Development of SNP set derived from single copy genes for MAB in Brassica oleracea

Abstract

Brassica oleracea is one of the 10 most cultivated crops in the world. According to reports, the competitiveness of Korean traditional breeding is world-class for B. oleracea. With more advanced molecular breeding, Korea is expected to have global competitiveness in B. oleracea. For the development of SNP array sets, resequencing data of 44 accessions that have various agricultural traits was mapped to the reference genome. From more than 3 million SNPs, SNPs that were genotyped from more than 40 accessions are filtered. After the filtering steps that enhance the accuracy of markers, 3,446 SNPs from genic regions were filtered. Since paralogous sequences can interfere with the fluorescent signal, paralogous sequences of flanking sequence containing the SNPs were filtered out. From 849 SNPs in single copy genes, 240 markers that are distributed throughout the genome were designed. After SNP array experiments, 192 markers that have high accordance rate with the resequencing data were selected, and these markers were applied to 92 samples from LG Farmhannong. 150 markers that can be used in marker assisted breeding (MAB) were ultimately selected with the criteria of no call rate and clustering form of data points. The phylogenetic trees that were drawn with 150 markers cluster cabbage in group 1 and other B. oleracea subspecies in group 2, and the result matched well with the phenotype data. These results showed that these markers are working well and can instantly be utilized to facilitate the shortening of the breeding period.

Keywords: Brassica oleracea, SNP array, MAB