Rui Chen, Ke Chen, Xingwei Yao, Xiaoli Zhang, Yingxia Yang, Xiao Su, Mingjie Lyu, Qian Wang, Guan Zhang, Mengmeng Wang, Yanhao Li, Lijin Duan, Tianyu Xie, Haichao Li, Yuyao Yang, Hong Zhang, Yutong Guo,Guiying Jia, Xianhong Ge, Panagiotis F. Sarris, Tao Lin, Deling Sun

NATURE GENETICS; Published online: 7 May 2024

ABSTRACT

Cauliflower (Brassica oleracea L. var. botrytis) is a distinctive vegetable that supplies a nutrient-rich edible inflorescence meristem for the human diet. However, the genomic bases of its selective breeding have not been studied extensively. Herein, we present a high-quality reference genome assembly C-8 (V2) and a comprehensive genomic variation map consisting of 971 diverse accessions of cauliflower and its relatives. Genomic selection analysis and deep-mined divergences were used to explore a stepwise domestication process for cauliflower that initially evolved from broccoli (Curd-emergence and Curd-improvement), revealing that three MADS-box genes, CAULIFLOWER1 (CAL1), CAL2 and FRUITFULL (FUL2), could have essential roles during curd formation. Genome-wide association studies identified nine loci significantly associated with morphological and biological characters and demonstrated that a zinc-finger protein (BOB06G 135460) positively regulates stem height in cauliflower. This study offers valuable genomic resources for better understanding the genetic bases of curd biogenesis and florescent development in crops.

See https://www.nature.com/articles/s41588-024-01744-4#Abs1

Fig. 1 | Genomic relationships of 971 B. oleracea accessions. a, Clades and groups including wild and major subspecies of B. oleracea, along with their relationships, illustrated using a phylogenetic tree. Different colors represent different groups as follows: gray, outgroup (B. rapa and B. nigra); black, wild and feral-type; cyan, Chinese kale; red, kohlrabi; dark green, lacinato kale; gold, curly kale; yellow, Brussels sprouts; dark blue, savoy cabbage; pink, kale; dark cyan, cabbage; green, broccoli; dark purple, purple cauliflower; magenta, ROM; blue, ELMC, purple, LMC; orange, EMC-1; brown, EMC-2. White and gray bars indicate 5 cm. b, Results of model-based clustering when K = 3, 4 and 5. Red dashed lines indicate three categories as labeled: Curdless, Green-curd and White-curd. c, PCA analysis based on 1,564 4d-SNPs. d, Summary of nucleotide diversity (π) and population divergence (FST) among major B. oleracea subspecies and each cauliflower group. e, LD decay. Dashed lines and colored dots indicate the half-maximum distance and corresponding r² values, respectively.