Natural Variations and Genome-Wide Association Studies in Crop Plants

被引：470

作者：

Huang, Xuehui ^{[1
]}

Han, Bin ^{[1
]}

机构：

[1] Chinese Acad Sci, Shanghai Inst Biol Sci, Shanghai Inst Plant Physiol & Ecol, Natl Ctr Gene Res, Shanghai 200233, Peoples R China

来源：

ANNUAL REVIEW OF PLANT BIOLOGY, VOL 65 | 2014年 / 65卷

基金：

中国国家自然科学基金;

关键词：

crop diversity; genotyping; GWAS; domestication; breeding; QUANTITATIVE TRAIT LOCI; MAP ALIGNMENT PROJECT; MIXED-MODEL APPROACH; COMPLEX TRAITS; GENETIC ARCHITECTURE; ALLELIC VARIATION; VARIATION REVEALS; AGRONOMIC TRAITS; DRAFT SEQUENCE; HAPLOTYPE MAP;

D O I：

10.1146/annurev-arplant-050213-035715

中图分类号：

Q94 [植物学];

学科分类号：

071001 ;

摘要：

Natural variants of crops are generated from wild progenitor plants under both natural and human selection. Diverse crops that are able to adapt to various environmental conditions are valuable resources for crop improvements to meet the food demands of the increasing human population. With the completion of reference genome sequences, the advent of high-throughput sequencing technology now enables rapid and accurate resequencing of a large number of crop genomes to detect the genetic basis of phenotypic variations in crops. Comprehensive maps of genome variations facilitate genome-wide association studies of complex traits and functional investigations of evolutionary changes in crops. These advances will greatly accelerate studies on crop designs via genomics-assisted breeding. Here, we first discuss crop genome studies and describe the development of sequencing-based genotyping and genome-wide association studies in crops. We then review sequencing-based crop domestication studies and offer a perspective on genomics-driven crop designs.

引用

页码：531 / 551

页数：21

共 140 条

[91] Green revolution: A mutant gibberellin-synthesis gene in rice - New insight into the rice variant that helped to avert famine over thirty years ago. [J].

Sasaki, A ;

Ashikari, M ;

Ueguchi-Tanaka, M ;

Itoh, H ;

Nishimura, A ;

Swapan, D ;

Ishiyama, K ;

Saito, T ;

Kobayashi, M ;

Khush, GS ;

Kitano, H ;

Matsuoka, M .

NATURE, 2002, 416 (6882) :701-702

[92] The genome sequence and structure of rice chromosome 1 [J].

Sasaki, T ;

Matsumoto, T ;

Yamamoto, K ;

Sakata, K ;

Baba, T ;

Katayose, Y ;

Wu, JZ ;

Niimura, Y ;

Cheng, ZK ;

Nagamura, Y ;

Antonio, BA ;

Kanamori, H ;

Hosokawa, S ;

Masukawa, M ;

Arikawa, K ;

Chiden, Y ;

Hayashi, M ;

Okamoto, M ;

Ando, T ;

Aoki, H ;

Arita, K ;

Hamada, M ;

Harada, C ;

Hijishita, S ;

Honda, M ;

Ichikawa, Y ;

Idonuma, A ;

Iijima, M ;

Ikeno, M ;

Ito, S ;

Ito, T ;

Ito, Y ;

Iwabuchi, A ;

Kamiya, K ;

Karasawa, W ;

Katagiri, S ;

Kikuta, A ;

Kobayashi, N ;

Kono, I ;

Machita, K ;

Maehara, T ;

Mizuno, H ;

Mizubayashi, T ;

Mukai, Y ;

Nagasaki, H ;

Nakashima, M ;

Nakama, Y ;

Nakamichi, Y ;

Nakamura, M .

NATURE, 2002, 420 (6913) :312-316

[93] The tomato genome sequence provides insights into fleshy fruit evolution [J].

Sato, Shusei ;

Tabata, Satoshi ;

Hirakawa, Hideki ;

Asamizu, Erika ;

Shirasawa, Kenta ;

Isobe, Sachiko ;

Kaneko, Takakazu ;

Nakamura, Yasukazu ;

Shibata, Daisuke ;

Aoki, Koh ;

Egholm, Michael ;

Knight, James ;

Bogden, Robert ;

Li, Changbao ;

Shuang, Yang ;

Xu, Xun ;

Pan, Shengkai ;

Cheng, Shifeng ;

Liu, Xin ;

Ren, Yuanyuan ;

Wang, Jun ;

Albiero, Alessandro ;

Dal Pero, Francesca ;

Todesco, Sara ;

Van Eck, Joyce ;

Buels, Robert M. ;

Bombarely, Aureliano ;

Gosselin, Joseph R. ;

Huang, Minyun ;

Leto, Jonathan A. ;

Menda, Naama ;

Strickler, Susan ;

Mao, Linyong ;

Gao, Shan ;

Tecle, Isaak Y. ;

York, Thomas ;

Zheng, Yi ;

Vrebalov, Julia T. ;

Lee, JeMin ;

Zhong, Silin ;

Mueller, Lukas A. ;

Stiekema, Willem J. ;

Ribeca, Paolo ;

Alioto, Tyler ;

Yang, Wencai ;

Huang, Sanwen ;

Du, Yongchen ;

Zhang, Zhonghua ;

Gao, Jianchang ;

Guo, Yanmei .

