Abstract
Seed traits are agronomically important for Cucurbita breeding, but the genes controlling seed size, seed weight and seed number have not been mapped in Cucurbita maxima (C. maxima). In this study, 100 F2 individual derived from two parental lines, “2013-12” and “9-6”, were applied to construct a 3,376.87-cM genetic map containing 20 linkage groups (LGs) with an average genetic distance of 0.47 cM using a total of 8,406 specific length amplified fragment (SLAF) markers in C. maxima. Ten quantitative trait loci (QTLs) of seed width (SW), seed length (SL) and hundred-seed weight (HSW) were identified using the composite interval mapping (CIM) method. The QTLs affecting SW, SL and HSW explained a maximum of 38.6%, 28.9% and 17.2% of the phenotypic variation and were detected in LG6, LG6 and LG17, respectively. To validate these results, an additional 150 F2 individuals were used for QTL mapping of SW and SL with cleaved amplified polymorphic sequence (CAPS) markers. We found that two major QTLs, SL6-1 and SW6-1, could be detected in both SLAF-seq and CAPS markers in an overlapped region. Based on gene annotation and non-synonymous single-nucleotide polymorphisms (SNPs) in the major SWand SL-associated regions, we found that two genes encoding a VQ motif and an E3 ubiquitin-protein ligase may be candidate genes influencing SL, while an F-box and leucinerich repeat (LRR) domain-containing protein is the potential regulator for SW in C. maxima. This study provides the first high-density linkage map of C. maxima using SNPs developed by SLAF-seq technology, which is a powerful tool for associated mapping of important agronomic traits, map-based gene cloning and marker-assisted selection (MAS)-based breeding in C. maxima.
Highlights
The squash Cucurbita maxima Duch (2x = 2n = 40) is an important cucurbitaceous plant that is widely grown worldwide as a commercial crop
According to seed trait data from the parents and 100 F2 individuals, correlation analysis showed that seed length (SL) was significantly correlated with seed width (SW) (r = 0.627), which indicated that long seeds always appeared together with wide seeds
By using 100 F2 populations from two morphologically diverse parents, a high-density genetic map of C. maxima was constructed by specific length amplified fragment (SLAF)-seq
Summary
The squash Cucurbita maxima Duch (2x = 2n = 40) is an important cucurbitaceous plant that is widely grown worldwide as a commercial crop. It has high nutritional value and healthprotective properties and has received increasing interest and popularity in breeding. The genetic maps of Cucurbita moschata were developed using SSR and SNP markers and spanned 1445.4–3087.03 cM (Gong et al, 2008b; Zhong et al, 2017). The high-density genetic map of C. moschata contained 3470 markers with an average genetic distance of 0.89 cM (Zhong et al, 2017) Compared with those of C. pepo and C. moschata, few maps of C. maxima with a limited number of markers have been published. A genetic map with a low density of markers has limited application for further fine QTL mapping and MAS in squash breeding; a high-density genetic map of C. maxima is urgently needed
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