Quantitative trait loci identification reveals zinc finger protein CONSTANS-LIKE 4 as the key candidate gene of stigma color in watermelon (Citrullus lanatus)

Abstract

Stigma color is a critical agronomic trait in watermelon that plays an important role in pollination. However, there are few reports on the regulation of stigma color in watermelon. In this study, a genetic analysis of the F2 population derived from ZXG1553 (P1, with orange stigma) and W1-17 (P2, with yellow stigma) indicated that stigma color is a quantitative trait and the orange stigma is recessive compared with the yellow stigma. Bulk segregant analysis sequencing (BSA-seq) revealed a 3.75 Mb segment on chromosome 6 that is related to stigma color. Also, a major stable effective QTL Clqsc6.1 (QTL stigma color) was detected in two years between cleaved amplified polymorphic sequencing (CAPS) markers Chr06_8338913 and Chr06_9344593 spanning a ~1.01 Mb interval that harbors 51 annotated genes. Cla97C06G117020 (annotated as zinc finger protein CONSTANS-LIKE 4) was identified as the best candidate gene for the stigma color trait through RNA-seq, quantitative real-time PCR (qRT-PCR), and gene structure alignment analysis among the natural watermelon panel. The expression level of Cla97C06G117020 in the orange stigma accession was lower than in the yellow stigma accessions with a significant difference. A nonsynonymous SNP site of the Cla97C06G117020 coding region that causes amino acid variation was related to the stigma color variation among nine watermelon accessions according to their re-sequencing data. Stigma color formation is often related to carotenoids, and we also found that the expression trend of ClCHYB (annotated as β-carotene hydroxylase) in the carotenoid metabolic pathway was consistent with Cla97C06G117020, and it was expressed in low amounts in the orange stigma accession. These data indicated that Cla97C06G117020 and ClCHYB may interact to form the stigma color. This study provides a theoretical basis for gene fine mapping and mechanisms for the regulation of stigma color in watermelon.