Identification of QTLs for grain size and characterization of the beneficial alleles of grain size genes in large grain rice variety BL129

doi:10.1016/S2095-3119(15)61043-7

Journal of Integrative Agriculture ›› 2016, Vol. 15 ›› Issue (1): 1-9.DOI: 10.1016/S2095-3119(15)61043-7

• 论文 • 下一篇

Identification of QTLs for grain size and characterization of the beneficial alleles of grain size genes in large grain rice variety BL129

GAO Xuan, ZHU Xu-dong, FANG Na, DUAN Peng-gen, WU Ying-bao, LUO Yue-hua, LI Yun-hai

1、Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources/Agricultural College, Hainan University, Haikou
570228, P.R.China
2、State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,
Hangzhou 310006, P.R.China
3、State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese
Academy of Sciences, Beijing 100101, P.R.China

收稿日期:2015-02-06 出版日期:2016-01-08 发布日期:2016-01-11
通讯作者: LUO Yue-hua, Tel: +86-898-66279259.E-mail: lyhhk@163.com; LI Yun-hai, Tel: +86-10-64807856,E-mail: yhli@genetics.ac.cn
作者简介:* These authors contributed equally to this study.
基金资助:
This work was supported by grants from the National Basic Research Program of China (2013CBA01401), the Strategic Priority Research Program of the Chinese Academy of Sciences (XDA08020108) and the Platform Construction Programs of Key Laboratory and Engineering Technology Research Center, Department of Science and Technology of Hainan Province, China (ZDZX2013023).

Identification of QTLs for grain size and characterization of the beneficial alleles of grain size genes in large grain rice variety BL129

GAO Xuan, ZHU Xu-dong, FANG Na, DUAN Peng-gen, WU Ying-bao, LUO Yue-hua, LI Yun-hai

1、Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources/Agricultural College, Hainan University, Haikou
570228, P.R.China
2、State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,
Hangzhou 310006, P.R.China
3、State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese
Academy of Sciences, Beijing 100101, P.R.China

Received:2015-02-06 Online:2016-01-08 Published:2016-01-11
Contact: LUO Yue-hua, Tel: +86-898-66279259.E-mail: lyhhk@163.com; LI Yun-hai, Tel: +86-10-64807856,E-mail: yhli@genetics.ac.cn
About author:* These authors contributed equally to this study.
Supported by:
This work was supported by grants from the National Basic Research Program of China (2013CBA01401), the Strategic Priority Research Program of the Chinese Academy of Sciences (XDA08020108) and the Platform Construction Programs of Key Laboratory and Engineering Technology Research Center, Department of Science and Technology of Hainan Province, China (ZDZX2013023).

摘要/Abstract

摘要： Grain size is one of the most important agronomic components of grain yield. Grain length, width and thickness are controlled by multiple quantitative trait loci (QTLs). To understand genetic basis of large grain shape and explore the beneficial alleles for grain size improvement, we perform QTL analysis using an F2 population derived from a cross between the japonica variety Beilu 129 (BL129, wide and thick grain) and the elite indica variety Huazhan (HZ, narrow and long grain). A total number of eight major QTLs are detected on three different chromosomes. QTLs for grain width (qGW), grain thickness (qGT), brown grain width (qBGW), and brown grain thickness (qBGT) explained 77.67, 36.24, 89.63, and 39.41% of total phenotypic variation, respectively. The large grain rice variety BL129 possesses the beneficial alleles of GW2 and qSW5/ GW5, which have been known to control grain width and weight, indicating that the accumulation of the beneficial alleles causes large grain shape in BL129. Further results reveal that the rare gw2 allele from BL129 increases grain width, thickness and weight of the elite indica variety Huazhan, which is used as a parental line in hybrid rice breeding. Thus, our findings will help breeders to carry out molecular design breeding on rice grain size and shape.

