Fine mapping and identification of candidate genes for fruit color in pepper (Capsicum chinense)

Abstract

The quality of pepper fruits is determined by numerous characteristics such as, flavor, color, and nutritional value. Through little is known about it, fruit color impacts breeding preferences in Capsicum chinense in a substantial way. In the present study, two C. chinense germplasms, HNUCC16 (dark green immature and yellow ripe fruit) and HNUCC22 (light green immature and red ripe fruit) were used to produce an F2 population. Based on genotyping-by-sequencing, we constructed a high-density genetic map of the F2 population with 1,347 bin markers and covered 1,206.37 cM in twelve pepper linkage groups. The trait segregation analysis of the F2 population show that the color of immature and mature fruits is controlled by a single locu . Bin markers 19 (chromosome 1) and 849 (Chromosome 6) were closely associated with the locus that regulates the color of immature and ripe fruits, respectively. The transformation of the two bin markers into dCAPS markers indicate that inactive shikimate kinase-like 2 (BC332_00870) may be a strong candidate gene for regulating immature fruit color, and the premature termination mutation of capsanthin–capsorubin synthase (BC332_17237) gene may possibly cause the yellow color in HNUCC16 pepper fruits. Overall, the findings of this study offer fundamental knowledge concerning the development of color and offer a new resource for pepper fruit color genetic improvement and molecular breeding.