Dataset Information

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 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.

SUBMITTER: Wang Y

PROVIDER: S-EPMC7046561 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Publications

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

Wang Yunli Y Wang Chaojie C Han Hongyu H Luo Yusong Y Wang Zhichao Z Yan Chundong C Xu Wenlong W Qu Shuping S

Frontiers in plant science 20200221

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) ma ...[more]

PMID: 32153597

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Project description:BackgroundSoybean is not only an important oil crop, but also an important source of edible protein and industrial raw material. Yield-traits and quality-traits are increasingly attracting the attention of breeders. Therefore, fine mapping the QTLs associated with yield-traits and quality-traits of soybean would be helpful for soybean breeders. In the present study, a high-density linkage map was constructed to identify the QTLs for the yield-traits and quality-traits, using specific length amplified fragment sequencing (SLAF-seq).ResultsSLAF-seq was performed to screen SLAF markers with 149 F8:11 individuals from a cross between a semi wild soybean, 'Huapidou', and a cultivated soybean, 'Qihuang26', which generated 400.91 M paired-end reads. In total, 53,132 polymorphic SLAF markers were obtained. The genetic linkage map was constructed by 5111 SLAF markers with segregation type of aa×bb. The final map, containing 20 linkage groups (LGs), was 2909.46 cM in length with an average distance of 0.57 cM between adjacent markers. The average coverage for each SLAF marker on the map was 81.26-fold in the male parent, 45.79-fold in the female parent, and 19.84-fold average in each F8:11 individual. According to the high-density map, 35 QTLs for plant height (PH), 100-seeds weight (SW), oil content in seeds (Oil) and protein content in seeds (Protein) were found to be distributed on 17 chromosomes, and 14 novel QTLs were identified for the first time. The physical distance of 11 QTLs was shorter than 100 Kb, suggesting a direct opportunity to find candidate genes. Furthermore, three pairs of epistatic QTLs associated with Protein involving 6 loci on 5 chromosomes were identified. Moreover, 13, 14, 7 and 9 genes, which showed tissue-specific expression patterns, might be associated with PH, SW, Oil and Protein, respectively.ConclusionsWith SLAF-sequencing, some novel QTLs and important QTLs for both yield-related and quality traits were identified based on a new, high-density linkage map. Moreover, 43 genes with tissue-specific expression patterns were regarded as potential genes in further study. Our findings might be beneficial to molecular marker-assisted breeding, and could provide detailed information for accurate QTL localization.

Dataset Information

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

Publications

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

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