endowments can be used in crop breeding to reduce agriculture´s footprints, as well as on the management of intellectual property for plant genetic resources, particularly in the light of increasing public-private partnerships on pre-breeding. The book content follows the order indicated in the program of this conference

Legume Crops Phylogeny and Genetic Diversity for Science and Breeding

Economically, legumes (Fabaceae) represent the second most important family of crop plants after the grass family, Poaceae. Grain legumes account for 27% of world crop production and provide 33% of the dietary protein consumed by humans, while pasture and forage legumes provide vital part of animal feed. Fabaceae, the third largest family of flowering plants, has traditionally been divided into the following three subfamilies: Caesalpinioideae, Mimosoideae, and Papilionoideae, all together with 800 genera and 20,000 species. The latter subfamily contains most of the major cultivated food and feed crops. Among the grain legumes are some of mankind's earliest crop plants, whose domestication parallelled that of cereals: Soybean in China; faba bean, lentil, chickpea and pea in the Fertile Crescent of the Near East; cowpeas and bambara groundnut in Africa; soybean and mungbeans in East Asia; pigeonpea and the grams in South Asia; and common bean, lima bean, scarlet runner bean, tepary bean and lupin in Central and South America. The importance of legumes is evidenced by their high representation in ex situ germplasm collections, with more than 1,000,000 accessions worldwide. A detailed knowledge of the phylogenetic relationships of the Fabaceae is essential for understanding the origin and diversification of this economically and ecologically important family of angiosperms. This review aims to combine the phylogenetic and genetic diversity approaches to better illustrate the origin, domestication history and preserved germplasm of major legume crops from 13 genera of six tribes and to indicate further potential both for science and agriculture

Improving the crown rot resistance and tolerance of wheat using marker-assisted recurrent selection

Crown rot disease (Fusarium pseudograminearum) of wheat causes significant yield losses across Australia. However, the genetic control of crown rot resistance and tolerance is complex and traditional breeding strategies have proven ineffective. Marker Assisted Recurrent Selection (MARS) was examined as a strategy to more effectively pyramid the many minor genes controlling plant response to crown rot. Populations were developed from three-way crosses to (i) optimize screening procedures for crown rot, (ii) examine the relationship between resistance and tolerance, (iii) identify quantitative trait loci (QTL) linked to resistance and tolerance, (iv) pyramid QTLs using MARS and (v) confirm response to selection. Disease severity in greenhouse pot tests was less reliable than field screening using managed inoculum; hence field screening was used for all subsequent evaluations. In the MARS approach, materials from each population were genotyped and phenotyped by F4 for crown rot response and QTLs linked to crown rot resistance and/or tolerance identified. Consistent QTL, mapped to unique chromosomal regions, were then recombined in crossing to pyramid markers. Following two cycles of recombination, the progeny from both cycles of MARS, the base population and the original parents were compared for resistance and/or tolerance depending on the population. Resistance and tolerance (determined as reduced yield loss in the presence of crown rot) were independently inherited. A significant and positive response to selection was observed with some recombinants significantly more resistant and higher yielding than their parents. The genotypes identified and developed in this study combine multiple sources of resistance and tolerance and these materials and their associated markers can be used by the Australian wheat industry to improve wheat yield in the presence of crown rot

Wheat Improvement

This open-access textbook provides a comprehensive, up-to-date guide for students and practitioners wishing to access in a single volume the key disciplines and principles of wheat breeding. Wheat is a cornerstone of food security: it is the most widely grown of any crop and provides 20% of all human calories and protein. The authorship of this book includes world class researchers and breeders whose expertise spans cutting-edge academic science all the way to impacts in farmers’ fields. The book’s themes and authors were selected to provide a didactic work that considers the background to wheat improvement, current mainstream breeding approaches, and translational research and avant garde technologies that enable new breakthroughs in science to impact productivity. While the volume provides an overview for professionals interested in wheat, many of the ideas and methods presented are equally relevant to small grain cereals and crop improvement in general. The book is affordable, and because it is open access, can be readily shared and translated -- in whole or in part -- to university classes, members of breeding teams (from directors to technicians), conference participants, extension agents and farmers. Given the challenges currently faced by academia, industry and national wheat programs to produce higher crop yields --- often with less inputs and under increasingly harsher climates -- this volume is a timely addition to their toolkit