Dataset Information

Construction of a high-density genetic map and identification of QTLs for cucumber mosaic virus resistance in pepper (Capsicum annuum L.) using specific length amplified fragment sequencing (SLAF-seq).

ABSTRACT: Pepper (Capsicum) is one of the most important vegetable and spice crops. Aphid-transmitted cucumber mosaic virus (CMV) causes significant damage to pepper crops across the world. The genetic basis of CMV resistance in pepper is complex, and the mechanisms underlying resistance remain largely unknown. Here, we employed a SLAF-seq approach to generate a high-density genetic map of pepper. The map spanned 1,785.46 cM, containing 12,727 markers on 12 chromosomes, with a mean marker distance of 0.16 cM between adjacent markers. We used this map and the interval mapping (IM) and multiple QTL mapping (MQM) procedures to detect genetic regions associated with quantitative trait for CMV resistance. Three QTLs, qcmv11.1, qcmv11.2 and qcmv12.1, conferred resistance to CMV and showed trait variation of 10.2%, 19.2% and 7.3% respectively. Our results will help to develop markers linked to CMV-resistant QTLs to improve pepper resistance to CMV.

SUBMITTER: Li N

PROVIDER: S-EPMC5982177 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature

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Construction of a high-density genetic map and identification of QTLs for cucumber mosaic virus resistance in pepper (<i>Capsicum annuum</i> L.) using specific length amplified fragment sequencing (SLAF-seq).

Li Ning N Yin Yanxu Y Wang Fei F Yao Minghua M

Breeding science 20180331 2

Pepper (<i>Capsicum</i>) is one of the most important vegetable and spice crops. Aphid-transmitted cucumber mosaic virus (CMV) causes significant damage to pepper crops across the world. The genetic basis of CMV resistance in pepper is complex, and the mechanisms underlying resistance remain largely unknown. Here, we employed a SLAF-seq approach to generate a high-density genetic map of pepper. The map spanned 1,785.46 cM, containing 12,727 markers on 12 chromosomes, with a mean marker distance ...[more]

PMID: 29875607

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Project description:BackgroundCucumber, Cucumis sativus L., is an economically important vegetable crop which is processed or consumed fresh worldwide. However, the narrow genetic base in cucumber makes it difficult for constructing high-density genetic maps. The development of massively parallel genotyping methods and next-generation sequencing (NGS) technologies provides an excellent opportunity for developing single nucleotide polymorphisms (SNPs) for linkage map construction and QTL analysis of horticultural traits. Specific-length amplified fragment sequencing (SLAF-seq) is a recent marker development technology that allows large-scale SNP discovery and genotyping at a reasonable cost. In this study, we constructed a high-density SNP map for cucumber using SLAF-seq and detected fruit-related QTLs.ResultsAn F2 population of 148 individuals was developed from an intra-varietal cross between CC3 and NC76. Genomic DNAs extracted from two parents and 148 F2 individuals were subjected to high-throughput sequencing and SLAF library construction. A total of 10.76 Gb raw data and 75,024,043 pair-end reads were generated to develop 52,684 high-quality SLAFs, out of which 5,044 were polymorphic. 4,817 SLAFs were encoded and grouped into different segregation patterns. A high-resolution genetic map containing 1,800 SNPs was constructed for cucumber spanning 890.79 cM. The average distance between adjacent markers was 0.50 cM. 183 scaffolds were anchored to the SNP-based genetic map covering 46% (168.9 Mb) of the cucumber genome (367 Mb). Nine QTLs for fruit length and weight were detected, a QTL designated fl3.2 explained 44.60% of the phenotypic variance. Alignment of the SNP markers to draft genome scaffolds revealed two mis-assembled scaffolds that were validated by fluorescence in situ hybridization (FISH).ConclusionsWe report herein the development of evenly dispersed SNPs across cucumber genome, and for the first time an SNP-based saturated linkage map. This 1,800-locus map would likely facilitate genetic mapping of complex QTL loci controlling fruit yield, and the orientation of draft genome scaffolds.

Dataset Information

Construction of a high-density genetic map and identification of QTLs for cucumber mosaic virus resistance in pepper (Capsicum annuum L.) using specific length amplified fragment sequencing (SLAF-seq).

Publications

Construction of a high-density genetic map and identification of QTLs for cucumber mosaic virus resistance in pepper (<i>Capsicum annuum</i> L.) using specific length amplified fragment sequencing (SLAF-seq).

Similar Datasets

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