Construction and Analysis of High-Density Linkage Map Using High-Throughput Sequencing Data

Dongyuan Liu; Chouxian Ma; Weiguo Hong; Long Huang; Min Liu; Hui Liu; Huaping Zeng; Dejing Deng; Huaigen Xin; Jun Song; Chunhua Xu; Xiaowen Sun; Xilin Hou; Xiaowu Wang; Hongkun Zheng

doi:10.1371/journal.pone.0098855

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Open Access

Peer-reviewed

Research Article

Construction and Analysis of High-Density Linkage Map Using High-Throughput Sequencing Data

Dongyuan Liu ,

Contributed equally to this work with: Dongyuan Liu, Chouxian Ma, Weiguo Hong, Long Huang

Affiliation Biomarker Technologies Corporation, Beijing, China
⨯
Chouxian Ma ,

Contributed equally to this work with: Dongyuan Liu, Chouxian Ma, Weiguo Hong, Long Huang

Affiliation Biomarker Technologies Corporation, Beijing, China
⨯
Weiguo Hong ,

Contributed equally to this work with: Dongyuan Liu, Chouxian Ma, Weiguo Hong, Long Huang

Affiliation Biomarker Technologies Corporation, Beijing, China
⨯
Long Huang ,

Contributed equally to this work with: Dongyuan Liu, Chouxian Ma, Weiguo Hong, Long Huang

Affiliation Biomarker Technologies Corporation, Beijing, China
⨯
Min Liu,

Affiliation Biomarker Technologies Corporation, Beijing, China
⨯
Hui Liu,

Affiliation Biomarker Technologies Corporation, Beijing, China
⨯
Huaping Zeng,

Affiliation Biomarker Technologies Corporation, Beijing, China
⨯
Dejing Deng,

Affiliation Biomarker Technologies Corporation, Beijing, China
⨯
Huaigen Xin,

Affiliation Biomarker Technologies Corporation, Beijing, China
⨯
Jun Song,

Affiliation Biomarker Technologies Corporation, Beijing, China
⨯
Chunhua Xu,

Affiliation Biomarker Technologies Corporation, Beijing, China
⨯
Xiaowen Sun,

Affiliation Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
⨯
Xilin Hou,

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
⨯
Xiaowu Wang ,

* E-mail: wangxw@mail.caas.net.cn (XWW) (XW); zhenghk@biomarker.com.cn (HKZ) (HZ)

Affiliations Biomarker Technologies Corporation, Beijing, China, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences (IVF, CAAS), Beijing, China
⨯
Hongkun Zheng

* E-mail: wangxw@mail.caas.net.cn (XWW) (XW); zhenghk@biomarker.com.cn (HKZ) (HZ)

Affiliation Biomarker Technologies Corporation, Beijing, China
⨯

Construction and Analysis of High-Density Linkage Map Using High-Throughput Sequencing Data

Dongyuan Liu,
Chouxian Ma,
Weiguo Hong,
Long Huang,
Min Liu,
Hui Liu,
Huaping Zeng,
Dejing Deng,
Huaigen Xin,
Jun Song

Published: June 6, 2014
https://doi.org/10.1371/journal.pone.0098855

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highly heterozygous loci

Posted by vaneck on 14 Jun 2015 at 20:51 GMT

Quote from the article text: RECORD has been developed to produce accurate marker orders in a relatively short time by employing the total number of observable recombination events between adjacent markers as a target function [24]. SMOOTH has been reported to eliminate genotyping errors from genetic linkage data during the mapping process and improve map quality [22]. However, neither RECORD nor SMOOTH is capable of handling populations with high heterozygous loci.
Questions: What are highly heterozygous loci? With homozygous loci it is not possible to construct a linkage map. A locus can be heterozygous only by having two different alleles.
I can assure that RECORD and SMOOTH can handle F2, RIL, BC1, HAP and DH populations

No competing interests declared.

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Construction and Analysis of High-Density Linkage Map Using High-Throughput Sequencing Data

Construction and Analysis of High-Density Linkage Map Using High-Throughput Sequencing Data

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highly heterozygous loci

Posted by vaneck on 14 Jun 2015 at 20:51 GMT