Abstract
High-density genetic map provides an essential framework for accurate and efficient genome assembly and QTL fine mapping. Construction of high-density genetic maps appears more feasible since the advent of next-generation sequencing (NGS), which eases SNP discovery and high-throughput genotyping of large population. In this research, a high-density genetic map of cucumber (Cucumis sativus L.) was successfully constructed across an F2 population by a recently developed Specific Length Amplified Fragment sequencing (SLAF-seq) method. In total, 18.69 GB of data containing 93,460,000 paired-end reads were obtained after preprocessing. The average sequencing depth was 44.92 in the D8 (female parent), 42.16 in the Jin5-508 (male parent), and 5.01 in each progeny. 79,092 high-quality SLAFs were detected, of which 6784 SLAFs were polymorphic, and 1892 of the polymorphic markers met the requirements for constructing genetic map. The genetic map spanned 845.87 cm with an average genetic distance of 0.45 cm. It is a reliable linkage map for fine mapping and molecular breeding of cucumber for its high marker density and well-ordered markers.
Highlights
Cucumber (Cucumis sativus L.), a diploid species (2n = 2x =14), is an important crop all over the world ranking fourth in quantity of world vegetable production after tomato, cabbage and onion (FAO STAT 2011, http://faostat.fao.org)
VALIDATION OF GENOTYPING RESULTS BASED ON SLAF-SEQ A total of 14 mapped SLAF markers were randomly selected from seven linkage groups for genotyping validation
Based on advanced generation sequencing, genotyping approaches including traditional methods (Illumina GoldenGate assay, Infinium assay), and next-generation sequencing (NGS)-based methods (Reduced-Representation Libraries (RRLs), RAD genotyping, and SLAF-seq (Baird et al, 2008; Sun et al, 2013) allow millions of SNPs to be identified in plant genome
Summary
Fazio et al (2003) developed a cucumber genetic map spanned 706 cm with 27 AFLPs, 62 RAPD, 14 SSR, 24 SCAR, one SNP, and three MTM molecular markers. Yuan et al (2008) constructed another map spanned 1005.8 cm included 206 SRAPs, 22 SSRs, 25 SCARs, one STS and three MTM. Miao et al (2011) developed a linkage map of cultivated cucumber with 248 SSR into seven linkage groups spanning 711.9 cm, with a mean marker interval of 2.8 cm. Yang et al (2013) constructed a map spanning 730.0 cm in seven linkage groups by integrating three component maps with a bin-mapping strategy, which has been considered to be the densest genetic maps of cucumber so far. Despite of significant improvements in map construction, marker density of these maps are still far from being satisfactory for many molecular marker-based applications such as marker-assisted breeding, map-based gene cloning or assembly of a more complete cucumber genome (Yang et al, 2013)
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