Genome-wide association studies dissect the genetic networks underlying agronomical traits in soybean

被引:327
作者
Fang, Chao [1 ,11 ]
Ma, Yanming [1 ]
Wu, Shiwen [2 ]
Liu, Zhi [1 ,11 ]
Wang, Zheng [1 ]
Yang, Rui [1 ]
Hu, Guanghui [3 ]
Zhou, Zhengkui [4 ]
Yu, Hong [2 ]
Zhang, Min [1 ]
Pan, Yi [1 ]
Zhou, Guoan [1 ]
Ren, Haixiang [5 ]
Du, Weiguang [6 ]
Yan, Hongrui [7 ]
Wang, Yanping [5 ]
Han, Dezhi [6 ]
Shen, Yanting [1 ,11 ]
Liu, Shulin [1 ,11 ]
Liu, Tengfei [1 ,11 ]
Zhang, Jixiang [1 ,11 ]
Qin, Hao [2 ]
Yuan, Jia [2 ]
Yuan, Xiaohui [8 ]
Kong, Fanjiang [9 ]
Liu, Baohui [9 ]
Li, Jiayang [2 ]
Zhang, Zhiwu [10 ]
Wang, Guodong [2 ,11 ]
Zhu, Baoge [1 ]
Tian, Zhixi [1 ,11 ]
机构
[1] Chinese Acad Sci, State Key Lab Plant Cell & Chromosome Engn, Inst Genet & Dev Biol, Beijing 100101, Peoples R China
[2] Chinese Acad Sci, State Key Lab Plant Genom, Inst Genet & Dev Biol, Beijing 100101, Peoples R China
[3] Heilongjiang Acad Agr Sci, Inst Maize Res, Harbin 150086, Heilongjiang, Peoples R China
[4] Chinese Acad Agr Sci, Inst Anim Sci, Beijing 100193, Peoples R China
[5] Heilongjiang Acad Agr Sci, Mudanjiang Branch, Mudanjiang 157041, Peoples R China
[6] Heilongjiang Acad Agr Sci, Inst Soybean Res, Harbin 150086, Heilongjiang, Peoples R China
[7] Heilongjiang Acad Agr Sci, Heihe Branch, Heihe 164300, Peoples R China
[8] Wuhan Univ Technol, Sch Comp Sci & Technol, Wuhan 430070, Hubei, Peoples R China
[9] Chinese Acad Sci, Key Lab Soybean Mol Design Breeding, Northeast Inst Geog & Agroecol, Harbin 130102, Heilongjiang, Peoples R China
[10] Washington State Univ, Dept Crop & Soil Sci, Pullman, WA 99164 USA
[11] Univ Chinese Acad Sci, Beijing 100039, Peoples R China
来源
GENOME BIOLOGY | 2017年 / 18卷
基金
中国国家自然科学基金; 美国食品与农业研究所;
关键词
Soybean; Agronomic traits; GWAS; Network; GROWTH HABIT; PLANT HEIGHT; ACID CONTENT; RESISTANCE; YIELD; EVOLUTION; MATURITY; IDENTIFICATION; ARCHITECTURE; SELECTION;
D O I
10.1186/s13059-017-1289-9
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
Background: Soybean (Glycine max [L.] Merr.) is one of the most important oil and protein crops. Ever-increasing soybean consumption necessitates the improvement of varieties for more efficient production. However, both correlations among different traits and genetic interactions among genes that affect a single trait pose a challenge to soybean breeding. Results: To understand the genetic networks underlying phenotypic correlations, we collected 809 soybean accessions worldwide and phenotyped them for two years at three locations for 84 agronomic traits. Genome-wide association studies identified 245 significant genetic loci, among which 95 genetically interacted with other loci. We determined that 14 oil synthesis-related genes are responsible for fatty acid accumulation in soybean and function in line with an additive model. Network analyses demonstrated that 51 traits could be linked through the linkage disequilibrium of 115 associated loci and these links reflect phenotypic correlations. We revealed that 23 loci, including the known Dt1, E2, E1, Ln, Dt2, Fan, and Fap loci, as well as 16 undefined associated loci, have pleiotropic effects on different traits. Conclusions: This study provides insights into the genetic correlation among complex traits and will facilitate future soybean functional studies and breeding through molecular design.
