title: An ultra-high density linkage map and QTL mapping for sex and growth-related traits of common carp (Cyprinus carpio).
abstract: High density genetic linkage maps are essential for QTL fine mapping, comparative genomics and high quality genome sequence assembly. In this study, we constructed a high-density and high-resolution genetic linkage map with 28,194 SNP markers on 14,146 distinct loci for common carp based on high-throughput genotyping with the carp 250 K single nucleotide polymorphism (SNP) array in a mapping family. The genetic length of the consensus map was 10,595.94 cM with an average locus interval of 0.75 cM and an average marker interval of 0.38 cM. Comparative genomic analysis revealed high level of conserved syntenies between common carp and the closely related model species zebrafish and medaka. The genome scaffolds were anchored to the high-density linkage map, spanning 1,357 Mb of common carp reference genome. QTL mapping and association analysis identified 22 QTLs for growth-related traits and 7 QTLs for sex dimorphism. Candidate genes underlying growth-related traits were identified, including important regulators such as KISS2, IGF1, SMTLB, NPFFR1 and CPE. Candidate genes associated with sex dimorphism were also identified including 3KSR and DMRT2b. The high-density and high-resolution genetic linkage map provides an important tool for QTL fine mapping and positional cloning of economically important traits, and improving common carp genome assembly.
authors.affiliation: College of Life Sciences, Shanghai Ocean University, Shanghai, 201306, China.|Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, 100141, China.
authors.forename: Wenzhu
authors.initials: W
authors.lastname: Peng
authors.affiliation: Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, 100141, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Xu
authors.affiliation: Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, 100141, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: College of Fishery, Henan Normal University, Xinxiang, 453007, China.
authors.forename: Jianxin
authors.initials: J
authors.lastname: Feng
authors.affiliation: College of Life Sciences, Shanghai Ocean University, Shanghai, 201306, China.|Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, 100141, China.
authors.forename: Chuanju
authors.initials: C
authors.lastname: Dong
authors.affiliation: College of Life Sciences, Shanghai Ocean University, Shanghai, 201306, China.|Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, 100141, China.
authors.forename: Likun
authors.initials: L
authors.lastname: Jiang
authors.affiliation: College of Life Sciences, Shanghai Ocean University, Shanghai, 201306, China.|Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, 100141, China.
authors.forename: Jingyan
authors.initials: J
authors.lastname: Feng
authors.affiliation: College of Life Sciences, Shanghai Ocean University, Shanghai, 201306, China.|Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, 100141, China.
authors.forename: Baohua
authors.initials: B
authors.lastname: Chen
authors.affiliation: College of Life Sciences, Shanghai Ocean University, Shanghai, 201306, China.|Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, 100141, China.
authors.forename: Yiwen
authors.initials: Y
authors.lastname: Gong
authors.affiliation: Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, 100141, China.|College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, PR China.
authors.forename: Lin
authors.initials: L
authors.lastname: Chen
authors.affiliation: Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, 100141, China.|Henan Academy of Fishery Science, Zhengzhou, 450044, China.
authors.forename: Peng
authors.initials: P
authors.lastname: Xu
mesh_terms: D000818:Animals; D002347:Carps / Q000235:genetics*; D002874:Chromosome Mapping; D008040:Genetic Linkage; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D015027:Zebrafish / Q000235:genetics