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Title: Genetic diversity and population structure of collard landraces and their relationship to other Brassica oleracea crops

item Branham, Sandra
item Couillard, David
item Stansell, Zachary
item Farnham, Mark

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/14/2015
Publication Date: 11/1/2015
Citation: Branham, S., Couillard, D.M., Stansell, Z.J., Farnham, M.W. 2015. Genetic diversity and population structure of collard landraces and their relationship to other Brassica oleracea crops. The Plant Genome. 8(3):1-11.

Interpretive Summary: Plant breeders require access to a diverse collection of plant varieties to provide different genes that can be exploited in crop improvement to meet the demand for food security in the face of an ever-increasing human population. Genetic erosion of the food supply is occurring by both an over reliance, on only a few major crop species, including corn, wheat and rice and through the wide-scale adoption of a limited number of cultivars for particular crops. The characterization and subsequent conservation of different varieties in the form of wild relatives, landraces, and underutilized crops is essential to ensure future availability of genetic resources for breeding efforts. USDA scientists working in Charleston, SC, evaluated a USDA landrace collection of the vitamin-rich specialty crop collard using DNA fingerprinting to assess its diversity and potential for improving the diverse crop types of the cabbage family, which includes broccoli, cauliflower, cabbage, brussels sprouts and kale. The collard landraces harbored substantial genetic variation as compared to collard cultivars and other cabbage family crops, supporting their role as an important source of genetic diversity for future crop improvement by vegetable breeders. The diversity results presented should prove useful to collection curators in managing the conservation of numerous varieties and allow for the preservation of this important genetic resource.

Technical 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 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 (52,157 SNPs) to: 1) evaluate genetic diversity and population structure of 75 collard landraces; 2) assess the potential of the collection for genome-wide association studies (GWAS) through characterization of genomic patterns of linkage disequilibrium; and 3) clarify the relationship of collard to the most economically important B. oleracea crop types. Confirming the collection as a valuable genetic resource, the collard landraces had twice the polymorphic markers (11,322 SNPs) and ten 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 600kb allowing for sufficient coverage of the genome for GWAS using the physical positions of the 8,273 SNPs polymorphic among the landraces. Although other relationships varied, the previous placement of collard with cabbage and Portuguese tronchuda cabbage was confirmed with STRUCTURE, PCoA, and phylogenetic analyses using 15,951 unlinked SNPs.