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Acta Agron Sin ›› 2017, Vol. 43 ›› Issue (10): 1434-1447.doi: 10.3724/SP.J.1006.2017.01434

• CROP GENETICS & BREEDING · GERMPLASM RESOURCES · MOLECULAR GENETICS • Previous Articles     Next Articles

Identification of QTLs Associated with High Yield of Super Rice Variety Zhongjiazao 17

HU Da-Wei1,**, SHENG Zhong-Hua1,**, CHEN Wei1,2, LI Qian-Long1,2, WEI Xiang-Jin1, SHAO Gao-Neng1, XIE Li-Hong1, JIAO Gui-Ai1, WANG Jian-Long2, HU Pei-Song1,2, TANG Shao-Qing1,*   

  1. 1 Key Laboratory of Rice Biology and Genetic Breeding of Ministry of Agriculture, State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; 2 Agricultural College of Hunan Agricultural University, Changsha 410128, China
  • Received:2017-01-18 Revised:2017-05-10 Online:2017-10-12 Published:2017-05-22
  • Contact: Kang shaoqing, E-mail: sqtang@126.com
  • Supported by:

    This research was financially supported by Zhejiang Science and Technology Projects (2015C32045), China Natural Science Foundation (31501285), the Central Level, Non-profit, Scientific Research Institute Basic R and D Operations Special Fund (2014RG002-1), the National Key Research and Development Program of China (2016YFD0101801), and the National Major Project for Developing New GM Crops (2016ZX08001006).

Abstract:

Rice yield has obvious effect on national food security. The further excavation of high yield related genes is of great significance. In this research, a doubled haploid population (DH population) of Zhongjiazao 17 (YK17) × D50 was constructed by using the anther culture technique. The yield related traits including effective panicles per plant, grain number per panicle, seed setting rate and 1000-grain weight in three different planting environments (Lingshui Hainan planting environment, high yield field in Hangzhou planting environment, low yield field in Hangzhou planting environment) were examined. Further, genetic linkage map of the DH population was constructed. A total of 74 QTLs for yield related traits were detected by QTL mapping, these QTLs were distributed on all the 12 chromosomes of rice with the contribution rate ranging from 3.7% to 43.2%. Among these QTLs, qPH1-1and qFLL12 were detected repeatedly in three different planting environments, and the contribution rate of them was 8.9%, 24.2%, 43.2% and 16.6%, 17.9%, 18.9%, respectively. In addition, qPH3, qFLL10-2, qFLW11-1, qPL11, qGNP11, qSSR3, and qTGW5-1 were detected repeatedly in two different planting environments with the contribution rate ranging from 7.4% to 42.2%. The analysis of QTL × environment interaction showed that qPH1-1, qFLW2, qEPP1,and qTGW5-1 had significant additive × environment interaction effects. GW5 sequencing, located in qTGW5-1, indicated that GW5 alleles of high yield lines and low yield lines were inherited from the parents YK17 and D50, respectively, which was consistent with that the additive effect of qTGW5-1 derived from YK17. This research provides theoretical basis and technical support for further excavation of rice yield related genes and breeding super high yield varieties by using molecular polymerization breeding.

