Genome-wide association study and selective sweep analysis uncover candidate genes controlling curd branch length in cauliflower.

Cauliflower is a distinct subspecies of the Brassica oleracea plants due to its specialized and edible floral organ. Cauliflower curd is composed of enlarged inflorescence meristems that developed by a series of precise molecular regulations. Based solely on the curd solidity, cauliflower is generally classified into two groups (compact-curd and loose-curd), where curd branch length acts as a crucial parameter to determine the curd morphological difference. Herein, to understand the genetic basis of curd branch development, we utilized a total of 298 inbred lines representing two groups of cauliflower to comprehensively investigate the causal genes and regulatory mechanisms. Phylogenetic and population structure analyses revealed that two subgroups could be further categorized into the compact-curd and the loose-curd groups, respectively. Integrating the genotype and phenotype data, we conducted a genome-wide association study for the length of the outermost branch (LOB) and secondary branch (LSB) of the curd. Sixty-four significant loci were identified that are highly associated with curd branch development. Evidence from genome-wide selective sweep analysis (F_ST and XP-EHH) narrowed down the major signal on chromosome 8 into an approximately 79 kb region which encodes eleven protein-coding genes. After further analysis of haplotypes, transcriptome profiling, and gene expression validation, we finally inferred that BOB08G028680, as a homologous counterpart of AtARR9, might be the causal gene for simultaneously regulating LOB and LSB traits in cauliflower. This result provides valuable information for improving curd solidity in future cauliflower breeding.