Peel color is an important factor affecting commodity quality in vegetables; however, the genes controlling this trait remain unclear in wax gourd. Here, we used two F2 genetic segregation populations to explore the inheritance patterns and to clone the genes associated with green and white skin in wax gourd. The F2 and BC1 trait segregation ratios were 3:1 and 1:1, respectively, and the trait was controlled by nuclear genes. Bulked segregant analysis of both F2 plants revealed peaks on Chr5 exceeding the confidence interval. Additionally, 6,244 F2 plants were used to compress the candidate interval into a region of 179 Kb; one candidate gene, Bch05G003950 (BhAPRR2), encoding two-component response regulator-like protein Arabidopsis pseudo-response regulator2 (APRR2), which is involved in the regulation of peel color, was present in this interval. Two bases (GA) present in the coding sequence of BhAPRR2 in green-skinned wax gourd were absent from white-skinned wax gourd. The latter contained a frameshift mutation, a premature stop codon, and lacked 335 residues required for the protein functional region. The chlorophyll content and BhAPRR2 expression were significantly higher in green-skinned than in white-skinned wax gourd. Thus, BhAPRR2 may regulate the peel color of wax gourd. This study provides a theoretical foundation for further studies of the mechanism of gene regulation for the fruit peel color of wax gourd.

Fruit shape is an important agronomic trait in wax gourds [Benincasa hispida (Thunb) Cogn.]. However, the candidate genes for this important trait, and their genetic mechanisms, remain unknown. In this study, we identi ed a candidate gene for fruit shape in wax gourds using a next-generation sequencing-based bulked segregant analysis in F 2 populations derived from a cross between GX-71 (long cylindrical fruit, FSI = 4.56) and MY-1 (round fruit, FSI = 1.06) genotypes. According to bulked segregant analysis, the candidate gene is located in the 17.18 Mb region on chromosome 2, and the kompetitive allele speci c polymerase chain reaction (KASP) marker was used to reduce it to the 19.6 Kb region. There is only one gene in the corresponding region of the reference genome, Bch02G016830 (designated BFS). We sequenced BFS in six wax gourd varieties with different fruit shapes. Sequence analysis showed that there were two non-synonymous mutations in the spherical wax gourd and one non-synonymous mutation in the cylindrical wax gourd. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis showed that the expression of BFS in round fruits was signi cantly higher than in long cylindrical fruits at the ovary formation stage. Therefore, BFS is a candidate gene for determination of the fruit shape of wax gourds. The predicted protein encoded by the BFS gene belongs to the IQD protein family, which have the structural characteristics of scaffold proteins and coordinate Ca 2+ CaM signaling from the membrane to the nucleus. The BFS gene can assist with the breeding of new varieties that possess ideal fruit shapes. Key MessageNon-synonymous mutations in the BFS gene, which encodes the IQD protein, are responsible for the shape of wax gourd fruits.

Soluble solids content (SSC) is an important quality trait of wax gourd, but reports about its regulatory genes are scarce. In this study, the SSC regulatory gene BhSSC2.1 in wax gourd was mined via quantitative trait locus (QTL) mapping based on high-density genetic mapping containing 12 linkage groups (LG) and bulked segregant analysis (BSA)-seq. QTL mapping and BSA-seq revealed for the first time that the SSC QTL (107.658–108.176 cM) of wax gourd was on Chr2 (LG2). The interpretable phenotypic variation rate and maximum LOD were 16.033% and 6.454, respectively. The QTL interval contained 13 genes. Real-time fluorescence quantitative expression analysis, functional annotation, and sequence analysis suggested that Bch02G016960, named BhSSC2.1, was a candidate regulatory gene of the SSC in wax gourd. Functional annotation of this gene showed that it codes for a NADP-dependent malic enzyme. According to BhSSC2.1 sequence variation, an InDel marker was developed for molecular marker-assisted breeding of wax gourd. This study will lay the foundation for future studies regarding breeding and understanding genetic mechanisms of wax gourd.

Bitter gourd (Momordica charantia) is cultivated widely as a vegetable and herbal medicine in many Asian and African countries. Two varieties (‘LS-5’ and ‘LS-22’) were re-sequenced by next-generation sequencing technology, and a set of InDel markers was developed. The genome of ‘Dali-11’ was the reference genome. Exactly 59098 and 73683 InDel loci were identified in ‘LS-5’ and ‘LS-22’, respectively. To verify the reliability of this set of InDel markers, 220 pairs of InDel primers were designed and synthesised. Primers were preliminarily detected by 8% polyacrylamide gel electrophoresis. Thereafter, 15 pairs of polymorphic primers were selected and employed to construct the DNA fingerprint of 27 bitter gourd varieties. The purity of five hybrid seed lots, ‘Zhongyu’, ‘Heiyu’, ‘Lvzhu’, ‘Shunliu 3’ and ‘Shunliu 8’, was determined using the specific primers. In this study, a batch of InDel primers with high polymorphism potential was developed based on resequencing. These primers can effectively distinguish some bitter gourd varieties. Therefore, this set of reliable and accurate InDel markers can provide a richer marker source for bitter gourd variety identification and seed purity determination.

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