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

Loading metrics

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

Reader Comments

Post a new comment on this article

Figure 1 is unclear

Posted by vaneck on 14 Jun 2015 at 21:25 GMT

Part A seems to show a homozygous diploid organism (2n=8)
The four pairs of homozygous chromosomes are green, pink, purple, gold.

Part B is not connected to A because gold changed into red?
Part B seems to display the F1 offspring of two non-inbred organisms (2n=2)
The genetic model is a father (heterozygous Green and Blue) x mother (Purple and Red)
In symbols the cross is : GB x PR
The segregating offspring displays a segregation ratio of 1:1:1:1 = GP:GR:BP:BR

Part D shows the integrated map including markers that segregate from one parent only
GB x 00 or 00xPR where the 00 is a dummy as suggested for the pseudo-testcross by Grattapaglia & Sederoff (1994) Genetics 137(4):1121-1137.

This paternal only or maternal only should cause cold or empty rows and columns in the heatmap because the product of male meiosis cannot display association with the product of female meiosis.

No competing interests declared.

Subject Areas
?

For more information about PLOS Subject Areas, click here.
We want your feedback. Do these Subject Areas make sense for this article? Click the target next to the incorrect Subject Area and let us know. Thanks for your help!

Linkage mapping
Is the Subject Area "Linkage mapping" applicable to this article?

Thanks for your feedback.
Genotyping
Is the Subject Area "Genotyping" applicable to this article?

Thanks for your feedback.
Gene mapping
Is the Subject Area "Gene mapping" applicable to this article?

Thanks for your feedback.
Carps
Is the Subject Area "Carps" applicable to this article?

Thanks for your feedback.
Next-generation sequencing
Is the Subject Area "Next-generation sequencing" applicable to this article?

Thanks for your feedback.
Genomics
Is the Subject Area "Genomics" applicable to this article?

Thanks for your feedback.
Algorithms
Is the Subject Area "Algorithms" applicable to this article?

Thanks for your feedback.
Genetic linkage
Is the Subject Area "Genetic linkage" applicable to this article?

Thanks for your feedback.

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

Reader Comments

Post Your Discussion Comment

Why should this posting be reviewed?

Thank You!

Figure 1 is unclear

Posted by vaneck on 14 Jun 2015 at 21:25 GMT