Comparative analysis of genetic diversity in Canadian barley assessed by SSR, DarT, and pedigree data

Abstract

The aim of this study was to measure genetic diversity and population structure among 92 Canadian barley cultivars using two types of molecular markers (SSRs and DArTs) and pedigree data. A total of 368 alleles were identified at 50 SSR loci. The number of alleles per locus ranged between 2 and 13 ([Formula: see text] = 7.36) and PIC values ranged from 0.34 to 0.86 ([Formula: see text] = 0.69). For the biallelic DArT markers, the genetic distance matrix was based on 971 markers whose PIC values ranged between 0.06 and 0.50 ([Formula: see text] = 0.39). A third distance matrix was computed based on the kinship coefficient. Clustering of genotypes was performed based on the genetic distance matrix and the three dendrograms obtained showed the genetic relationships among barley cultivars. The topological similarity of the three dendrograms was estimated using a congruence index and showed the three dendrograms to be in very good agreement. Statistical analysis also showed a highly significant correlation between the SSR and DArT matrices (r = 0.80, p < 0.002) compared with lower yet significant correlations of the pedigree data with both marker types (r = 0.46, p < 0.002; r = 0.52, p < 0.002). Finally, we assessed linkage disequilibrium in this germplasm and found it to be quite extensive, as the mean distance between marker pairs with significant (P < 0.001) r2 values >0.5 was 3.8 cM. Information obtained from comparing results of different genetic diversity estimation methods should be useful for the improvement and conservation of barley genetic resources.