The Impact of Genetic Relationship and Linkage Disequilibrium on Genomic Selection

Supplemental Files
Date
2015-01-01
Authors
Liu, Hongjun
Zhou, Huangkai
Lubberstedt, Thomas
Wu, Youngsheng
Li, Xiao
Zhao, Jing
Zuo, Tao
Zhang, Xuan
Zhang, Yongzhong
Liu, Sisi
Shen, Yaou
Lin, Haijian
Zhang, Zhiming
Abertondo, Victor
Lee, Michael
Huang, Kaijian
Lubberstedt, Thomas
Pan, Guangtang
Major Professor
Advisor
Committee Member
Journal Title
Journal ISSN
Volume Title
Publisher
Altmetrics
Authors
Research Projects
Organizational Units
Agronomy
Organizational Unit
Journal Issue
Series
Department
Agronomy
Abstract

Genomic selection is a promising research area due to its practical application in breeding. In this study, impact of realized genetic relationship and linkage disequilibrium (LD) on marker density and training population size required was investigated and their impact on practical application was further discussed. This study is based on experimental data of two populations derived from the same two founder lines (B73, Mo17). Two populations were genotyped with different marker sets at different density: IBM Syn4 and IBM Syn10. A high-density marker set in Syn10 was imputed into the Syn4 population with low marker density. Seven different prediction scenarios were carried out with a random regression best linear unbiased prediction (RR-BLUP) model. The result showed that the closer the real genetic relationship between training and validation population, the fewer markers were required to reach a good prediction accuracy. Taken the short-term cost for consideration, relationship information is more valuable than LD information. Meanwhile, the result indicated that accuracies based on high LD between QTL and markers were more stable over generations, thus LD information would provide more robust prediction capacity in practical applications.

Comments

This article is published as Liu, Hongjun, Huangkai Zhou, Yongsheng Wu, Xiao Li, Jing Zhao, Tao Zuo, Xuan Zhang et al. "The impact of genetic relationship and linkage disequilibrium on genomic selection." PloS one 10, no. 7 (2015): e0132379. doi: 10.1371/journal.pone.0132379. Posted with permission.

Description
Keywords
Citation
DOI
Collections