Abstract
BackgroundHigh-density map is a valuable tool for genetic and genomic analysis. Although wax gourd is a widely distributed vegetable of Cucurbitaceae and has important medicinal and health value, no genetic map has been constructed because of the lack of efficient markers. Specific-locus amplified fragment sequencing (SLAF-seq) is a newly developed high-throughput strategy for large-scale single nucleotide polymorphism (SNP) discovery and genotyping.ResultsIn our present study, we constructed a high-density genetic map by using SLAF-seq and identified a locus controlling pericarp color in wax gourd. An F2 population of 140 individuals and their two parents were subjected to SLAF-seq. A total of 143.38 M pair-end reads were generated. The average sequencing depth was 26.51 in the maternal line (B214), 27.01 in the parental line (B227), and 5.11 in each F2 individual. When filtering low-depth SLAF tags, a total of 142,653 high-quality SLAFs were detected, and 22,151 of them were polymorphic, with a polymorphism rate of 15.42 %. And finally, 4,607 of the polymorphic markers were selected for genetic map construction, and 12 linkage groups (LGs) were generated. The map spanned 2,172.86 cM with an average distance between adjacent markers for 0.49 cM. The inheritance of pericarp color was also studied, which showed that the pericarp color was controlled by one single gene. And based on the newly constructed high-density map, a single locus locating on chromosome 5 was identified for controlling the pericarp color of wax gourd.ConclusionsThis is the first report of high-density genetic map construction and gene mapping in wax gourd, which will be served as an invaluable tool for gene mapping, marker assisted breeding, map-based gene cloning, comparative mapping and draft genome assembling of wax gourd.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2220-y) contains supplementary material, which is available to authorized users.
Highlights
High-density map is a valuable tool for genetic and genomic analysis
SLAF sequencing and genotyping After SLAF library construction and high-throughput sequencing, 143.38 M pair-end reads was obtained with a length of 100 bp
For 160 BC1 plants, 75 of them had dark green fruit, while the remaining had yellow fruit (χ2 = 0.51 for 1 dark green to 1 yellow segregation ratio). These results indicated that the pericarp color was controlled by one single gene, with dark green dominant to yellow
Summary
High-density map is a valuable tool for genetic and genomic analysis. wax gourd is a widely distributed vegetable of Cucurbitaceae and has important medicinal and health value, no genetic map has been constructed because of the lack of efficient markers. Wax gourd (Benincasa hispida (Thunb.) Cogn, 2n = 2x = 24) is a monotypic genus, which belongs to Cucurbitaceae and is a widely distributed vegetable in India, China and many other tropical countries [1]. It is called white gourd, white pumpkin, tallow gourd, and so on, which is named after an Italian count, Giuseppe. The storage of wax gourd is quite long, which makes it play a significant role in ensuring the annual supply and regulating off-seasons of vegetables It is recommended for treatment of peptic ulcer, hemorrhages from internal organs, epilepsy and other neurological disorders [3, 4]. In spite of its economic importance, no genetic map has been constructed in
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