Genetic analysis and phenotypic associations for drought tolerance in Hordeum spontaneum introgression lines using SSR and SNP markers

Associations between markers and drought related traits were investigated on a set of 57 advanced barley breeding lines, carrying various levels of introgression from Hordeum spontaneum lines 41-1 and 41-5, the best sources of drought tolerance in the ICARDA barley breeding program, using 74 simple sequences repeats (SSR) and 20 single nucleotide polymorphism markers. The 57 lines were evaluated for grain yield and drought related traits for three years (2003/04, 2004/05, 2005/06) in nine Mediterranean low rainfall environments. A high level of polymorphism was found with SSR markers, and the mean polymorphism information content and gene diversity values were 0.67 and 0.71, respectively. The number of alleles per locus varied from 2 to 11, with an average of 5.8 alleles per marker. Considering all the 57 lines, the linkage disequilibrium (LD) analysis was significant at a comparison-wise P < 0.01 level in nearly 9 % of the SSR marker pairs used and a decay of LD was observed to a value of r2 < 0.2 at a genetic distance of 40 cM. The association analysis revealed a total of 147 significant marker–trait associations for grain yield and drought related traits. A total of 72 (49 %) marker–trait associations showed favorable effects of the exotic germplasm where the H. spontaneum lines contributed to an improvement of the trait under drought stress conditions. The number of significant marker–trait associations per trait were: 12 for growth habit; 2 for growth vigor; 11 for peduncle extrusion; 5 for number of grains per spike; 20 for peduncle length; 16 for days to heading; 20 for plant height; 8 for spike length; 17 for thousand kernel weight; 30 for grain yield; 4 for harvest index and 2 for biological yield. The phenotypic variation explained by individual marker–trait associations ranged from 7.6 % to 36.2 %. The identification of genomic regions associated with grain yield and drought related traits is useful for the genetic improvement of cultivars better adapted to drought stress environments. Thus, the present study is encouraging in identifying significant marker–trait associations through LD based association mapping analysis, which could complement and augment previous quantitative trait loci information for the potential use of Marker Assisted Selection for drought.