关键词: rice , quantitative trait , grain size , GW2 , GW5

Abstract: Grain size is one of the most important agronomic components of grain yield. Grain length, width and thickness are controlled by multiple quantitative trait loci (QTLs). To understand genetic basis of large grain shape and explore the beneficial alleles for grain size improvement, we perform QTL analysis using an F2 population derived from a cross between the japonica variety Beilu 129 (BL129, wide and thick grain) and the elite indica variety Huazhan (HZ, narrow and long grain). A total number of eight major QTLs are detected on three different chromosomes. QTLs for grain width (qGW), grain thickness (qGT), brown grain width (qBGW), and brown grain thickness (qBGT) explained 77.67, 36.24, 89.63, and 39.41% of total phenotypic variation, respectively. The large grain rice variety BL129 possesses the beneficial alleles of GW2 and qSW5/ GW5, which have been known to control grain width and weight, indicating that the accumulation of the beneficial alleles causes large grain shape in BL129. Further results reveal that the rare gw2 allele from BL129 increases grain width, thickness and weight of the elite indica variety Huazhan, which is used as a parental line in hybrid rice breeding. Thus, our findings will help breeders to carry out molecular design breeding on rice grain size and shape.

Key words: rice , quantitative trait , grain size , GW2 , GW5

GAO Xuan, ZHU Xu-dong, FANG Na, DUAN Peng-gen, WU Ying-bao, LUO Yue-hua, LI Yun-hai. Identification of QTLs for grain size and characterization of the beneficial alleles of grain size genes in large grain rice variety BL129[J]. Journal of Integrative Agriculture, 2016, 15(1): 1-9.

参考文献

Chakravorty D, Trusov Y, Zhang W, Acharya B R, Sheahan M B,McCurdy D W, Assmann S M, Botella J R. 2011. An atypicalheterotrimeric G-protein gamma-subunit is involved in guardcell K-channel regulation and morphological developmentin Arabidopsis thaliana. The Plant Journal, 67, 840-851

Fan C, Xing Y, Mao H, Lu T, Han B, Xu C, Li X, Zhang Q.2006. GS3, a major QTL for grain length and weight andminor QTL for grain width and thickness in rice, encodes aputative transmembrane protein. Theoretical and AppliedGenetics, 112, 1164-1171

Hu Z, He H, Zhang S, Sun F, Xin X, Wang W, Qian X, YangJ, Luo X. 2012. A kelch motif-containing serine/threonineprotein phosphatase determines the large grain QTL traitin rice. Journal of Integrative Plant Biology, 54, 979-990

Ishimaru K, Hirotsu N, Madoka Y, Murakami N, Hara N, OnoderaH, Kashiwagi T, Ujiie K, Shimizu B, Onishi A, MiyagawaH, Katoh E. 2013. Loss of function of the IAA-glucosehydrolase gene TGW6 enhances rice grain weight andincreases yield. Nature Genetics, 45, 707-711

Li S, Liu Y, Zheng L, Chen L, Li N, Corke F, Lu Y, Fu X, ZhuZ, Bevan M W, Li Y. 2012. The plant-specific G proteingamma subunit AGG3 influences organ size and shapein Arabidopsis thaliana. New Phytologist, 194, 690-703

Li Y, Fan C, Xing Y, Jiang Y, Luo L, Sun L, Shao D, Xu C, LiX, Xiao J, He Y, Zhang Q. 2011. Natural variation in GS5plays an important role in regulating grain size and yield inrice. Nature Genetics, 43, 1266-1269

Li Y, Lee K K, Walsh S, Smith C, Hadingham S, Sorefan K,Cawley G, Bevan M W. 2006. Establishing glucose- andABA-regulated transcription networks in Arabidopsis by microarray analysis and promoter classification usinga Eelevance Vector Machine. Genome Research, 16,414-427

Li Y, Qian Q, Zhou Y, Yan M, Sun L, Zhang M, Fu Z, Wang Y,Han B, Pang X, Chen M, Li J. 2003. BRITTLE CULM1, whichencodes a COBRA-like protein, affects the mechanicalproperties of rice plants. The Plant Cell, 15, 2020-2031

Li Y, Zheng L, Corke F, Smith C, Bevan M W. 2008. Controlof final seed and organ size by the DA1 gene family inArabidopsis thaliana. Genes Development, 22, 1331-1336

Mao H, Sun S, Yao J, Wang C, Yu S, Xu C, Li X, Zhang Q.2010. Linking differential domain functions of the GS3protein to natural variation of grain size in rice. Proceedingsof the National Academy of Sciences of the United Statesof America, 107, 19579-19584

