assessment of genetic diversity and population structure of barley breeding lines and landraces using snp markers

Genetic diversity is critical for developing broadly adapted cultivars with desirable traits. this research aimed to investigate the genetic diversity, population structure, and genome-wide linkage disequilibrium (ld) of 108 barley genotypes, including rainfed and irrigated breeding lines, cultivars, and landraces with the 50k illuminatm iselect single nucleotide polymorphism (snp) array. after quality control, 14,943 polymorphic snps were subjected to estimate shannon’s information index (i), nei’s gene diversity (h), polymorphic information content (pic), fixation index (fst), and principal component analysis (pca). the i and h indices were 0.74 and 0.336, respectively. the pic values were 0.367 and 0.178 for six and two-rowed barley, respectively. pca using nei’s genetic distance identified three subpopulations. subpopulations 1 and 2 had 0.38, and 0.29 pic values, respectively, and were more diverse than subpopulation 3 (0.09). the fst value was 0.381. subpopulations 1 and 3 indicated the highest (0.379) and the lowest (0.040) genetic diversity within subpopulations, respectively. the average ld for two-rowed genotypes and subpopulation 3 was more than that for six-roweded genotypes. a high level of genetic variation and genetic differentiation among subpopulations was observed in this panel. the irrigated six-rowed types and landraces indicated higher genetic diversity, whereas rainfed two-rowed barley indicated the highest ld and the lowest genetic variation due to high selection intensity. this panel could be used for genome-wide association studies to identify the trait-marker associations in future genetic improvement programs for barley.

assessment of genetic diversity and population structure of barley breeding lines and landraces using snp markers

genetic diversity is critical for developing broadly adapted cultivars with desirable traits. this research aimed to investigate the genetic diversity, population structure, and genome-wide linkage disequilibrium (ld) of 108 barley genotypes, including rainfed and irrigated breeding lines, cultivars, and landraces with the 50k illuminatm iselect single nucleotide polymorphism (snp) array. after quality control, 14,943 polymorphic snps were subjected to estimate shannon’s information index (i), nei’s gene diversity (h), polymorphic information content (pic), fixation index (fst), and principal component analysis (pca). the i and h indices were 0.74 and 0.336, respectively. the pic values were 0.367 and 0.178 for six and two-rowed barley, respectively. pca using nei’s genetic distance identified three subpopulations. subpopulations 1 and 2 had 0.38, and 0.29 pic values, respectively, and were more diverse than subpopulation 3 (0.09). the fst value was 0.381. subpopulations 1 and 3 indicated the highest (0.379) and the lowest (0.040) genetic diversity within subpopulations, respectively. the average ld for two-rowed genotypes and subpopulation 3 was more than that for six-roweded genotypes. a high level of genetic variation and genetic differentiation among subpopulations was observed in this panel. the irrigated six-rowed types and landraces indicated higher genetic diversity, whereas rainfed two-rowed barley indicated the highest ld and the lowest genetic variation due to high selection intensity. this panel could be used for genome-wide association studies to identify the trait-marker associations in future genetic improvement programs for barley.