Key words: Yield related traits, QTL mapping, DH population, Zhongjiazao17, Rice

[1] 许凌, 张亚东, 朱镇, 赵凌, 赵庆勇, 张巧凤, 王才林. 不同年份水稻产量性状的QTL分析. 中国水稻科学, 2008, 22: 370–376
Xu L, Zhang Y D, Zhu Z, Zhao L, Zhao Q Y, Zhang Q F, Wang C L. Dissection of QTLs in two years for yield component traits in rice (Oryza sativa). Chin J Rice Sci, 2008, 22: 370–376 (in Chinese with English abstract)
[2] 占小登, 于萍, 林泽川, 陈代波, 沈希宏, 张迎信, 付君林, 程式华, 曹立勇. 利用大粒籼/小粒粳重组自交系定位水稻生育期及产量相关性状QTL. 中国水稻科学, 2014, 28: 570–580
Zhan X D, Yu P, Lin Z C, Chen D B, Shen X H, Zhang Y X, Fu J L, Cheng S H, Cao L Y. QTL mapping of heading date and yield-related traits in rice using a recombination inbred lines (RILs) population derived from BG1/XLJ. Chin J Rice Sci, 2014, 28: 570–580 (in Chinese with English abstract)
[3] 王兰, 李智, 郑杏梅, 蔡英钦, 罗敏, 聂益勇. 普通野生稻矮化突变体的株高与分蘖基因的QTL定位及主效基因的遗传分析. 华北农学报, 2014, 29: 5–9
Wang L, Li Z, Zheng X M, Cai Y Q, Luo M, Nie Y Y. Mapping quantitative trait loci associated with height and tillers of Oryza rufipogon Griff. dwarf mutant and genetic analysis of major quantitative locus. Acta Agric Boreali-Sin, 2014, 29: 5–9 (in Chinese with English abstract)
[4] 陈明亮, 熊焕金, 胡兰香, 罗世友, 刘志辉, 肖叶青. 水稻产量相关数量性状基因研究进展. 江西农业学报, 2014, 26: 16–20
Chen M L, Xiong H J, Hu L X, Luo S Y, Liu Z H, Xiao Y Q. Research advances in genes of yield-related quantitative traits in rice. Acta Agric Jiangxi, 2014, 26: 16–20 (in Chinese with English abstract)
[5] Li Y B, Fan C C, Xing Y Z, Jiang Y H, Luo L J, Sun L, Shao D, Xu C J, Li X H, Xiao J H, He Y Q, Zhang Q F. Natural variation in GS5 plays an important role in regulating grain size and yield in rice. Nat Genet, 2011, 43: 1266–1269
[6] Yan S, Zou G H, Li S J, Wang H, Liu H Q, Zhai G W, Guo P, Song H M, Yan C J, Tao Y Z. Seed size is determined by the combinations of the genes controlling different seed characteristics in rice. Theor Appl Genet, 2011, 123: 1173–1181
[7] Wang S K, Wu K, Yuan Q B, Liu X Y, Liu Z B, Lin X Y, Zeng R Z, Zhu H T, Dong G J, Qian Q, Zhang G Q, Fu X D. Control of grain size, shape and quality by OsSPL16 in rice. Nat Genet, 2012, 44: 950–954
[8] Xue W Y, Xing Y Z, Weng X Y, Zhao Y, Tang W J, Wang L, Zhou H J, Yu S B, Xu C G, Li X H, Zhang Q F. Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nat Genet, 2008, 40: 761–767
[9] Wei X J, Xu J F, Guo H G, Jiang L, Chen S H, Yu C Y, Zhou Z L, Hu P S, Zhai H Q, Wan J M. DTH8 suppresses flowering in rice, influencing plant height and yield potential simultaneously. Plant Physiol, 2010, 153: 1747–1758
[10] Tan L B, Li X R, Liu F X, Sun X Y, Li C G, Zhu Z F, Fu Y C, Cai H W, Wang X K, Xie D X, Sun C Q. Control of a key transition from prostrate to erect growth in rice domestication. Nat Genet, 2008, 40:1360–1364
[11] Jin J, Huang W, Gao J P, Yang J, Shi M, Zhu M Z, Luo D, Lin H X. Genetic control of rice plant architecture under domestication. Nat Genet, 2008, 40: 1365–1369
[12] Jiao Y Q, Wang Y H, Xue D W, Wang J, Yan M X, Liu G F, Dong G J, Zeng D L, Lu Z F, Zhu X D, Qian Q, Li J Y. Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice. Nat Genet, 2010, 42: 541–544
