title: Construction and analysis of high-density linkage map using high-throughput sequencing data.
abstract: Linkage maps enable the study of important biological questions. The construction of high-density linkage maps appears more feasible since the advent of next-generation sequencing (NGS), which eases SNP discovery and high-throughput genotyping of large population. However, the marker number explosion and genotyping errors from NGS data challenge the computational efficiency and linkage map quality of linkage study methods. Here we report the HighMap method for constructing high-density linkage maps from NGS data. HighMap employs an iterative ordering and error correction strategy based on a k-nearest neighbor algorithm and a Monte Carlo multipoint maximum likelihood algorithm. Simulation study shows HighMap can create a linkage map with three times as many markers as ordering-only methods while offering more accurate marker orders and stable genetic distances. Using HighMap, we constructed a common carp linkage map with 10,004 markers. The singleton rate was less than one-ninth of that generated by JoinMap4.1. Its total map distance was 5,908 cM, consistent with reports on low-density maps. HighMap is an efficient method for constructing high-density, high-quality linkage maps from high-throughput population NGS data. It will facilitate genome assembling, comparative genomic analysis, and QTL studies. HighMap is available at http://highmap.biomarker.com.cn/.
authors.affiliation: Biomarker Technologies Corporation, Beijing, China.
authors.forename: Dongyuan
authors.initials: D
authors.lastname: Liu
authors.affiliation: Biomarker Technologies Corporation, Beijing, China.
authors.forename: Chouxian
authors.initials: C
authors.lastname: Ma
authors.affiliation: Biomarker Technologies Corporation, Beijing, China.
authors.forename: Weiguo
authors.initials: W
authors.lastname: Hong
authors.affiliation: Biomarker Technologies Corporation, Beijing, China.
authors.forename: Long
authors.initials: L
authors.lastname: Huang
authors.affiliation: Biomarker Technologies Corporation, Beijing, China.
authors.forename: Min
authors.initials: M
authors.lastname: Liu
authors.affiliation: Biomarker Technologies Corporation, Beijing, China.
authors.forename: Hui
authors.initials: H
authors.lastname: Liu
authors.affiliation: Biomarker Technologies Corporation, Beijing, China.
authors.forename: Huaping
authors.initials: H
authors.lastname: Zeng
authors.affiliation: Biomarker Technologies Corporation, Beijing, China.
authors.forename: Dejing
authors.initials: D
authors.lastname: Deng
authors.affiliation: Biomarker Technologies Corporation, Beijing, China.
authors.forename: Huaigen
authors.initials: H
authors.lastname: Xin
authors.affiliation: Biomarker Technologies Corporation, Beijing, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Song
authors.affiliation: Biomarker Technologies Corporation, Beijing, China.
authors.forename: Chunhua
authors.initials: C
authors.lastname: Xu
authors.affiliation: Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China.
authors.forename: Xiaowen
authors.initials: X
authors.lastname: Sun
authors.affiliation: State Key laboratory of Crop Genetic and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China.
authors.forename: Xilin
authors.initials: X
authors.lastname: Hou
authors.affiliation: Biomarker Technologies Corporation, Beijing, China; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences (IVF, CAAS), Beijing, China.
authors.forename: Xiaowu
authors.initials: X
authors.lastname: Wang
authors.affiliation: Biomarker Technologies Corporation, Beijing, China.
authors.forename: Hongkun
authors.initials: H
authors.lastname: Zheng
mesh_terms: D000465:Algorithms; D000818:Animals; D002347:Carps / Q000235:genetics; D002874:Chromosome Mapping; D005819:Genetic Markers / Q000235:genetics; D023281:Genomics / Q000379:methods*; D060005:Genotyping Techniques; D059014:High-Throughput Nucleotide Sequencing
chemical_list: D005819:Genetic Markers