title: The Impact of Genetic Relationship and Linkage Disequilibrium on Genomic Selection.
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.
authors.affiliation: Maize Research Institute of Sichuan Agricultural University, Chengdu, China.
authors.forename: Hongjun
authors.initials: H
authors.lastname: Liu
authors.affiliation: Guangzhou Genedenovo Biotechnology Co., Ltd, Guangzhou, China.
authors.forename: Huangkai
authors.initials: H
authors.lastname: Zhou
authors.affiliation: Guangxi Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China.
authors.forename: Yongsheng
authors.initials: Y
authors.lastname: Wu
authors.affiliation: Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, China.
authors.forename: Xiao
authors.initials: X
authors.lastname: Li
authors.affiliation: Department of Agronomy, Iowa State University, Ames, IA, United States of America.
authors.forename: Jing
authors.initials: J
authors.lastname: Zhao
authors.affiliation: Interdepartmental genetics program, Iowa State University, Ames, IA, United States of America.
authors.forename: Tao
authors.initials: T
authors.lastname: Zuo
authors.affiliation: Guangzhou Genedenovo Biotechnology Co., Ltd, Guangzhou, China.
authors.forename: Xuan
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Maize Research Institute of Sichuan Agricultural University, Chengdu, China.
authors.forename: Yongzhong
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Maize Research Institute of Sichuan Agricultural University, Chengdu, China.
authors.forename: Sisi
authors.initials: S
authors.lastname: Liu
authors.affiliation: Maize Research Institute of Sichuan Agricultural University, Chengdu, China.
authors.forename: Yaou
authors.initials: Y
authors.lastname: Shen
authors.affiliation: Maize Research Institute of Sichuan Agricultural University, Chengdu, China.
authors.forename: Haijian
authors.initials: H
authors.lastname: Lin
authors.affiliation: Maize Research Institute of Sichuan Agricultural University, Chengdu, China.
authors.forename: Zhiming
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: Guangxi Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China.
authors.forename: Kaijian
authors.initials: K
authors.lastname: Huang
authors.affiliation: Department of Agronomy, Iowa State University, Ames, IA, United States of America.
authors.forename: Thomas
authors.initials: T
authors.lastname: Lübberstedt
authors.affiliation: Maize Research Institute of Sichuan Agricultural University, Chengdu, China.
authors.forename: Guangtang
authors.initials: G
authors.lastname: Pan
mesh_terms: D015810:Linkage Disequilibrium; D008957:Models, Genetic; D012641:Selection, Genetic; D003313:Zea mays / Q000235:genetics*