Genome diversity and population structure analysis of Iranian landrace and improved barley (Hordeum vulgare L.) genotypes using arbitrary functional gene-based molecular markers

Abstract

Barley (Hordeum vulgare L. subsp. vulgare) is one of the earliest domesticated crop plants, which originated in Fertile Crescent. Genetic diversity analysis in primary gene pool and landraces is an effective strategy for germplasm conservation and utilization in breeding programs. In this study, Eighty-two barley genotypes comprised 22 Iranian improved cultivars and 60 landrace accessions collected from different zones of Iran were assumed for genetic diversity analysis using three gene targeted markers, start codon targeted (SCoT) polymorphism, conserved DNA-derived polymorphism (CDDP) and CAAT box-derived polymorphism (CBDP) in comparison with sequence-related amplified polymorphism (SRAP) markers. A total of 40 primers (10 primers from each marker) detected genetic polymorphism among barley genotypes. Four different marker types showed high level of polymorphism and SRAP markers produced higher number of polymorphic bands (67) in comparisons with SCoT, CDDP and CBDP. Average PIC values for SCoT, CDDP, CBDP and SRAP were 0.33, 0.37, 0.37 and 0.31, respectively. Marker index (MI) in SRAP and CBDP markers was higher than SCoT and CDDP markers. Cluster analysis using CDDP, CBDP and SRAP markers grouped barley genotypes in three distinct groups, while SCoT markers divided genotypes in four clusters. There were positive correlations between similarity matrixes obtained by each marker types. The results from cluster analysis and STRUCTURE analysis using combined data grouped barley genotypes in three clusters and the grouping of genotypes was strongly in agreement with their origins. Results showed that genotypes from west and north-west of Iran grouped in distinct clusters from those originated from north-east and center of Iran. To our knowledge, this is the first detailed report of using gene targeted molecular marker for genetic diversity analysis in barley. Our results showed the efficiency of these markers for genetic diversity analysis in barley and their potential for genome diversity and germplasm conservation.