Cauliflower is an important variety of Brassica oleracea and is planted worldwide. Here, the high-quality genome sequence of cauliflower was reported. The assembled cauliflower genome was 584.60 Mb in size, with a contig N50 of 2.11 Mb, and contained 47,772 genes; 56.65% of the genome was composed of repetitive sequences. Among these sequences, long terminal repeats (LTRs) were the most abundant (32.71% of the genome), followed by transposable elements (TEs) (12.62%). Comparative genomic analysis confirmed that after an ancient paleohexaploidy (γ) event, cauliflower underwent two whole-genome duplication (WGD) events shared with Arabidopsis and an additional whole-genome triplication (WGT) event shared with other Brassica species. The present cultivated cauliflower diverged from the ancestral B. oleracea species ~3.0 million years ago (Mya). The speciation of cauliflower (~2.0 Mya) was later than that of B. oleracea L. var. capitata (approximately 2.6 Mya) and other Brassica species (over 2.0 Mya). Chromosome no. 03 of cauliflower shared the most syntenic blocks with the A, B, and C genomes of Brassica species and its eight other chromosomes, implying that chromosome no. 03 might be the most ancient one in the cauliflower genome, which was consistent with the chromosome being inherited from the common ancestor of Brassica species. In addition, 2,718 specific genes, 228 expanded genes, 2 contracted genes, and 1,065 positively selected genes in cauliflower were identified and functionally annotated. These findings provide new insights into the genomic diversity of Brassica species and serve as a valuable reference for molecular breeding of cauliflower.

Cauliflower is a nutritious vegetable with inflorescences that are specialized to form the edible organs called curds. Uncovering key genes underlying important traits is crucial for the genetic improvement of this important crop. However, the genetic basis of many important agronomic traits, including curd performance and plant architecture in cauliflower, remains unclear. GWASs have proved to be powerful tools to study agronomic traits in many crops. To reveal the genetic basis of four important agronomic traits, namely, the main stem height (MSH), purplish curd (PC), external leaf wing (ELW) and weight of a single curd (WSC), we selected 220 core accessions of loose-curd cauliflower for resequencing, phenotypic investigation and GWAS. The approach revealed significant novel loci. We detected several significant associations: on C02 for MSH and PC, on C06 for ELW and on C01 for WSC. More interestingly, we identified a significant single-peak signal for the weight of a single curd (WSC), an important yield trait, and within this signal interval, we identified the BOB01G136670 gene with five SNPs encoding nonsynonymous mutations in the CDS region; these mutations resulted in two haplotypes with significant differences in curd weight. The weight of a single curd was significantly increased in the varieties with the BOB01G136670 ^Hap1 allele compared to those with BOB01G136670 ^Hap2. BOB01G136670 was highly conserved with the homologous genes that encode serine carboxypeptidase and belong to the S10 family in other species, including GS5, which functions as a positive regulator of grain size in rice, wheat and maize. Additionally, BOB01G136670 was highly expressed specifically at the curd enlargement stage, with low or even no expression at all in other tissues and stages, indicating that BOB01G136670 is a plausible candidate gene for WSC. Overall, this study identified genomic loci for four important agronomic traits that are relevant for accelerating biological breeding and the improvement of cauliflower varieties.