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

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 F 2 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 F 2 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 markerassisted selection (MAS)-based breeding in C. maxima.

A wildCucurbitagenome reveals the role of structural variants and introgression in domestication

“…Previous studies have also identified an association between variants in ABC transporter proteins and seed size in Cucurbita maxima and Linum usitatissimum (Guo et al, 2019), further suggesting that ABA may be deregulated via selective pressures on ABC transporters to enhance seed size in C. argyrosperma during its domestication. Variants in a serine/threonineprotein kinase, as the ones we found in our selective scans, have also been associated with seed size in C. maxima (Wang et al, 2019). We found SPP as a CNV loss in argyrosperma, whose ortholog in C. maxima has been predicted as a major QTL for seed length (Wang et al, 2019).…”

Quantitative Trait Loci for Seed Size Variation in Cucurbits – A Review

“…As discussed early (see section "Introduction, " Supplementary Table S1), the ubiquitination pathway may play important roles in control of seed size (e.g., Song et al, 2007;Li et al, 2010;Su et al, 2011;Xia et al, 2013;Wang et al, 2016;Dong et al, 2017). From our recent study in pumpkin, the E3 ubiquitin-protein ligase gene was located in the SL6-1 and SW6-1 major-effect QTL region (Wang et al, 2019). In rice, a gene encoding a zinc finger protein has been verified in control grain weight (Huang et al, 2011).…”

“…Tan et al (2013) developed an F 2 population using the Indian large-grain '0515-1' and the small-grain '0460-1-1' pumpkin lines; QTL analysis detected 4 major-effect QTL controlling SWD on LG2, LG3 and LG4 with PVE from 2.9 to 29.7%. In C. maxima, Wang et al (2019) developed a high-density genetic map with the F 2 population from the cross between two squash inbred lines ('2013-12' and '9-6'). In QTL mapping, they identified 10 QTL on six chromosomes (Chr) (Chr4,5,6,8,17,and 18), including 4 for SL, 4 for SW, and 2 for HSW (100-hundred-seed weight) with the PVE ranging from 7.0 to 38.6%.…”

Identification of Fruit-Associated QTLs in Winter Squash (Cucurbita maxima Duchesne) Using Recombinant Inbred Lines

“…Despite biological and horticultural interest in C. maxima, knowledge of its genetics and genomic resources is limited in comparison with other economically important cucurbit crops. Recently, the first detailed genetic maps were developed for C. maxima [2,[19][20][21]. Additionally, the nuclear genome of C. maxima cv.…”

“…For C. maxima, the genetic bases of fruit-associated traits are largely unknown [4]. The only QTLs described so far for C. maxima have been for a dwarf vine identified in an F 2 population [19], seed-related traits using an F 2:3 population [21] and fruit flesh color and carotenoid content-identified using F 6 RILs [20].…”