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页数:13
相关论文
共 69 条
[11]   Post-green revolution trends in yield potential of temperate maize in the north-central United States [J].
Duvick, DN ;
Cassman, KG .
CROP SCIENCE, 1999, 39 (06) :1622-1630
[12]   STAGE OF DEVELOPMENT DESCRIPTIONS FOR SOYBEANS, GLYCINE-MAX (L) MERRILL [J].
FEHR, WR ;
CAVINESS, CE ;
BURMOOD, DT ;
PENNINGTON, JS .
CROP SCIENCE, 1971, 11 (06) :929-+
[13]  
Felsenstein J., 2005, PHYLIP (phylogeny inference package) version 3.6
[14]   Identification of uncommon plant metabolites based on calculation of elemental compositions using gas chromatography and quadrupole mass spectrometry [J].
Fiehn, O ;
Kopka, J ;
Trethewey, RN ;
Willmitzer, L .
ANALYTICAL CHEMISTRY, 2000, 72 (15) :3573-3580
[15]   Genetic characteristics of soybean resistance to HG type 0 and HG type 1.2.3.5.7 of the cyst nematode analyzed by genome-wide association mapping [J].
Han, Yingpeng ;
Zhao, Xue ;
Cao, Guanglu ;
Wang, Yan ;
Li, Yinghui ;
Liu, Dongyuan ;
Teng, Weili ;
Zhang, Zhiwu ;
Li, Dongmei ;
Qiu, Lijuan ;
Zheng, Hongkun ;
Li, Wenbin .
BMC GENOMICS, 2015, 16
[16]   A novel GmFAD3-2a mutant allele developed through TILLING reduces α-linolenic acid content in soybean seed oil [J].
Hoshino, Tomoki ;
Watanabe, Satoshi ;
Takagi, Yutaka ;
Anai, Toyoaki .
BREEDING SCIENCE, 2014, 64 (04) :371-377
[17]   Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm [J].
Huang, Xuehui ;
Zhao, Yan ;
Wei, Xinghua ;
Li, Canyang ;
Wang, Ahong ;
Zhao, Qiang ;
Li, Wenjun ;
Guo, Yunli ;
Deng, Liuwei ;
Zhu, Chuanrang ;
Fan, Danlin ;
Lu, Yiqi ;
Weng, Qijun ;
Liu, Kunyan ;
Zhou, Taoying ;
Jing, Yufeng ;
Si, Lizhen ;
Dong, Guojun ;
Huang, Tao ;
Lu, Tingting ;
Feng, Qi ;
Qian, Qian ;
Li, Jiayang ;
Han, Bin .
NATURE GENETICS, 2012, 44 (01) :32-U53
[18]   Genome-wide association studies of 14 agronomic traits in rice landraces [J].
Huang, Xuehui ;
Wei, Xinghua ;
Sang, Tao ;
Zhao, Qiang ;
Feng, Qi ;
Zhao, Yan ;
Li, Canyang ;
Zhu, Chuanrang ;
Lu, Tingting ;
Zhang, Zhiwu ;
Li, Meng ;
Fan, Danlin ;
Guo, Yunli ;
Wang, Ahong ;
Wang, Lu ;
Deng, Liuwei ;
Li, Wenjun ;
Lu, Yiqi ;
Weng, Qijun ;
Liu, Kunyan ;
Huang, Tao ;
Zhou, Taoying ;
Jing, Yufeng ;
Li, Wei ;
Lin, Zhang ;
Buckler, Edward S. ;
Qian, Qian ;
Zhang, Qi-Fa ;
Li, Jiayang ;
Han, Bin .
NATURE GENETICS, 2010, 42 (11) :961-U76
[19]   A genome-wide association study of seed protein and oil content in soybean [J].
Hwang, Eun-Young ;
Song, Qijian ;
Jia, Gaofeng ;
Specht, James E. ;
Hyten, David L. ;
Costa, Jose ;
Cregan, Perry B. .
BMC GENOMICS, 2014, 15
[20]   Impacts of genetic bottlenecks on soybean genome diversity [J].
Hyten, David L. ;
Song, Qijian ;
Zhu, Youlin ;
Choi, Ik-Young ;
Nelson, Randall L. ;
Costa, Jose M. ;
Specht, James E. ;
Shoemaker, Randy C. ;
Cregan, Perry B. .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2006, 103 (45) :16666-16671