Genome-wide SNP-based diversity analysis and association mapping in linseed (Linum usitatissimum L.)

The present study was aimed to characterize linseed accessions for genetic diversity, population structure and establish marker-trait association using SNP markers. A total of 10057 SNPs were identified in 86 accessions through genotyping by sequencing approach of next-generation sequencing. The polymorphism information content (PIC) value was found to be in the range from 0.08 to 0.30 with an average of 0.27 +/- 0.09. Moderate value of PIC (0.30-0.60) was shown by 48% SNPs while remaining had low PIC values. Based on Jaccard's similarity coefficient, the genetic distance varied from 0.17 to 0.65 with an average of 0.42 +/- 0.07. Based on genetic relatedness among the accessions, CG 79, CG 86, GP 25, GP 31 GP 33, GP 47, and GP 49 were found to be most divergent and could be potential accessions for the future breeding program of linseed to create further genetic variability. The neighbor-joining clustering revealed that 86 genotypes were grouped into four clusters with 28, 8, 21 and 29 accessions respectively. An admixture model-based clustering method in STRUCTURE was also implemented which grouped all the accessions in four subpopulations (K=4) as similar to NJ clustering. One pleiotropic SNPs was observed for capsule weight/plant and seed weight/plant which could assist in their simultaneous improvement during the breeding programme.