Population Genomic and Genome-Wide Association Analysis of Morphological Traits in Brassica rapa

Increasing the growth of Chinese cabbage in short time with stress tolerance and disease resistance, is essential in the context to climate change. Discovering the candidate genes and introducing by molecular breeding are the keys for global food security. We have identified ~2.2 million single nucleotide polymorphisms from 201 diverse inbred lines which adopted to different morphological and geographical backgrounds. Re-sequencing the genome of 9 elite lines with over 10 fold coverage and other 192 with 3 to 5 fold coverage helped to generate the genome-wide genetic map with respect to characterize the population structure of morphotypes. Further we analyzed nucleotide variation diversity, linkage disequilibrium and recombination rates throughout the genome to discover the genomic patterns of Chinese cabbage. To understand the influence of variations on major morphological traits, we performed genome wide association studies (GWAS) for 24 morphological traits in Chinese cabbage. Several candidate genes were traced with GWAS and classical QTL maps; like DWF, NAC biding transcription factor and protein kinase were identified as highly influencing genes for plant height, leaf length and number of leaves, respectively. In final we have found 55 potential genes underlying with nucleotide variation, for 24 traits of Chinese cabbage. The first GWAS study of morphological traits in B. rapa will be the basis of trait improvement through marker-assisted breeding and genomic selection.