Insertion of a CACTA-like transposable element disrupts the function of the BoCCD4 gene in yellow-petal Chinese kale

Abstract

Brassica oleracea comprises several important subspecies, including cabbage, broccoli, cauliflower, Chinese kale, and kohlrabi. The petal color of Chinese kale is mostly white and sometimes yellow. To explore the genetic basis of petal color variation in Chinese kale, F2 and BC1 (backcross) populations were constructed from the cross of two inbred lines, 2114 (yellow petal) and 2116 (white petal). Genetic analysis of the F2 and BC1 populations demonstrated that yellow petal color was controlled by a single recessive nuclear gene, termed cpc-2. Insertion-deletion (InDel) markers, designed based on the parental resequencing data, were used to map cpc-2. The fine mapping results indicated that the cpc-2 gene was located in a 569-kb interval on chromosome C03 flanked by InDel markers ZB636 and ZB692, with genetic distances of 0.3 cM and 0.6 cM, respectively. By analyzing the nucleotide variations and annotations of the genes in this interval, a CCD4 family gene was predicted to be a candidate for cpc-2 and renamed BoCCD4.2. In addition, insertion of the CACTA-like transposable element (TE3) interrupted the function of the BoCCD4 gene, which may have resulted in the loss of function of BoCCD4 and the petal color transition from white to yellow. The TE3 insertion in the BoCCD4 gene was also present in 63 cabbage inbred lines among 159 accessions, which revealed that the TE3-type null allele of BoCCD4 formed before the divergence of the two subspecies cabbage and Chinese kale and that Chinese kale evolved much earlier than cabbage. This study lays the foundation for cloning BoCCD4.2 and revealing the molecular mechanism underlying petal color formation in Chinese kale.