The USDA Barley Core Collection:Genetic Diversity, Population Structure, and Potential for Genome-Wide Association Studies

New sources of genetic diversity must be incorporated into plant breeding programs if they are to continue increasing grain yield and quality, and tolerance to abiotic and biotic stresses. Germplasm collections provide a source of genetic and phenotypic diversity, but characterization of these resources is required to increase their utility for breeding programs. We used a barley SNP iSelect platform with 7,842 SNPs to genotype 2,417 barley accessions sampled from the USDA National Small Grains Collection of 33,176 accessions. Most of the accessions in this core collection are categorized as landraces or cultivars/breeding lines and were obtained from more than 100 countries. Both STRUCTURE and principal component analysis identified five major subpopulations within the core collection, mainly differentiated by geographical origin and spike row number (an inflorescence architecture trait). Different patterns of linkage disequilibrium (LD) were found across the barley genome and many regions of high LD contained traits involved in domestication and breeding selection. The genotype data were used to define 'mini-core' sets of accessions capturing the majority of the allelic diversity present in the core collection. These 'mini-core' sets can be used for evaluating traits that are difficult or expensive to score. Genome-wide association studies (GWAS) of 'hull cover', 'spike row number', and 'heading date' demonstrate the utility of the core collection for locating genetic factors determining important phenotypes. The GWAS results were referenced to a new barley consensus map containing 5,665 SNPs. Our results demonstrate that GWAS and high-density SNP genotyping are effective tools for plant breeders interested in accessing genetic diversity in large germplasm collections

Chickpea

The narrow genetic base of cultivated chickpea warrants systematic collection, documentation and evaluation of chickpea germplasm and particularly wild Cicer species for effective and efficient use in chickpea breeding programmes. Limiting factors to crop production, possible solutions and ways to overcome them, importance of wild relatives and barriers to alien gene introgression and strategies to overcome them and traits for base broadening have been discussed. It has been clearly demonstrated that resistance to major biotic and abiotic stresses can be successfully introgressed from the primary gene pool comprising progenitor species. However, many desirable traits including high degree of resistance to multiple stresses that are present in the species belonging to secondary and tertiary gene pools can also be introgressed by using special techniques to overcome pre- and post-fertilization barriers. Besides resistance to various biotic and abiotic stresses, the yield QTLs have also been introgressed from wild Cicer species to cultivated varieties. Status and importance of molecular markers, genome mapping and genomic tools for chickpea improvement are elaborated. Because of major genes for various biotic and abiotic stresses, the transfer of agronomically important traits into elite cultivars has been made easy and practical through marker-assisted selection and marker-assisted backcross. The usefulness of molecular markers such as SSR and SNP for the construction of high-density genetic maps of chickpea and for the identification of genes/QTLs for stress resistance, quality and yield contributing traits has also been discussed

Chromosomal locations of the maize (Zea mays L.) HtP and rt genes that confer resistance to Exserohilum turcicum

We used 125 microsatellite markers to genotype the maize (Zea mays L.) near isogenic lines (NIL) L30HtPHtPRtRt and L30htphtpRtRt and the L40htphtprtrt line which contrast regarding the presence of the recently described dominant HtP and the recessive rt genes that confer resistance to Exserohilum turcicum. Five microsatellite markers revealed polymorphisms between the NIL and were considered candidate linked markers for the HtP resistance gene. Linkage was confirmed by bulked segregant sample (BSS) analysis of 32 susceptible and 34 resistant plants from a BC1F1 population derived from the cross (L30HtPHtPRtRt x L40htphtprtrt) x L40htphtprtrt. The bnlg198 and dupssr25 markers, both located on maize chromosome 2L (bin 2.08), were polymorphic between bulks. Linkage distances were estimated based on co-segregation data of the 32 susceptible plants and indicated distances of 28.7 centimorgans (cM) between HtP and bnlg198 and 23.5 cM between HtP and dupssr25. The same set of susceptible plants was also genotyped with markers polymorphic between L30HtPHtPRtRt and L40htphtprtrt in order to find markers linked to the rt gene. Marker bnlg197, from chromosome 3L (bin 3.06), was found linked to rt at a distance of 9.7 cM. This is the first report on the chromosomal locations of these newly described genes