Genetic Diversity and Population Structure of Collard Landraces and their Relationship to Other Brassica oleracea Crops

Abstract

Landraces have the potential to provide a reservoir of genetic diversity for crop improvement to combat the genetic erosion of the food supply. A landrace collection of the vitamin-rich specialty crop collard (Brassica oleracea L. var. viridis) was genetically characterized to assess its potential for improving the diverse crop varieties of B. oleracea. We used the Illumina 60K Brassica SNP BeadChip array with 52,157 single nucleotide polymorphisms (SNPs) to (i) clarify the relationship of collard to the most economically important B. oleracea crop types, (ii) evaluate genetic diversity and population structure of 75 collard landraces, and (iii) assess the potential of the collection for genome-wide association studies (GWAS) through characterization of genomic patterns of linkage disequilibrium. Confirming the collection as a valuable genetic resource, the collard landraces had twice the polymorphic markers (11,322 SNPs) and 10 times the variety-specific alleles (521 alleles) of the remaining crop types examined in this study. On average, linkage disequilibrium decayed to background levels within 600 kilobase (kb), allowing for sufficient coverage of the genome for GWAS using the physical positions of the 8273 SNPs polymorphic among the landraces. Although other relationships varied, the previous placement of collard with the cabbage family was confirmed through phylogenetic analysis and principal coordinates analysis (PCoA).