不同环境下水稻株高和穗长的QTL分析

doi:10.3864/j.issn.0578-1752.2015.03.01

Abstract

Abstract: 【Objective】Panicle length and plant height are two important factors affecting rice production. Breeding varieties with large panicle and the ideal plant architecture traits are significant for increasing the grain yield of rice. To explore the genetic basis of plant height and panicle length in rice, quantitative genetic analysis was conducted in three different environments. In this study, stable expressed QTLs for plant height and panicle length were identified. The results of this study help us to understand the genetic basis of plant height and panicle length, and provide us with useful information for marker-assisted improvement of the plant type in rice.【Method】The recombinant inbred lines (RILs) derived from the cross between Shennong 265 (japonica) and Lijiangxintuanheigu (japonica) consisting of 126 lines were used to identify QTLs for plant height and panicle length in three different environments (Shenyang, 2011; Hainan, 2012; Shenyang, 2013). Nine QTLs were mapped by QTL IciMapping v3.0 software, using ICIM method for plant height and panicle length. In addition, based on the QTL results and the published literature and rice database data, the major QTLs in 3 environments were analyzed. These results were further confirmed the reliability of the QTL. Finally, in order to narrow the interval of the major QTLs, the QTL-BSA(Bulked Segregant Analysis of Major QTL) was used fine mapping.【Result】Analysis of variance test showed that a significant difference was detected between the parents under three different conditions. A normal distribution of phenotypic values for panicle length and plant height were observed, which indicated that panicle length and plant height were controlled by multiple genes. A total of nine QTLs for the plant height and panicle length were mapped. Five QTLs affecting plant height were detected on the chromosomes 6, 7, 9 and 12, with the LOD values ranged from 2.67 to 19.39, the additive effect from -17.68 to 2.90, and the range of individually explaining phenotypic variation was from 4.25% to 37.35%. A total of four QTLs for the panicle length were mapped on the chromosomes 6, 7 and 9, with the LOD values ranged from 3.57 to 23.18, the additive effect from -3.22 to 1.42, and the range of individually explaining phenotypic variation was from 11.30% to 61.62%. Of these, five were identified in more than one environments, four were significant in two or three environments, indicating that these QTLs are stable across years or environments. Among them, qPL9a and qPH9 were detected on the same region of chromosome 9 in three environments. qPH7 and qPL7b were mapped on the same interval of chromosome 7 in two or three environments, respectively. These QTLs’ alleles from LTH parent increased plant height and panicle length in this population. In addition, the analysis of major QTL-BSA mapping narrowed the qPHL9 (qPH9 and qPL9a)to a 522.46 kb region flanked by simple sequence repeat marker RM1189 and RM24457. qPHL7 (qPH7 and qPL7b) was mapped to a 856.49 kb interval flanked by simple sequence repeat marker RM478 and RM429 on chromosome 7. 【Conclusion】In this study, the recombinant inbred lines (RILs) derived from the cross between Shennong 265 (japonica) and Lijiangxintuanheigu (japonica) were used for mapping QTLs of plant height and panicle length. Five QTLs affecting plant height and four QTLs affecting panicle length were identified. Pleiotropic QTL region on the chromosome 9 could be detected in three environments. A novel plant height and panicle length pleiotropic QTL-qPHL7 was located on chromosome 7 in two environments.

Key words: rice, plant height, panicle length, QTL

YAO Xiao-yun, LI Qing, LIU Jin, JIANG Shu-kun, YANG Sheng-long, WANG Jia-yu, XU Zheng-jin. Dissection of QTLs for Plant Height and Panicle Length Traits in Rice Under Different Environment[J].Scientia Agricultura Sinica, 2015, 48(3): 407-414.

References

[1] Xing Y Z, Zhang Q F. Genetic and molecular bases of rice yield. Annual Review of Plant Biology, 2010, 61: 421-442.

[2] 邱丽娟, 郭勇, 黎裕, 王晓波, 周国安, 刘章雄, 周时荣, 李新海, 马有志, 王建康, 万建民. 中国作物新基因发掘: 现状、挑战与展望. 作物学报, 2011, 37(1): 1-17.

Qiu L J, Guo Y, Li Y, Wang X B, Zhou G A, Liu Z X, Zhou S R, Li X H, Ma Y Z, Wang J K, Wan J M. Novel gene discovery of crops in China: status, challenging, and perspective. Acta Agronomica Sinica, 2011, 37(1): 1-17. (in Chinese)

[3] 姜树坤, 徐正进, 陈温福. 水稻QTL 图位克隆的特征分析. 遗传, 2008, 30(9): 1121-1126.

Jiang S K, Xu Z J, Chen W F. Analysis of features of 15 successful positional cloning of QTL in rice. Hereditas, 2008, 30(9): 1121-1126. (in Chinese)

[4] Ashikari M, Sakakibara H, Lin S Y, Yamamoto T, Takashi T, Nishimura A R, Angeles E, Qian Q, Kitano H, Matsuoka M. Cytokinin oxidase regulates rice grain production. Science, 2005, 309(5735): 741-745.