[13] Miura K, Ikeda M, Matsubara A, Song X J, Ito M, Asano K, Matsuoka M, Kitano H, Ashikari M. OsSPL14 promotes panicle branching and higher grain productivity in rice. Nat Genet, 2010, 42: 545–549
[14] Liu W, Zhang D C, Tang M F, Li D Y, Zhu Y X, Zhu L H, Chen C Y. THIS1 is a putative lipase that regulates tillering, plant height, and spiklelet fertility in rice. J Exp Bot, 2013, 64: 4389–4402
[15] Ashikari M, Sakakibara H, Lin S Y, Yamamoto T, Takashi T, Nishimura A, Angeles E R, Qian Q, Kitano H, Matsuoka M. Cytokinin oxidase regulates rice grain production. Science, 2005, 309: 741–745
[16] Huang X Z, Qian Q, Liu Z B, Sun H Y, He S Y, Luo D, Xia G M, Chu C C, Li J Y, Fu X D. Natural variation at the DEP1 locus enhances grain yield in rice. Nat Genet, 2009, 41: 494–497
[17] Zhou Y, Zhu J Y, Li Z Y, Yi C D, Liu J, Zhang H G, Tang S Z, Gu M H, Liang G H. Deletion in a quantitative trait gene qPE9-1 associated with panicle erectness improves plant architecture during rice domestication. Genetics, 2009, 183: 315–324
[18] Fan C C, Xing Y Z, Mao H L, Lu T T, Han B, Xu C G, Li X H, Zhang Q F. GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor Appl Genet, 2006, 112: 1164–1171
[19] Weng J F, Gu S H, Wan X Y, Gao H, Guo T, Su N, Lei C L, Zhang X, Cheng Z J, Guo X P, Wang J L, Jiang L, Zhai H Q, Wan J M. Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight. Cell Res, 2008, 18: 1199–1209
[20] Ishimaru K, Hirotsu N, Madoka Y, Murakami N, Hara N, Onodera H, Kashiwagi T, Ujiie K, Shimizu B, Onishi A, Miyagawa H, Katoh E. Loss of function of the IAA-glucose hydrolase gene TGW6 enhances rice grain weight and increases yield. Nat Genet, 2013, 45: 707–711
[21] Si L Z, Chen J Y, Huang X H, Gong H, Luo J H, Hou Q Q, Zhou T Y, Lu T T, Zhu J J, Shangguan Y Y, Chen E W, Gong C X, Zhao Q, Jing Y F, Zhao Y, Li Y, Cui L L, Fan D L, Lu Y Q, Weng Q J, Wang Y C, Zhan Q L, Liu K Y, Wei X H, An K, An G, Han B. OsSPL13 controls grain size in cultivated rice. Nat Genet, 2016, 48: 447–456
[22] 穆平, 黄超, 李君霞, 刘立峰, 刘弋菊, 李自超. 低磷胁迫下水稻产量性状变化及其QTL定位. 作物学报, 2008, 34: 1137–1142
Mu P, Huang C, Li J X, Liu L F, Liu U J, Li Z C. Yield trait variation and QTL mapping in a DH population of rice under phosphorus deficiency. Acta Agron Sin, 2008, 34: 1137–1142 (in Chinese with English abstract)
[23] 杨小林, 戚华雄, 殷得所, 曾凡松, 张舒, 喻大昭. 水稻稻瘟病抗性QTL的定位分析. 植物病理学报, 2012, 42: 600–607
Yang X L, Qi H X, Yin D S, Zeng F S, Zhang S, Yu D Z. Mapping QTLs for rice blast resistance in DH line derived from Muwanggu and E’ wan8. Acta Phytopathol Sin, 2012, 42: 600–607 (in Chinese with English abstract)
[24] 王小虎, 方云霞, 祝阳舟, 潘斌清, 余海平, 张栋, 曾大力, 胡江, 钟卫国, 俞良, 端木银熙, 梁国华, 钱前. 水稻水培抗倒伏相关性状的QTL分析. 核农学报, 2016, 30: 850–858
Wang X H, Fang Y X, Zhu Y Z, Pan B Q, Yu H P, Zhang D, Zeng D L, Hu J, Zhong W G, Yu L, Duan-Mu Y X, Liang G H, Qian Q. Identification of QTLs associated with hydroponics resistance to lodging in rice. J Nuclear Agric Sci, 2016, 30: 850–858 (in Chinese)
[25] 罗炬, 邵高能, 魏祥进, 陈明亮, 唐绍清, 焦桂爱, 谢黎虹, 胡培松. 一个控制水稻株高QTL qPH3的遗传分析. 中国水稻科学, 2012, 26: 417–422