Qi P, Lin Y S, Song X J, Shen J B, Huang W, Shan J X, Zhu M Z,Jiang L, Gao J P, Lin H X. 2012. The novel quantitative traitlocus GL3.1 controls rice grain size and yield by regulatingCyclin-T1;3. Cell Research, 22, 1666-1680

Shomura A, Izawa T, Ebana K, Ebitani T, Kanegae H, KonishiS, Yano M. 2008. Deletion in a gene associated with grainsize increased yields during rice domestication. NatureGenetics, 40, 1023-1028

Song X J, Huang W, Shi M, Zhu M Z, Lin H X. 2007. A QTLfor rice grain width and weight encodes a previouslyunknown RING-type E3 ubiquitin ligase. Nature Genetics,39, 623-630

Song X J, Kuroha T, Ayano M, Furuta T, Nagai K, KomedaN, Segami S, Miura K, Ogawa D, Kamura T, SuzukiT, Higashiyama T, Yamasaki M, Mori H, Inukai Y, WuJ, Kitano H, Sakakibara H, Jacobsen S E, Ashikari M.2015. Rare allele of a previously unidentified histone H4acetyltransferase enhances grain weight, yield, and plantbiomass in rice. Proceedings of the National Academy ofSciences of the United States of America, 112, 76-81

Takano-Kai N, Jiang H, Kubo T, Sweeney M, MatsumotoT, Kanamori H, Padhukasahasram B, Bustamante C,Yoshimura A, Doi K, McCouch S R. 2009. Evolutionaryhistory of GS3, a gene conferring grain size in rice. Genetics,182, 1323-1334

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. Nature Genetics,44, 950-954

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 QTLassociated with rice grain width and weight. Cell Research,18, 1199-1209

Xia T, Li N, Dumenil J, Li J, Kamenski A, Bevan M W, Gao F,Li Y. 2013. The ubiquitin receptor DA1 interacts with theE3 ubiquitin ligase DA2 to regulate seed and organ size inArabidopsis. The Plant Cell, 25, 3347-3359

Xing Z, Tan F, Hua P, Sun L, Xu G, Zhang Q. 2002.Characterization of the main effects, epistatic effects andtheir environmental interactions of QTLs on the geneticbasis of yield traits in rice. Theoretical and Applied Genetics,105, 248-257

Ying J Z, Gao J P, Shan J X, Zhu M Z, Shi M, Lin H X. 2012.Dissecting the genetic basis of extremely large grain shapein rice cultivar ‘JZ1560’. Journal of Genetics and Genomics,39, 325-333

Zhang X, Wang J, Huang J, Lan H, Wang C, Yin C, Wu Y, TangH, Qian Q, Li J, Zhang H. 2012. Rare allele of OsPPKL1associated with grain length causes extra-large grain and asignificant yield increase in rice. Proceedings of the NationalAcademy of Sciences of the United States of America, 109,21534-21539

