植物学报 ›› 2016, Vol. 51 ›› Issue (4): 411-415.doi: 10.11983/CBB16121

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全基因组关联分析实现水稻粒型自然变异的分子解析

厉新民, 林鸿宣*()   

  1. 中国科学院上海生命科学研究院植物生理生态研究所, 植物分子遗传国家重点实验室/分子植物卓越中心, 上海 200032
  • 收稿日期:2016-06-01 接受日期:2016-06-13 出版日期:2016-07-01 发布日期:2016-08-05
  • 通讯作者: 林鸿宣 E-mail:hxlin@sibs.ac.cn
  • 作者简介:

    # 共同第一作者

Genome-wide Association Study Opens a Window to Molecular Dissection of Rice Grain Size

Xinmin Li, Hongxuan Lin*   

  1. National Key Laboratory of Plant Molecular Genetics, Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
  • Received:2016-06-01 Accepted:2016-06-13 Online:2016-07-01 Published:2016-08-05
  • Contact: Lin Hongxuan E-mail:hxlin@sibs.ac.cn
  • About author:

    # Co-first authors

摘要:

全基因组关联分析(GWAS)近年来被广泛应用于解析生物自然变异的遗传基础。但限于其遗传定位精度, 在水稻(Oryza sativa)遗传学研究中, 该方法尚无法取代传统的图位克隆法在克隆复杂性状调控基因中的作用。近期, 中国科学家在应用GWAS等大数据来克隆控制水稻粒长和粒重等复杂性状的QTL方面取得了新突破。

Abstract:

High-throughput sequencing technologies bring us the genomics age, consequently facilitates genome-wide association studies (GWAS) of complex traits in crops. But GWAS has not yet been successful in detecting the genetic basis of phenotypic variations in rice due to limited mapping resolution. Recently, chinese scientists have cloned a QTL for rice grain length and weight using GWAS combining with functional investigations and propelled the molecular dissection of rice QTL from genetics to genomics. Their study provided us not only a model for investigating rice complex traits and evolutionary changes using “omics” resources but also a valuable gene for rice breeding.

