title: High-density genetic map construction and gene mapping of pericarp color in wax gourd using specific-locus amplified fragment (SLAF) sequencing.
abstract: BACKGROUND
  High-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.
  
  
  RESULTS
  In 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.
  
  
  CONCLUSIONS
  This 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.
authors.affiliation: Vegetable Research Institute, Guangdong Academy of Agriculture Science, Guangzhou, 510640, China.|Guangdong Provincial Key Lab for New Technology Research on Vegetables, Guangzhou, 510640, China.
authors.forename: Biao
authors.initials: B
authors.lastname: Jiang
authors.affiliation: Vegetable Research Institute, Guangdong Academy of Agriculture Science, Guangzhou, 510640, China.|Guangdong Provincial Key Lab for New Technology Research on Vegetables, Guangzhou, 510640, China.
authors.forename: Wenrui
authors.initials: W
authors.lastname: Liu
authors.affiliation: Vegetable Research Institute, Guangdong Academy of Agriculture Science, Guangzhou, 510640, China. xiedasen@126.com.|Guangdong Provincial Key Lab for New Technology Research on Vegetables, Guangzhou, 510640, China. xiedasen@126.com.
authors.forename: Dasen
authors.initials: D
authors.lastname: Xie
authors.affiliation: Vegetable Research Institute, Guangdong Academy of Agriculture Science, Guangzhou, 510640, China.
authors.forename: Qingwu
authors.initials: Q
authors.lastname: Peng
authors.affiliation: Vegetable Research Institute, Guangdong Academy of Agriculture Science, Guangzhou, 510640, China.|Guangdong Provincial Key Lab for New Technology Research on Vegetables, Guangzhou, 510640, China.
authors.forename: Xiaoming
authors.initials: X
authors.lastname: He
authors.affiliation: Vegetable Research Institute, Guangdong Academy of Agriculture Science, Guangzhou, 510640, China.
authors.forename: Yu'e
authors.initials: Y
authors.lastname: Lin
authors.affiliation: Vegetable Research Institute, Guangdong Academy of Agriculture Science, Guangzhou, 510640, China.
authors.forename: Zhaojun
authors.initials: Z
authors.lastname: Liang
mesh_terms: D001947:Breeding; D002874:Chromosome Mapping / Q000379:methods*; D019662:Cucurbitaceae / Q000235:genetics*; D008040:Genetic Linkage; D023281:Genomics / Q000379:methods*; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D019655:Quantitative Trait, Heritable