A high-density linkage map and QTL mapping of fruit-related traits in pumpkin (Cucurbita moschata Duch.)

Abstract

Pumpkin (Cucurbita moschata) is an economically worldwide crop. Few quantitative trait loci (QTLs) were reported previously due to the lack of genomic and genetic resources. In this study, a high-density linkage map of C. moschata was structured by double-digest restriction site-associated DNA sequencing, using 200 F2 individuals of CMO-1 × CMO-97. By filtering 74,899 SNPs, a total of 3,470 high quality SNP markers were assigned to the map spanning a total genetic distance of 3087.03 cM on 20 linkage groups (LGs) with an average genetic distance of 0.89 cM. Based on this map, both pericarp color and strip were fined mapped to a novel single locus on LG8 in the same region of 0.31 cM with phenotypic variance explained (PVE) of 93.6% and 90.2%, respectively. QTL analysis was also performed on carotenoids, sugars, tuberculate fruit, fruit diameter, thickness and chamber width with a total of 12 traits. 29 QTLs distributed in 9 LGs were detected with PVE from 9.6% to 28.6%. It was the first high-density linkage SNP map for C. moschata which was proved to be a valuable tool for gene or QTL mapping. This information will serve as significant basis for map-based gene cloning, draft genome assembling and molecular breeding.

Quantitative Trait Loci (QTL) Analysis of Fruit and Agronomic Traits of Tropical Pumpkin (Cucurbita moschata) in an Organic Production System

“…The resulting genetic map consisted of 24 linkage groups with an overall genetic length of 2665 cM and an average spacing of 3.7 cMs (Figure 1). The mapping was unable to achieve a chromosome level resolution as in recent studies [21] due to an insufficient number of markers, but the map did provide close to a chromosome-level number of linkage groups that provide utility in tropical pumpkin breeding.…”

“…Individual GBS reads that contained a SNP that showed a statistically significant association with any given trait in the QTL analysis were aligned against the pumpkin genome [21] that is publicly available through the Cucurbit Genomics Database [22] using the BLAST tool [23]. Coordinates and annotations are summarized in Table S1.…”

Construction of a High-Density Genetic Map and Analysis of Seed-Related Traits Using Specific Length Amplified Fragment Sequencing for Cucurbita maxima

“…The high-density genetic map of C. pepo contained 7,718 markers with an average genetic distance between markers of 0.4 cM (Monteropau et al, 2017). 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).…”

“…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.…”

“…Recently, a new high-throughput strategy for de novo SNP discovery called specific length amplified fragment sequencing (SLAF-seq) has been developed and successfully applied to construct high-density maps of grape (Wang et al, 2017a), gingko (Liu et al, 2017), pear (Wang et al, 2017b), tobacco (Gong et al, 2016), matsudana (Zhang et al, 2016), cauliflower (Zhao et al, 2016), soybean (Qi et al, 2014), sesame (Zhang et al, 2013), watermelon (Shang et al, 2016), and cucumber (Xu et al, 2015). This strategy has also been applied for QTL mapping of important economic and nutritional traits in sesame (Mei et al, 2017), soybean (Li et al, 2017), spinach (Qian et al, 2017), cucumber (Zhu et al, 2016), wax gourd (Jiang et al, 2015), and pumpkin (Zhong et al, 2017). However, SLAF-seq has not been successfully applied in squash.…”