Identification of QTLs and Candidate Genes Associated with Agronomic Traits in Brassica oleracea var. Italica

Optimizing crop growing and harvesting efficiency requires the elucidation of genetic variation of agronomic traits in diverse crop culitvars. In this study, a genome-wide association study (GWAS) on 112 Brassica oleracea var. italica diversity lines was conducted to identify significant loci and candidate genes important to over 20 agronomic traits. A QK mixed model was applied in order to appropriately account for population structure. With replication over two years, an average of 6 QTLs were identified for each trait. The QTL regions were searched for candidate genes from a list aggregated from the scientific literature by a Natural Language Processing software. For example, the QTL regions associated with black rot trait, caused by the Xanthomonas campestris bacteria, contained defense related genes such as pathogenesis-thaumatin, defensin (DEFL), disease resistance (TIR-NBS-LRR), and hypersensitive response lesion-inducing candidate genes. Identifying candidate genes associated with complex agronomic traits provides a great resource for genetic and breeding research to further improve broccoli agronomics and allow greater access to broccoli’s plethora of human health benefits.