[5] Li S B, Qian Q, Fu Z M, Zeng D L, Meng X B, Kyozuka J, Maekawa M, Zhu X D, Zhang J, Li J Y, Wang Y H. Short panicle1 encodes a putative PTR family transporter and determines rice panicle size. The Plant Journal, 2009, 58(4): 592-605.

[6] Li M, Tang D, Wang K J, Wu X R, Lu L L, Yu H X, Gu M H, Yan C G, Cheng Z K. Mutations in the F-box gene LARGER PANICLE improve the panicle architecture and enhance the grain yield in rice. Plant Biotechnology Journal, 2011, 9(9): 1002-1013.

[7] 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. Nature Genetics, 2008, 40(6): 761-767.

[8] 姜树坤, 张喜娟, 黄成, 邢亚南, 郑旭, 徐正进, 陈温福. 基于粳稻F₂和F_2:6群体的连锁图谱及剑叶性状QTL比较分析. 中国水稻科学, 2010, 24(4): 372-378.

Jiang S K, Zhang X J, Huang C, Xing Y N, Zheng X, Xu Z J, Chen W F. Comparison of genetic linkage map and QTLs controlling flag leaf traits based on F₂ and F_2:6 populations derived from japonica rice. Chinese Journal of Rice Science, 2010, 24(4): 372-378. (in Chinese)

[9] Wang J K, Li H H, Zhang L Y, Li C H, Lei M. Users’ Manual of QTL IciMapping v3.0 2011.Webpage: http://www.isbreeding.net.

[10] McCouch S R, Cho Y G, Yano M, Paul E, Blinstrub M, Morishima H, Kinoshita T. Report on QTL nomenclature. Rice Genet Newsletter, 1997, 14: 11-13.

[11] Wang G L, Paterson A H. Assessment of DNA pooling strategies for mapping of QTLs. Theoretical and Applied Genetics, 1994, 88: 355-361.

[12] Shashidar H E, Vinod M S, Naveen S, Sharma G V, Krishnamurthy K. Markers linked to grain yield using bulk segregant analysis approach in rice (Oryza sativa L.). Rice Genetics Newsletter, 2005, 22: 69-71.

[13] Venuprasad R, Dalid C O, Del Valle M, Zhao D, Espiritu M, Sta Cruz M T, Amante M, Kumar A, Atlin G N. Identification and characterization of large-effect quantitative trait loci for grain yield under lowland drought stress in rice using bulk-segregant analysis. Theoretical and Applied Genetics, 2009, 120: 177-190.

[14] Salunkhe A S, Poornima R, Prince K S J, Kanagaraj P, Sheeba J A, Amudha K, Suji K K, Senthil A, Babu R C. Fine mapping QTL for drought resistance traits in rice (Oryza sativa L.) using bulk segregant analysis. Molecular Biotechnology, 2011, 49: 90-95.

[15] 沈希宏, 曹立勇, 陈深广, 占小登, 吴伟明, 程式华. 超级杂交稻协优9308重组自交系群体的穗部性状QTL分析. 中国水稻科学, 2009, 23(4): 354-362.

Shen X H, Cao L Y, Chen S H, Zhan X D, Wu W M, Cheng S H. Dissection of QTLs for panicle traits in recombinant inbred lines derived from super hybrid rice, Xieyou9308. Chinese Journal of Rice Science, 2009, 23(4): 354-362. (in Chinese)

[16] 樊叶杨, 庄杰云, 李强, Sala F, 郑康乐. 水稻株高QTL分析及其与产量QTL的关系. 作物学报, 2001, 27(6): 915-922.

Fan Y Y, Zhuang J Y, Li Q, Sala F, Zheng K L. Analysis of quantitative trait loci(QTL) for plant height and the relation between these QTL and QTL for yield traits in rice. Acta Agronomica Sinica, 2001, 27(6): 915-922. (in Chinese)

[17] 何风华, 席章营, 曾瑞珍, Akshay Talu Kdar, 张桂权. 利用单片段代换系鉴定水稻株高及其构成因素的QTL. 中国水稻科学, 2005, 19(5): 387-392.

He F H, Xi Z Y , Zeng R Z, Akshay T K, Zhang G Q. Identification of QTL for plant height and its components by using single segment substitution lines in rice (Oryza sativa). Chinese Journal of Rice Science, 2005, 19(5): 387-392. (in Chinese)

[18] 郭小蛟, 张涛, 蒋开锋, 杨莉, 曹应江, 杨乾华, 游书梅, 万先齐, 罗婧, 李昭祥, 高磊, 郑家奎. 水稻籼粳交F₈、F₂群体穗长QTL比较分析. 中国农业科学, 2013, 46(23): 4849-4857.