[1]	RONG Rui-juan, WU Peng-cheng, LAN Jin-ping, WEI Han-fu, WEI Jian, CHEN Hao, SHI Jia-nan, HAO Yu-jie, LIU Li-juan, DOU Shi-juan, LI Li-yun, WU Lin, LIU Si-qi, YIN Chang-cheng, LIU Guo-zhen. Western blot detection of PMI protein in transgenic rice[J]. Journal of Integrative Agriculture, 2016, 15(4): 726-734.
[2]	Elsheikh Y M Ahmed, ZHANG Yan-pei, YU Jian-ping, Rashid M A Rehman, ZHANG Hong-l. Mapping of three QTLs for seed setting and analysis on the candidate gene for qSS-1 in rice (Oryza sativa L.)[J]. Journal of Integrative Agriculture, 2016, 15(4): 735-743.
[3]	CHE Sheng-guo, ZHAO Bing-qiang, LI Yan-ting, YUAN Liang, LIN Zhi-an, HU Shu-wen, SHEN Bing. Nutrient uptake requirements with increasing grain yield for rice in China[J]. Journal of Integrative Agriculture, 2016, 15(4): 907-917.
[4]	LI Gang-hua, CHEN Yi-lu, DING Yan-feng, GENG Chun-miao, LI Quan, LIU Zheng-hui, WANG Shao-hua, TANG She. Charactering protein fraction concentrations as influenced by nitrogen application in low-glutelin rice cultivars[J]. Journal of Integrative Agriculture, 2016, 15(3): 537-544.
[5]	LIU Jing-na, ZHU Bo, YI Li-xia, DAI Hong-cui, XU He-shui, ZHANG Kai, HU Yue-gao, ZENG Zhao-hai. Winter cover crops alter methanotrophs community structure in a double-rice paddy soil[J]. Journal of Integrative Agriculture, 2016, 15(3): 553-565.
[6]	ZENG Yan-hua, ZAHNG Yu-ping, XIANG Jing, WU Hui, CHEN Hui-zhe, ZHANG Yi-kai, ZHU De-feng. Effects of chilling tolerance induced by spermidine pretreatment on antioxidative activity, endogenous hormones and ultrastructure of indica-japonica hybrid rice seedlings[J]. Journal of Integrative Agriculture, 2016, 15(2): 295-308.
[7]	WEI Huan-he, LI Chao, XING Zhi-peng, WANG Wen-ting, DAI Qi-gen, ZHOU Gui-shen, WANG Li, XU Ke, HUO Zhong-yang, GUO Bao-wei, WEI Hai-yan, ZHANG Hong-cheng. Suitable growing zone and yield potential for late-maturity type of Yongyou japonica/indica hybrid rice in the lower reaches of Yangtze River, China[J]. Journal of Integrative Agriculture, 2016, 15(1): 50-62.
[8]	XIAO Gui-qing, ZHANG Hai-wen, LU Xiang-yang, HUANG Rong-feng. Characterization and mapping of a novel light-dependent lesion mimic mutant lmm6 in rice (Oryza sativa L.)[J]. Journal of Integrative Agriculture, 2015, 14(9): 1687-1696.
[9]	SONG Wen-en, CHEN Shi-bao, LIU Ji-fang, CHEN Li, SONG Ning-ning, LI Ning, LIU Bin. Variation of Cd concentration in various rice cultivars and derivation of cadmium toxicity thresholds for paddy soil by species-sensitivity distribution[J]. Journal of Integrative Agriculture, 2015, 14(9): 1845-1854.
[10]	David Norman. Transitioning from paternalism to empowerment of farmers in lowincome countries: Farming components to systems[J]. Journal of Integrative Agriculture, 2015, 14(8): 1490-1499.
[11]	CHEN Zhong-du, ZHANG Hai-lin, S Batsile Dikgwatlhe, XUE Jian-fu, QIU Kang-cheng, TANG Hai-ming, CHEN fu. Soil carbon storage and stratification under different tillage/ residue-management practices in double rice cropping system[J]. Journal of Integrative Agriculture, 2015, 14(8): 1551-1560.
[12]	YAN Xing-ying, QU Cun-min, LI Jia-na, CHEN Li, LIU Lie-zhao. QTL analysis of leaf photosynthesis rate and related physiological traits in Brassica napus[J]. Journal of Integrative Agriculture, 2015, 14(7): 1261-1268.
[13]	JIANG Peng, XIE Xiao-bing, HUANG Min, ZHOU Xue-feng, ZHANG Rui-chun, CHEN Jia-na, WU Dan-dan, XIA Bing, XU Fu-xian, XIONG Hong, ZOU Ying-bin. Comparisons of yield performance and nitrogen response between hybrid and inbred rice under different ecological conditions in southern China[J]. Journal of Integrative Agriculture, 2015, 14(7): 1283-1294.
[14]	DENG Qi-de, YONG Ming-li, LI Dan-yang, LAI Chao-hui, CHEN Hong-ming, FAN Jing, HU Dong-wei. Survey and examination of the potential alternative hosts of Villosiclava virens, the pathogen of rice false smut, in China[J]. Journal of Integrative Agriculture, 2015, 14(7): 1332-1337.
[15]	CHENG Ya-hao, Zhifeng Gao, James Seale Jr.. Changing structure of China’s meat imports[J]. Journal of Integrative Agriculture, 2015, 14(6): 1081-1091.

Identification of QTLs for grain size and characterization of the beneficial alleles of grain size genes in large grain rice variety BL129

Identification of QTLs for grain size and characterization of the beneficial alleles of grain size genes in large grain rice variety BL129

PDF

可视化

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 15

编辑推荐

Metrics