Luo J, Shao G N, Wei X J, Chen M L, Tang S Q, Jiao G A, Xie L H, Hu P S. Genetic analysis of a OTL qPH3 for plant height in rice. Chin J Rice Sci, 2012, 26: 417–422 (in Chinese with English abstract)
[26] van Ooijen J W. Join Map 4, Software for the Calculation of Genetic Linkage Maps in Experimental Populations. Wageningen, Netherlands, 2006
[27] Wang S, Basten C J, Zeng Z B. Windows QTL Cartographer 2.5 Department of Statistics. Raleigh, USA: North Carolina State University, 2006
[28] McCouch S R. Gene nomenclature system for rice. Rice, 2008, 1: 72–84
[29] 赵建国, 蒋开锋, 杨莉, 杨乾华, 万先齐, 曹应江, 游书梅, 罗婧, 张涛, 郑家奎. 水稻产量相关性状QTL定位. 中国水稻科学, 2013, 27: 344–352
Zhao J G, Jiang K F, Yang L, Yang Q H, Wan X Q, Cao Y J, You S M, Luo J, Zhang T, Zheng J K. QTL mapping for yield related components in a RIL population of rice. Chin J Rice Sci, 2013, 27: 344–352 (in Chinese with English abstract)
[30] Liu G F, Yang J, Zhu J. Mapping QTL for biomass yield and its components in rice (Oryza sativa). Acta Genet Sin, 2006, 33: 607–616
[31] 郭龙彪, 罗利军, 邢永忠, 徐才国, 梅捍卫, 王一平, 钟代彬, 钱前, 应存山, 石春海. 水稻重要农艺性状的两年QTL分析. 中国水稻科学, 2003, 17: 211–218
Guo L B, Luo L J, Xing Y Z, Xu C G, Mei H W, Wang Y P, Zhong D B, Qian Q, Ying C S, Shi C H. Dissection of QTLs in two years for important agronomic traits in rice (Oryza sativa L.). Chin J Rice Sci, 2003, 17: 211–218 (in Chinese with English abstract)
[32] 邓家耀. 水稻光合与产量相关性状的QTL分析. 福建农林大学硕士学位论文, 福建福州, 2007
Deng J Y. QTL Mapping Associated with the Traits of Photosynthesis and Yield Components in Rice (Oryza sativa L.). MS Thesis of Fujian Agriculture and Forestry University, Fuzhou, China, 2007 (in Chinese with English abstract)
[33] 冯跃, 翟荣荣, 林泽川, 曹立勇, 魏兴华, 程式华. 不同供氮水平下水稻产量性状的QTL分析. 中国水稻科学, 2013, 27: 577–584
Feng Y, Zhai R R, Lin Z C, Cao L Y, Wei X H, Cheng S H. QTL Analysis for yield traits in rice under two nitrogen levels. Chin J Rice Sci, 2013, 27: 577–584 (in Chinese with English abstract)
[34] 苏相文. 水稻重组自交系产量及其相关性状的QTL分析. 四川农业大学硕士学位论文, 四川成都, 2010
Su X W. QTL Analysis for Rice Yield and Its Related Traits by Recombinant Inbred Line. MS Thesis of Sichuan Agricultural University, Chengdu, China, 2010 (in Chinese with English abstract)
[35] 文飘. 东乡野生稻产量性状的QTL分析. 江西师范大学硕士学位论文, 江西南昌, 2012
Wen P. QTL Analysis for Controlling Yield Traits in Dongxiang Wild Rice (Oryza rufipogon Griff.). MS Thesis of Jiangxi Normal University, Nanchang, China, 2012 (in Chinese with English abstract)
[36] 杨益善, 邓启云, 陈立云, 邓化冰, 庄文, 熊跃东. 野生稻高产QTL导入晚稻恢复系的增产效果. 分子植物育种, 2006, 4: 59-64
Yang Y S, Deng Q Y, Chen L Y, Deng H B, Zhuang W, Xiong Y D. Yield-increasing effect of yield-enhancing QTL from Oryza Rufipogon after being transferred into late-season rice restorer line. Mol Plant Breed, 2006, 4: 59-64 (in Chinese with English abstract)
[37] 邓化冰, 邓启云, 陈立云, 杨益善, 熊跃东, 孔凡娜, 王斌, 袁隆平. 马来西亚普通野生稻增产QTL的分子标记辅助选择及其育种效果. 中国水稻科学, 2007, 21: 605-611
Deng H B, Deng Q Y, Chen L Y, Yang Y S, Xiong Y D, Kong F N, Wang B, Yuan L P. Marker-assisted selection for yield-enhancing QTLs in the Progeny of “9311×Oryza rufipogon” and its effects in rice breeding. Chin J Rice Sci, 2007, 21: 605-611 (in Chinese with English abstract)

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