Fine mapping of the major gene BhHLS1 controlling seed size in wax gourd (Benincasa hispida)

Abstract

Introduction/BackgroundThe seed size of wax gourds is an important agronomic trait; however, the associated genes have not yet been reported.MethodsIn this study, we used a high-density genetic map constructed based on F8 recombinant inbred line populations derived from a cross between MY-1 (large seed) and GX-71 (small seed) strains to detect quantitative trait locis (QTLs) for seed-size-related traits in wax gourd over a two-year period.ResultsTwo stable QTLs (qSL10 and qSW10) for seed length (SL) and seed width (SW) on chromosome 10 were repeatedly detected over two years (2021–2022). qSL10 had a phenotypic variation rate of 75.30% and 80.80% in 2021 and 2022, respectively. Whereas, qSW10 had a phenotypic variation rate of 66.60% and 73.80% in 2021 and 2022, respectively. Further, a single nucleotide polymorphism mutation was found to cause early termination of Bch10G006400 (BhHLS1) translation in GX-71 through sequencing analysis of candidate genes. Based on gene functional annotation and quantitative real-time PCR analyses, BhHLS1 encoded a probable N-acetyltransferase HLS1-like protein and its expression level was significantly different between parents. Therefore, BhHLS1 is a major candidate gene associated with a one-factor polymorphism regulating the SL and SW of wax gourds. Finally, based on variation in the BhHLS1 sequence, a cleaved amplified polymorphic sequence marker was developed for the molecular marker-assisted breeding of wax gourds.DiscussionOverall, this study is of great significance for the genetic improvement of seed size, verification of gene functions, and cultivation of specific germplasm resources for wax gourds.

Natural Allelic Variations of Bch10G006400 Controlling Seed Size in Chieh-qua (Benincasa hispida Cogn. var. Chieh-qua How)

“…Finally, the seed size gene was localized within the 48.8 Kb range and contained only one gene (Bch10G006400) (Figure 4b), which encodes a family of Nacetyltransferase proteins. It is speculated that this gene is an important candidate for determining the seed size of chieh-qua, which was consistent with the findings of previous studies of the wax gourd seed size gene [22].…”

“…The results showed that the seed phenotype of the F 1 population was similar to that of the large-seed parent P 1 (Table 1 and Figure 1a), and the seeds of the F 2 population exhibited a bimodal distribution (Figure 1b-d). These findings are consistent with the results for the seed size of wax gourd [22]. However, some researchers believe that seed size is a quality trait, which may be caused by differences in the materials, planting methods, or statistical methods used.…”

“…These three loci constitute four haplotypes (G-G-AGA, C-G-AGA, G-T-AGA, and G-G), of which only G-G-AGA is a large seed, and the other three haplotypes are small seeds. It is worth noting that in wax gourd, Bch10G006400 did not involve the other two loci (SNP_314 and InDel_551), which may be caused by different materials [22]. On the other hand, they verified that most of the materials used were large seed materials, so it was easy to ignore the other two sites where small seed materials existed.…”

“…At present, Bch10G006400 has been reported to be related to seed size in wax gourd [22], and the SNP (G to T) at 400 bp, named SNP_400, caused early termination of translation. However, the SNP was not found in the two chieh-qua parents in this study, so we speculated that the mutation of this gene varies among different materials.…”