Guo X J, Zhang T, Jiang K F, Yang L, Cao Y J, Yang Q H, You S M, Wan X Q, Luo J, Li Z X, Gao L, Zheng J K. Comparison of panicle length QTL based on F₂and F₈ populations derived from rice subspecies cross. Scientia Agricultura Sinica, 2013, 46(23): 4849-4857. (in Chinese)

[19] 韩龙植, 乔永利, 张三元, 曹桂兰, 叶昌荣, 徐福荣, 戴陆园, 芮钟斗, 高熙宗. 不同生长环境下水稻主要农艺性状的QTL分析. 中国农业科学, 2005, 38(6): 1080-1087.

Han L Z, Qiao Y L, Zhang S Y, Cao G L, Ye C R, Xu F R, Dai L Y, Ye J D, Koh H J. QTL analysis of some agronomic traits in rice under different growing environments. Scientia Agricultura Sinica, 2005, 38(6): 1080-1087. (in Chinese)

[20] Liu T, Li L, Zhang Y, Xu C, Li X, Xing Y. Comparison of quantitative trait loci for rice yield, panicle length and spikelet density across three connected populations. Journal of Genetics, 2011, 90(2): 377-382.

[21] 江建华, 张晚霞, 刘晓丽, 刘强明, 卢超, 党小景, 赵其兵, 洪德林. 多环境下粳稻株高动态QTL分析. 中国水稻科学, 2012, 26(1): 55-64.

Jiang J H, Zhang W X, Liu X L, Liu Q M, Lu C, Dang X J, Zhao Q B, Hong D L. QTL dissection of plant height at different growth stages under multi-environments in japonica rice. Chinese Journal of Rice Science, 2012, 26(1): 55-64. (in Chinese)

[22] 祝莉莉, 谭光轩, 任翔, 翁清妹, 何光存. 5种重要农艺性状基因在水稻重组自交系群体中的定位. 武汉大学学报: 理学版, 2003, 49(6): 787-792.

Zhu L L, Tan G X, Ren X, Weng Q M, He G C. Mapping five agronomic character loci of rice based on a recombinant inbred line population. Journal of Wuhan University: Natural Science Edition, 2003, 49(6): 787-792. (in Chinese)

[23] 王军, 朱金燕, 周勇, 杨杰, 王中德, 范方军, 梁国华, 仲维功. 基于CSSSLs的水稻穗长QTL的定位. 华北农学报, 2012, 27(1): 68-73.

Wang J, Zhu J Y, Zhou Y, Yang J, Wang Z D, Fan F J, Liang G H, Zhong W G. Mapping of QTLs for panicle length using CSSSLs in rice (Oryza sativa L.). Acta Agriculturae Boreali-Sinica, 2012, 27(1): 68-73. (in Chinese)

[24] 张振华, 郭梁, 朱玉君, 樊叶杨, 庄杰云. 籼稻不同定位群体抽穗期和株高的QTL比较研究. 中国农业科学, 2011, 44(15): 3069-3077.

Zhang Z H, Guo L, Zhu Y J, Fan Y Y, Zhuang J Y. Mapping of quantitative trait loci for heading date and plant height in two populations of indica rice. Scientia Agricultura Sinica, 2011, 44(15): 3069-3077. (in Chinese)

[25] Hittalmani S, Huang N, Courtois B, Venuprasad R, Venuprasad R, Shashidhar H E, Zhuang J Y, Zheng K L, Liu G F, Wang G C, Sidhu J S, Srivantaneeyakul S, Singh V P, Bagali P G, Prasanna H C, McLaren G, Khush G S. Identification of QTL for growth and grain yield related traits in rice across nine locations of Asia. Theoretical and Applied Genetics, 2003, 107: 679-690.

[26] Ishimaru K, Ono K, Kashiwagi T. Identification of a new gene controlling plant height in rice using the candidate-gene strategy. Planta, 2004, 218: 388-395.

[27] 潘英华, 余建平, 张强, 熊海燕, 朱汝财, 李自超. 水稻穗粒数相关基因的初步定位. 华北农学报, 2013, 28(3): 19-24.

Pan Y H, Yu J P, Zhang Q, Xiong H Y, Zhu R C, Li Z C. Mapping QTL associated with grain number of rice. Acta Agriculturae Boreali-Sinica, 2013, 28(3): 19-24. (in Chinese)

[28] Yan C J, Zhou J H, Yan S, Chen F, Yeboah M, Tang S Z, Liang G H, Gu M H. IdentiWcation and characterization of a major QTL responsible for erect panicle trait in japonica rice (Oryza sativa L.). Theoretical and Applied Genetics, 2007, 115(8): 1093-1100.

[29] Wang J Y, Nakazaki T, Chen S Q, Chen W F, Saito H, Tsukiyama T, Okumoto Y, Xu Z J, Tanisaka T. Identification and characterization of the erect-pose panicle gene EP conferring high grain yield in rice (Oryza sativa L.). Theoretical and Applied Genetics, 2009, 119(1): 85-91.

[30] 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(4): 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 componentsin a RIL population of rice. Chinese Journal of Rice Science, 2013, 27(4): 344-352. (in Chinese)

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