群体构成方式对大豆百粒重全基因组选择预测准确度的影响

doi:10.3724/SP.J.1006.2018.00043

作物学报 ›› 2018, Vol. 44 ›› Issue (01): 43-52.doi: 10.3724/SP.J.1006.2018.00043

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

群体构成方式对大豆百粒重全基因组选择预测准确度的影响

马岩松^1,2,13,刘章雄¹,文自翔³,魏淑红⁴,杨春明⁵,王会才⁶,杨春燕⁷,卢为国⁸,徐冉⁹,张万海¹⁰,吴纪安¹¹,胡国华¹²,栾晓燕¹³,付亚书¹⁴,郭泰¹⁵,王曙明⁵,韩天富¹,张孟臣⁷,张磊¹⁶,苑保军¹⁷,郭勇¹,Jochen C. REIF¹⁸,江勇¹⁸,李文滨²,王德春³,邱丽娟^1,*

1 中国农业科学院作物科学研究所 / 国家农作物基因资源与遗传改良重大科学工程 / 农业部作物种质资源与生物技术重点开放实验室，北京100081；2 东北农业大学农学院，黑龙江哈尔滨150030；3 Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing MI 48824, USA；4 黑龙江省农业科学院育种研究所，黑龙江哈尔滨150081；5 吉林省农业科学院大豆研究所，吉林长春130033；6 内蒙古赤峰市农科所，内蒙古赤峰024031；7 河北省农业科学院粮油作物研究所，河北石家庄050031；8 河南省农业科学院经作所，河南郑州450002；9 山东省农业科学院作物研究所，山东济南250010；10 内蒙古呼伦贝尔市农科所，内蒙古呼伦贝尔021000；11 黑龙江省农业科学院黑河分院，黑龙江黑河164300；12 黑龙江省农垦科研育种中心，黑龙江哈尔滨150090；13 黑龙江省农业科学院大豆研究所，黑龙江哈尔滨150086；14 黑龙江省农业科学院绥化分院，黑龙江绥化152052；15 黑龙江省农业科学院佳木斯分院，黑龙江佳木斯154007；16 安徽省农业科学院作物研究所，安徽合肥230031；17 河南省周口市农业科学院，河南周口466001；18 Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben 06466, Germany

收稿日期:2017-02-10 修回日期:2017-09-10 出版日期:2018-01-12 网络出版日期:2017-10-30
基金资助:
本研究由国家转基因生物新品种培育重大专项(2014ZX08004001)和中国农业科学院农业科技创新项目资助。

Effect of Population Structure on Prediction Accuracy of Soybean 100-Seed Weight by Genomic Selection MA Yan-Song1,2,13, LIU Zhang-Xiong1, WEN Zi-Xiang3, WEI Shu-Hong4, YANG Chun-Ming5, WANG Hui-Cai6, YANG

MA Yan-Song^1,2,13, LIU Zhang-Xiong¹, WEN Zi-Xiang³, WEI Shu-Hong⁴, YANG Chun-Ming⁵, WANG Hui-Cai⁶,YANG Chun-Yan⁷, LU Wei-Guo⁸, XU Ran⁹, ZHANG Wan-Hai¹⁰, WU Ji-An¹¹, HU Guo-Hua¹², LUAN Xiao-Yan¹³, FU Ya-Shu¹⁴, GUO Tai¹⁵, WANG Shu-Ming⁵, HAN Tian-Fu¹, ZHANG Meng-Chen⁷, ZHANG Lei¹⁶, YUAN Bao-Jun¹⁷, GUO Yong¹, Jochen C. REIF¹⁸, JIANG Yong¹⁸, LI Wen-Bin², WANG De-Chun³,QIU Li-Juan^1,*

1 National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; 2 College of Agriculture, Northeast Agricultural University, Harbin 150030, China; 3 Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing MI 48824, United States of America; 4 Institute of Crop Breeding, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, Heilongjiang, China; 5 Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun 130033, Jilin, China; 6 Chifeng Institute of Agricultural Sciences, Chifeng 024031, Inner Mongolia, China; 7 Institution of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050031, Hebei, China; 8 Economic Crops Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, Henan, China; 9 Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250010, Shandong, China; 10 Hulunbeier Institute of Agricultural Sciences, Hulunbeier 021000, Inner Mongolia, China; 11 Heihe Branch Institute, Heilongjiang Academy of Agricultural Sciences, Heihe 164300, Heilongjiang, China; 12 The Crop Research and Breeding Center of Land-Reclamation, Harbin 150090, Heilongjiang, China; 13 Soybean Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, Heilongjiang, China; 14 Suihua Branch Institute, Heilongjiang Academy of Agricultural Sciences, Suihua 152052, Heilongjiang, China; 15 Jiamusi Branch Institute, Heilongjiang Academy of Agricultural Sciences, Jiamusi 154007, Heilongjiang, China; 16 Crop Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, Anhui, China; 17 Zhoukou Institute of Agricultural Sciences, Zhoukou 466001, Henan, China; 18 Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben 06466, Germany

Received:2017-02-10 Revised:2017-09-10 Published:2018-01-12 Published online:2017-10-30
Supported by:
This study was supported by the National Major Project for Developing New GM Crops (2014ZX08004001) and the Agricultural Science and Technology Innovation Program (ASTIP) of Chinese Academy of Agricultural Sciences.

