title: Potential of marker selection to increase prediction accuracy of genomic selection in soybean (Glycine maxL.).
abstract: Genomic selection is a promising molecular breeding strategy enhancing genetic gain per unit time. The objectives of our study were to (1) explore the prediction accuracy of genomic selection for plant height and yield per plant in soybean [Glycine max(L.) Merr.], (2) discuss the relationship between prediction accuracy and numbers of markers, and (3) evaluate the effect of marker preselection based on different methods on the prediction accuracy. Our study is based on a population of 235 soybean varieties which were evaluated for plant height and yield per plant at multiple locations and genotyped by 5361 single nucleotide polymorphism markers. We applied ridge regression best linear unbiased prediction coupled with fivefold cross-validations and evaluated three strategies of marker preselection. For plant height, marker density and marker preselection procedure impacted prediction accuracy only marginally. In contrast, for grain yield, prediction accuracy based on markers selected with a haplotype block analyses-based approach increased by approximately 4 % compared with random or equidistant marker sampling. Thus, applying marker preselection based on haplotype blocks is an interesting option for a cost-efficient implementation of genomic selection for grain yield in soybean breeding.
authors.affiliation: College of Agriculture, Northeast Agricultural University, Harbin, 150030 China ; The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China ; Soybean Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086 China.
authors.forename: Yansong
authors.initials: Y
authors.lastname: Ma
authors.affiliation: Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany.
authors.forename: Jochen C
authors.initials: JC
authors.lastname: Reif
authors.affiliation: Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany.
authors.forename: Yong
authors.initials: Y
authors.lastname: Jiang
authors.affiliation: Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824 USA.
authors.forename: Zixiang
authors.initials: Z
authors.lastname: Wen
authors.affiliation: Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824 USA.
authors.forename: Dechun
authors.initials: D
authors.lastname: Wang
authors.affiliation: The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China.
authors.forename: Zhangxiong
authors.initials: Z
authors.lastname: Liu
authors.affiliation: The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China.
authors.forename: Yong
authors.initials: Y
authors.lastname: Guo
authors.affiliation: Heilongjiang Academy of Agricultural Sciences, Harbin, 150086 China.
authors.forename: Shuhong
authors.initials: S
authors.lastname: Wei
authors.affiliation: Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun, 130033 China.
authors.forename: Shuming
authors.initials: S
authors.lastname: Wang
authors.affiliation: Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun, 130033 China.
authors.forename: Chunming
authors.initials: C
authors.lastname: Yang
authors.affiliation: Chifeng Institute of Agricultural Sciences, Chifeng, 024031 China.
authors.forename: Huicai
authors.initials: H
authors.lastname: Wang
authors.affiliation: Institution of Cereal and Oil Crops Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050031 China.
authors.forename: Chunyan
authors.initials: C
authors.lastname: Yang
authors.affiliation: Economic Crops Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450002 China.
authors.forename: Weiguo
authors.initials: W
authors.lastname: Lu
authors.affiliation: Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250010 China.
authors.forename: Ran
authors.initials: R
authors.lastname: Xu
authors.affiliation: Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062 China.
authors.forename: Rong
authors.initials: R
authors.lastname: Zhou
authors.affiliation: Institute of Crop Sciences, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200 China.
authors.forename: Ruizhen
authors.initials: R
authors.lastname: Wang
authors.affiliation: Institute of Economical Crops, Guangxi Academy of Agricultural Sciences, Nanning, 530007 China.
authors.forename: Zudong
authors.initials: Z
authors.lastname: Sun
authors.affiliation: Institute of Economical Crops, Guangxi Academy of Agricultural Sciences, Nanning, 530007 China.
authors.forename: Huaizhu
authors.initials: H
authors.lastname: Chen
authors.affiliation: Hulun Buir Institute of Agricultural Sciences, Hulun Buir, 021000 China.
authors.forename: Wanhai
authors.initials: W
authors.lastname: Zhang
authors.affiliation: Heihe Branch Institute, Heilongjiang Academy of Agricultural Sciences, Heihe, 164300 China.
authors.forename: Jian
authors.initials: J
authors.lastname: Wu
authors.affiliation: The Crop Research and Breeding Center of Land-Reclamation, Harbin, 150090 Heilongjiang China.
authors.forename: Guohua
authors.initials: G
authors.lastname: Hu
authors.affiliation: The Crop Research and Breeding Center of Land-Reclamation, Harbin, 150090 Heilongjiang China.
authors.forename: Chunyan
authors.initials: C
authors.lastname: Liu
authors.affiliation: Soybean Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086 China.
authors.forename: Xiaoyan
authors.initials: X
authors.lastname: Luan
authors.affiliation: Suihua Branch Institute, Heilongjiang Academy of Agricultural Sciences, Suihua, 152052 China.
authors.forename: Yashu
authors.initials: Y
authors.lastname: Fu
authors.affiliation: Jiamusi Branch Institute, Heilongjiang Academy of Agricultural Sciences, Jiamusi, 154007 China.
authors.forename: Tai
authors.initials: T
authors.lastname: Guo
authors.affiliation: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China.
authors.forename: Tianfu
authors.initials: T
authors.lastname: Han
authors.affiliation: Institution of Cereal and Oil Crops Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050031 China.
authors.forename: Mengchen
authors.initials: M
authors.lastname: Zhang
authors.affiliation: Hulun Buir Institute of Agricultural Sciences, Hulun Buir, 021000 China.
authors.forename: Bincheng
authors.initials: B
authors.lastname: Sun
authors.affiliation: Crop Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031 Anhui China.
authors.forename: Lei
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Suihua Branch Institute, Heilongjiang Academy of Agricultural Sciences, Suihua, 152052 China.
authors.forename: Weiyuan
authors.initials: W
authors.lastname: Chen
authors.affiliation: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China.
authors.forename: Cunxiang
authors.initials: C
authors.lastname: Wu
authors.affiliation: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China.
authors.forename: Shi
authors.initials: S
authors.lastname: Sun
authors.affiliation: Zhoukou Institute of Agricultural Sciences, Zhoukou, 466001 Henan China.
authors.forename: Baojun
authors.initials: B
authors.lastname: Yuan
authors.affiliation: Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062 China.
authors.forename: Xinan
authors.initials: X
authors.lastname: Zhou
authors.affiliation: Heihe Branch Institute, Heilongjiang Academy of Agricultural Sciences, Heihe, 164300 China.
authors.forename: Dezhi
authors.initials: D
authors.lastname: Han
authors.affiliation: Heihe Branch Institute, Heilongjiang Academy of Agricultural Sciences, Heihe, 164300 China.
authors.forename: Hongrui
authors.initials: H
authors.lastname: Yan
authors.affiliation: College of Agriculture, Northeast Agricultural University, Harbin, 150030 China.
authors.forename: Wenbin
authors.initials: W
authors.lastname: Li
authors.affiliation: The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China.
authors.forename: Lijuan
authors.identifier: 0000-0003-1746-3653
authors.initials: L
authors.lastname: Qiu
keywords: Genomic selection; Glycine max; Prediction accuracy; Sampling method