Campus Units

Agronomy

Document Type

Article

Publication Version

Published Version

Publication Date

2015

Journal or Book Title

PloS One

Volume

10

Issue

7

First Page

e0132379

DOI

10.1371/journal.pone.0132379

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.

Creative Commons License

Creative Commons Attribution 4.0 License
This work is licensed under a Creative Commons Attribution 4.0 License.

Copyright Owner

The Authors

Language

en

File Format

application/pdf

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