1 Che R, Tong H, Shi B, Liu Y, Fang S, Liu D, Xiao Y, Hu B, Liu L, Wang H, Zhao M, Chu C (2015). Control of grain size and rice yield by GL2-mediated brassinosteroid responses.Nat Plants 2, 15195.
2 Duan P, Ni S, Wang J, Zhang B, Xu R, Wang Y, Chen H, Zhu X, Li Y (2015). Regulation of OsGRF4 by OsmiR396 controls grain size and yield in rice.Nat Plants 2, 15203.
3 Hu J, Wang Y, Fang Y, Zeng L, Xu J, Yu H, Shi Z, Pan J, Zhang D, Kang S, Zhu L, Dong G, Guo L, Zeng D, Zhang G, Xie L, Xiong G, Li J, Qian Q (2015). A rare allele of GS2 enhances grain size and grain yield in rice.Mol Plant 8, 1455-1465.
4 Huang X, Han B (2014). Natural variations and genome-wide association studies in crop plants.Annu Rev Plant Biol 65, 531-551.
5 Huang X, Kurata N, Wei X, Wang ZX, Wang A, Zhao Q, Zhao Y, Liu K, Lu H, Li W, Guo Y, Lu Y, Zhou C, Fan D, Weng Q, Zhu C, Huang T, Zhang L, Wang Y, Feng L, Furuumi H, Kubo T, Miyabayashi T, Yuan X, Xu Q, Dong G, Zhan Q, Li C, Fujiyama A, Toyoda A, Lu T, Feng Q, Qian Q, Li J, Han B (2012a). A map of rice genome variation reveals the origin of cultivated rice.Nature 490, 497-501.
6 Huang X, Qian Q, Liu Z, Sun H, He S, Luo D, Xia G, Chu C, Li J, Fu X (2009). Natural variation at the DEP1 locus enhances grain yield in rice.Nat Genet 41, 494-497.
7 Huang X, Wei X, Sang T, Zhao Q, Feng Q, Zhao Y, Li C, Zhu C, Lu T, Zhang Z, Li M, Fan D, Guo Y, Wang A, Wang L, Deng L, Li W, Lu Y, Weng Q, Liu K, Huang T, Zhou T, Jing Y, Li W, Lin Z, Buckler ES, Qian Q, Zhang QF, Li J, Han B (2010). Genome-wide association studies of 14 agronomic traits in rice landraces.Nat Genet 42, 961-967.
8 Huang X, Zhao Y, Wei X, Li C, Wang A, Zhao Q, Li W, Guo Y, Deng L, Zhu C, Fan D, Lu Y, Weng Q, Liu K, Zhou T, Jing Y, Si L, Dong G, Huang T, Lu T, Feng Q, Qian Q, Li J, Han B (2012b). Genome-wide association study of flower- ing time and grain yield traits in a worldwide collection of rice germplasm.Nat Genet 44, 32-39.
9 Ishimaru K, Hirotsu N, Madoka Y, Murakami N, Hara N, Onodera H, Kashiwagi T, Ujiie K, Shimizu B, Onishi A, Miyagawa H, Katoh E (2013). Loss of function of the IAA-glucose hydrolase gene TGW6 enhances rice grain weight and increases yield.Nat Genet 45, 707-711.
10 Jiao Y, Wang Y, Xue D, Wang J, Yan M, Liu G, Dong G, Zeng D, Lu Z, Zhu X, Qian Q, Li J (2010). Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice.Nat Genet 42, 541-544.
11 Li Y, Fan C, Xing Y, Jiang Y, Luo L, Sun L, Shao D, Xu C, Li X, Xiao J, He Y, Zhang Q (2011). Natural variation in GS5 plays an important role in regulating grain size and yield in rice.Nat Genet 43, 1266-1269.
12 Mao H, Sun S, Yao J, Wang C, Yu S, Xu C, Li X, Zhang Q (2010). Linking differential domain functions of the GS3 protein to natural variation of grain size in rice. Proc Natl Acad Sci USA 107, 19579-19584.
13 Miura K, Ikeda M, Matsubara A, Song XJ, Ito M, Asano K, Matsuoka M, Kitano H, Ashikari M (2010). OsSPL14 promotes panicle branching and higher grain productivity in rice. Nat Genet 42, 545-549.
14 Qi P, Lin YS, Song XJ, Shen JB, Huang W, Shan JX, Zhu MZ, Jiang L, Gao JP, Lin HX (2012). The novel quan- titative trait locus GL3.1 controls rice grain size and yield by regulating Cyclin-T1;3.Cell Res 22, 1666-1680.
15 Shomura A, Izawa T, Ebana K, Ebitani T, Kanegae H, Konishi S, Yano M (2008). Deletion in a gene associated with grain size increased yields during rice domestication.Nat Genet 40, 1023-1028.
16 Si LZ, Chen JY, Huang XH, Gong H, Luo JH, Hou QQ, Zhou TY, Lu TT, Zhu JJ, Shangguan YY, Chen EW, Gong CX, Zhao Q, Jing YF, Zhao Y, Li Y, Cui LL, Fan DL, Lu YQ, Weng QJ, Wang YC, Zhan QL, Liu KY, Wei XH, An K, An G, Han B (2016). OsSPL13 controls grain size in cultivated rice.Nat Genet 48, 447-456.
17 Song XJ, Huang W, Shi M, Zhu MZ, Lin HX (2007). A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase.Nat Genet 39, 623-630.
18 Song XJ, Kuroha T, Ayano M, Furuta T, Nagai K, Kom- eda N, Segami S, Miura K, Ogawa D, Kamura T, Su- zuki T, Higashiyama T, Yamasaki M, Mori H, Inukai Y, Wu J, Kitano H, Sakakibara H, Jacobsen SE, Ashikari M (2015). Rare allele of a previously unidentified histone H4 acetyltransferase enhances grain weight, yield, and plant biomass in rice.Proc Natl Acad Sci USA 112, 76-81.
19 Wang H, Wang H (2015). The miR156/SPL module, a regu- latory hub and versatile toolbox, gears up crops for enhan- ced agronomic traits.Mol Plant 8, 677-688.
20 Wang S, Wu K, Yuan Q, Liu X, Liu Z, Lin X, Zeng R, Zhu H, Dong G, Qian Q, Zhang G, Fu X (2012). Control of grain size, shape and quality by OsSPL16 in rice.Nat Genet 44, 950-954.
21 Wang S, Li S, Liu Q, Wu K, Zhang J, Wang S, Wang Y, Chen X, Zhang Y, Gao C, Wang F, Huang H, Fu X (2015a). The OsSPL16-GW7 regulatory module determines grain shape and simultaneously improves rice yield and grain quality.Nat Genet 47, 949-954.
22 Wang Y, Xiong G, Hu J, Jiang L, Yu H, Xu J, Fang Y, Zeng L, Xu E, Xu J, Ye W, Meng X, Liu R, Chen H, Jing Y, Wang Y, Zhu X, Li J, Qian Q (2015b). Copy number variation at the GL7 locus contributes to grain size diversity in rice.Nat Genet 47, 944-948.
23 Weng J, Gu S, Wan X, Gao H, Guo T, Su N, Lei C, Zhang X, Cheng Z, Guo X, Wang J, Jiang L, Zhai H, Wan J (2008). Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight.Cell Res 18, 1199-1209.
24 Zhang X, Wang J, Huang J, Lan H, Wang C, Yin C, Wu Y, Tang H, Qian Q, Li J, Zhang H (2012). Rare allele of OsPPKL1 associated with grain length causes extra-large grain and a significant yield increase in rice.Proc Natl Acad Sci USA 109, 21534-21539.
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[2] 刘德立. 植物热激蛋白及其功能[J]. 植物学报, 1996, 13(01): 14 -19 .
[3] 丁承强 马丹 王绍华 丁艳锋. 水稻蛋白质组双向电泳优化流程及方法[J]. 植物学报, 2011, 46(1): 67 -73 .
[4] 宋克敏. 植物的磷营养:磷酸盐运转系统及其调节[J]. 植物学报, 1999, 16(03): 251 -256 .
[5] 杨洪强 接玉玲 李军. 植物根源逆境信使及其产生和传输[J]. 植物学报, 2002, 19(01): 56 -62 .
[6] 李辉, 张光灿, 谢会成, 许景伟, 李传荣, 孙居文. 苯酚废水对垂柳叶片光合生理参数的影响[J]. 植物学报, 2016, 51(1): 31 -39 .
[7] 刘林德 王仲礼 田国伟 申家恒. 刺五加胚与胚乳发育的研究[J]. 植物学报, 1996, 13(专辑): 97 -98 .
[8] 刘晓梅, 方建, 张婧, 林吴颖, 樊廷录, 冯虎元. 长期施肥对麦田土壤微生物垂直分布的影响[J]. 植物生态学报, 2009, 33(2): 397 -404 .
[9] 王仁卿. 山东半岛和辽东半岛植被的比较研究[J]. 植物生态学报, 1984, 8(1): 41 -51 .
[10] 宋永昌. 第二届欧洲生态学学术讨论会和第十届德国生态学年会[J]. 植物生态学报, 1981, 5(2): 151 -166 .