Genome-wide association analysis reveals a novel QTL CsPC1 for pericarp color in cucumber

Abstract

Background Cucumber is an important melon crop in the world, with different pericarp colors. However, the candidate genes and the underlying genetic mechanism for such an important trait in cucumber are unknown. In this study, a locus controlling pericarp color was found on chromosome 3 of cucumber genome. Results In this study, the light green inbred line G35 and the dark green inbred line Q51 were crossed to produce one F2 population. Consequently, we identified a major locus CsPC1 (Pericarp color 1). Next, we mapped the CsPC1 locus to a 94-kb region chromosome 3 which contains 15 genes. Among these genes, Csa3G912920, which encodes a GATA transcription factor, was expressed at a higher level in the pericarp of the NIL-1334 line (with light-green pericarp) than in that of the NIL-1325 line (with dark-green pericarp). This study provides a new allele for the improvement of cucumber pericarp color. Conclusion A major QTL that controls pericarp color in cucumber, CsPC1, was identified in a 94-kb region that harbors the strong candidate gene CsGATA1.

Morphological and Genetic Diversity of Cucumber (Cucumis sativus L.) Fruit Development

“…The presence and density of trichomes and warts has been associated with homologs of numerous transcription factors regulating trichome development in other species as well as genes influencing auxin and cytokinin levels and transport [ 87 , 88 , 90 , 96 , 97 , 98 , 111 , 113 , 114 ]. Variation in traits such as cuticle thickness and composition and skin and flesh color has been found to be mediated by structural genes encoding biosynthetic enzymes for cutin, wax, chlorophyll, and beta-carotene synthesis, as well as transcription factors regulating cuticle deposition and pigment biosynthesis [ 118 , 120 , 124 , 127 , 135 , 136 , 137 , 138 , 139 , 140 , 141 , 143 ]. Collectively, these findings demonstrate the complex interplay between structural genes, transcription factors, and hormone signaling leading to morphological diversity in cucumber.…”

“…A recessive white immature fruit trait has been associated with QTL on chromosomes 3 and 5 [ 134 ]. Fruit with lighter colors also have been produced via mutagenesis, influencing genes such as a Ycf54-like protein implicated in the cyclase step of chlorophyll biosynthesis [ 135 ]; a gene homologous to Arabidopsis ARC5 important for chloroplast division [ 136 ]; the transcription factor, MYB36 reducing chlorophyll content and causing a yellow green peel [ 137 ]; and a GATA transcription family member that has been implicated in other systems to regulate chlorophyll synthesis [ 138 ]. Mutations resulting in white fruit with fewer chloroplasts and reduced chlorophyll content include a premature stop in the w gene encoding a putative two-component response regulator (RR)-like protein, APRR2 [ 139 , 140 , 141 ].…”