摘要/Abstract

摘要：

百粒重是大豆产量的重要构成因子，在一定条件下与产量呈显著正相关。百粒重是一个复杂的数量性状，用传统的育种方法其遗传增益不明显。本研究对280份大豆品种多年多点田间鉴定，通过混合线性模型预测获得品种百粒重的最佳线性无偏预测值。同时利用分布在大豆全基因组的5361个SNP标记鉴定参试品种基因型，结合随机回归最佳线性无偏预测模型和交互验证方法，探讨了群体构成方式对大豆百粒重的全基因组选择预测准确度的影响。结果表明，大豆百粒重的全基因组选择预测准确度变化范围为–0.15~ +0.75；群体构成方式对百粒重的预测准确度影响明显；亚群内的预测准确度(0.24~0.75)高于亚群间(?0.15~ +0.29)；当群体间遗传距离由0.1566增加到0.2201时，预测准确度下降27.87%；相比随机构建的训练群体，基于群体遗传结构构建的训练群体能将百粒重的预测准确度提高2.34%。本研究明确了大豆百粒重的全基因组选择预测准确度，阐明了群体结构对大豆百粒重的全基因组选择预测准确度的影响，为大豆分子育种提供了新的思路和方法。

关键词: 大豆, 百粒重, 全基因组选择, 预测准确度, 遗传结构

Abstract:

Hundred-seed weight is an important yield component and has positive relationship with soybean yield under certain conditions. The genetic gain of 100-seed weight based on traditional breeding or markers assisted-selection is limited because it is controlled by plenty of small effect genes. Genomic selection offers an approach to accelerate the soybean 100-seed weight breeding. However, the effect of population structure on soybean 100-seed weight prediction accuracy has not been elaborated. In our study 280 soybean varieties with phenotypic data evaluated in multi-location in 2008–2012 and 5361 SNPs genotype were used to explore the effect of population structure on 100-seed weight prediction accuracy. The best linear unbiased prediction of 100-seed weight of each variety was calculated according to mixed linear model. Ridge regression best linear unbiased prediction and five-fold cross validation were used to estimate the 100-seed weight prediction accuracy. Our research showed that the range of 100-seed weight, which was from –0.15 to 0.75. Hundred-seed weight prediction accuracy was affected by population structure significantly. The prediction accuracy within subset (0.24 to 0.75) was higher than that between subsets (?0.15 to +0.29). When the genetic distance between subsets increased from 0.1566 to 0.2201, the 100-seed weight prediction accuracy was decreased by 27.87%. Compared with random sampling training population, the training population composed based on genetic structure improved 100-seed weight prediction accuracy by 2.34%. In summary we are clear about the soybean 100-seed weight genomic selection accuracy and the effect of population structure on genomic selection accuracy. The genomic selection is an efficient method to improve the soybean breeding.

Key words: Glycine max, 100-seed weight, Genomic selection, Prediction accuracy, Genetic structure

马岩松,刘章雄,文自翔,魏淑红,杨春明,王会才,杨春燕,卢为国,徐冉,张万海,吴纪安,胡国华,栾晓燕,付亚书,郭. 群体构成方式对大豆百粒重全基因组选择预测准确度的影响[J]. 作物学报, 2018, 44(01): 43-52.

MA Yan-Song, LIU Zhang-Xiong, WEN Zi-Xiang, WEI Shu-Hong, YANG Chun-Ming, WANG Hui-Cai6, YANG Chun-Yan, LU Wei-Guo, XU Ran, ZHANG Wan-Hai, WU Ji-An, HU Guo-Hua, LUAN Xiao-Yan, FU . Effect of Population Structure on Prediction Accuracy of Soybean 100-Seed Weight by Genomic Selection MA Yan-Song1,2,13, LIU Zhang-Xiong1, WEN Zi-Xiang3, WEI Shu-Hong4, YANG Chun-Ming5, WANG Hui-Cai6, YANG[J]. Acta Agron Sin, 2018, 44(01): 43-52.

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链接本文: https://zwxb.chinacrops.org/CN/10.3724/SP.J.1006.2018.00043

https://zwxb.chinacrops.org/CN/Y2018/V44/I01/43

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群体构成方式对大豆百粒重全基因组选择预测准确度的影响

Effect of Population Structure on Prediction Accuracy of Soybean 100-Seed Weight by Genomic Selection MA Yan-Song1,2,13, LIU Zhang-Xiong1, WEN Zi-Xiang3, WEI Shu-Hong4, YANG Chun-Ming5, WANG Hui-Cai6, YANG

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