Abstract
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.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-1158) contains supplementary material, which is available to authorized users.
Highlights
Cucumber, Cucumis sativus L., is an economically important vegetable crop which is processed or consumed fresh worldwide
Cucumber linkage maps were mostly composed of dominant markers [i.e. random amplified polymorphic DNAs (RAPDs), and amplified fragment length polymorphisms (AFLPs)], and did not reach saturated due to insufficient marker number [5,6,7,8,9]
High-throughput Specific-length amplified fragments (SLAF) sequencing and genotyping A total of 10.76 Gb raw data was generated from Illumina sequencing and SLAF library construction, which contained 75,024,043 pair-end reads with a length of 100 bp
Summary
Cucumis sativus L., is an economically important vegetable crop which is processed or consumed fresh worldwide. We constructed a high-density SNP map for cucumber using SLAF-seq and detected fruit-related QTLs. Cucumber (Cucumis sativus L., 2n = 2x = 14) is one of the most important vegetable crops cultivated worldwide, immature fruits of which are consumed cooked, processed, or fresh in a considerable amount. Two consensus maps were developed in cucumber to increase marker density, which were constructed by Zhang et al (1369 marker loci) [25], and Yang et al (1681 marker loci), respectively [26] Both of them employed the Gy14 × PI 183967 map with 995 SSRs for map integration [16], whereas marker orders in recombination suppression regions in the 1369-point map were not well placed. Despite the high marker density in consensus maps, it is still difficult to construct saturated maps for F2 or RIL populations derived from intra-varietal crosses to conduct QTL analysis and molecular mapping in certain populations
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