NATURE, 2012, 485 (7400) :635-641

[94] Patterns of population epigenomic diversity [J].

Schmitz, Robert J. ;

Schultz, Matthew D. ;

Urich, Mark A. ;

Nery, Joseph R. ;

Pelizzola, Mattia ;

Libiger, Ondrej ;

Alix, Andrew ;

McCosh, Richard B. ;

Chen, Huaming ;

Schork, Nicholas J. ;

Ecker, Joseph R. .

NATURE, 2013, 495 (7440) :193-198

[95] Genome sequence of the palaeopolyploid soybean [J].

Schmutz, Jeremy ;

Cannon, Steven B. ;

Schlueter, Jessica ;

Ma, Jianxin ;

Mitros, Therese ;

Nelson, William ;

Hyten, David L. ;

Song, Qijian ;

Thelen, Jay J. ;

Cheng, Jianlin ;

Xu, Dong ;

Hellsten, Uffe ;

May, Gregory D. ;

Yu, Yeisoo ;

Sakurai, Tetsuya ;

Umezawa, Taishi ;

Bhattacharyya, Madan K. ;

Sandhu, Devinder ;

Valliyodan, Babu ;

Lindquist, Erika ;

Peto, Myron ;

Grant, David ;

Shu, Shengqiang ;

Goodstein, David ;

Barry, Kerrie ;

Futrell-Griggs, Montona ;

Abernathy, Brian ;

Du, Jianchang ;

Tian, Zhixi ;

Zhu, Liucun ;

Gill, Navdeep ;

Joshi, Trupti ;

Libault, Marc ;

Sethuraman, Anand ;

Zhang, Xue-Cheng ;

Shinozaki, Kazuo ;

Nguyen, Henry T. ;

Wing, Rod A. ;

Cregan, Perry ;

Specht, James ;

Grimwood, Jane ;

Rokhsar, Dan ;

Stacey, Gary ;

Shoemaker, Randy C. ;

Jackson, Scott A. .

NATURE, 2010, 463 (7278) :178-183

[96] The B73 Maize Genome: Complexity, Diversity, and Dynamics [J].

Schnable, Patrick S. ;

Ware, Doreen ;

Fulton, Robert S. ;

Stein, Joshua C. ;

Wei, Fusheng ;

Pasternak, Shiran ;

Liang, Chengzhi ;

Zhang, Jianwei ;

Fulton, Lucinda ;

Graves, Tina A. ;

Minx, Patrick ;

Reily, Amy Denise ;

Courtney, Laura ;

Kruchowski, Scott S. ;

Tomlinson, Chad ;

Strong, Cindy ;

Delehaunty, Kim ;

Fronick, Catrina ;

Courtney, Bill ;

Rock, Susan M. ;

Belter, Eddie ;

Du, Feiyu ;

Kim, Kyung ;

Abbott, Rachel M. ;

Cotton, Marc ;

Levy, Andy ;

Marchetto, Pamela ;

Ochoa, Kerri ;

Jackson, Stephanie M. ;

Gillam, Barbara ;

Chen, Weizu ;

Yan, Le ;

Higginbotham, Jamey ;

Cardenas, Marco ;

Waligorski, Jason ;

Applebaum, Elizabeth ;

Phelps, Lindsey ;

Falcone, Jason ;

Kanchi, Krishna ;

Thane, Thynn ;

Scimone, Adam ;

Thane, Nay ;

Henke, Jessica ;

Wang, Tom ;

Ruppert, Jessica ;

Shah, Neha ;

Rotter, Kelsi ;

Hodges, Jennifer ;

Ingenthron, Elizabeth ;

Cordes, Matt .

SCIENCE, 2009, 326 (5956) :1112-1115

[97] Fast-forward genetics enabled by new sequencing technologies [J].

Schneeberger, Korbinian ;

Weigel, Detlef .

TRENDS IN PLANT SCIENCE, 2011, 16 (05) :282-288

[98] SHOREmap: simultaneous mapping and mutation identification by deep sequencing [J].

Schneeberger, Korbinian ;

Ossowski, Stephan ;

Lanz, Christa ;

Juul, Trine ;

Petersen, Annabeth Hogh ;

Nielsen, Kare Lehmann ;

Jorgensen, Jan-Elo ;

Weigel, Detlef ;

Andersen, Stig Uggerhoj .

NATURE METHODS, 2009, 6 (08) :550-551

[99] An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations [J].

Segura, Vincent ;

Vilhjalmsson, Bjarni J. ;

Platt, Alexander ;

Korte, Arthur ;

Seren, Uemit ;

Long, Quan ;

Nordborg, Magnus .

NATURE GENETICS, 2012, 44 (07) :825-U144

[100] GWAPP: A Web Application for Genome-Wide Association Mapping in Arabidopsis [J].

Seren, Uemit ;

Vilhjalmsson, Bjarni J. ;

Horton, Matthew W. ;

Meng, Dazhe ;

Forai, Petar ;

Huang, Yu S. ;

Long, Quan ;

Segura, Vincent ;

Nordborg, Magnus .

PLANT CELL, 2012, 24 (12) :4793-4805

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