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Acta Agron Sin ›› 2017, Vol. 43 ›› Issue (11): 1650-1657.doi: 10.3724/SP.J.1006.2017.01650


QTL Mapping for Leaf Morphological Traits of Rice Using Chromosome Segment Substitution Lines

ZHOU Yong,TAO Ya-Jun,YAO Rui,LI Chang,TAN Wen-Chen,YI Chuan-Deng,GONG Zhi-Yun, LIANG Guo-Hua*   

  1. Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University / Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou 225009, China
  • Received:2017-02-06 Revised:2017-05-10 Online:2017-11-12 Published:2017-05-06
  • Contact: Jiang guohua, E-mail: ricegb@yzu.edu.cn E-mail:zhouyong@yzu.edu.cn


Leaf morphology is an important component of ideal plant architecture in rice. Therefore, identification of genes associated with leaf morphologic traits is helpful to shape rice ideal architecture and reach the aim of super high-yield. A set of chromosome segment substitution lines (CSSLs) derived from Guanglu’ai 4 (recipient) and Nipponbare (donor) were employed to detect quantitative trait loci (QTL) for the length and width of top three leaves (flag leaf, the second and third leaf from top). We also examined the correlation between the leaf traits and grain yield per plant, indicating that except for flag leaf width, other leaf traits were significantly and positively correlated with grain yield per plant. One-way ANOVA and Dunnett’s test were used to detect QTL related to size of rice top three leaves. Thirteen and seven QTL, for leaf length and width, respectively, were identified. Among them, eight and four QTL had positive effects, respectively. Identification of these QTL provides useful information for improving rice leaf morphologic traits.

Key words: Rice, Leaf morphology, Chromosome segment substitution lines, Quantitative trait loci

[1] Zhang Q F. Strategies for developing green super rice. Proc Natl Acad Sci USA, 2007, 104: 16402–16409
[2] Yuan L P. Hybrid rice breeding for super high yield. Hybrid Rice, 1997, 12: 1–6
[3] 朱德峰. 国际水稻研究所水稻新株型的研究现状与新动向. 作物研究, 1996, (1): 35–36
   Zhu D F. Current status and new trends of research on new plant type of rice in international rice research institute. Crop Res, 1996, (1): 35–36 (in Chinese)
[4] 薛大伟, 钱前. 中国超级稻遗传基础与资源创新. 沈阳农业大学学报, 2007, 38: 667–675
Xue D W, Qian Q. Genetic basis and resources innovation of super rice breeding in China. J Shenyang Agric Univ, 2007, 38: 667–675 (in Chinese with English abstract)
[5] 唐文邦, 陈立云, 肖应辉, 蔡义东, 兰海. 水稻功能叶形态及光合速率与产量构成因素的相关研究. 湖南农业科学, 2004, (2): 29–31
   Tang W B, Chen L Y, Xiao Y H, Cai Y D, Lan H. Relations of photosynthetic ability and functional leaves features to rice yield and yield components. Hunan Agric Sci, 2004, (2): 29–31 (in Chinese with English abstract)
[6] 王永锐. 水稻生理育种. 北京: 科学技术文献出版社, 1995. pp 131–133
   Wang Y R. Physiological Breeding of Rice. Beijing: Scientific and Technical Documentation Press, 1995. pp 131–133 (in Chinese)
[7] Qi J, Qian Q, Bu Q Y, Li S Y, Chen Q, Sun J Q, Liang W X, Zhou Y H, Chu C C, Li X G. Mutation of the rice narrow leaf1 gene, which encodes a novel protein, affects vein patterning and polar auxin transport. Plant Physiol, 2008, 147: 1947–1959
[8] Zhang G H, Xu Q, Zhu X D, Qian Q, Xue H W. SHALLOT-LIKE1 is a KANADI transcription factor that modulates rice leaf rolling by regulating leaf abaxial cell development. Plant Cell, 2009, 21: 719–735
[9] Yoon D B, Kang K H, Kim H J, Ju H G, Kwon S J, Suh J P, Jeong O Y, Ahn S N. Mapping quantitative trait loci for yield components and morphological traits in an advanced backcross population between Oryza grandiglumis and the Oryza sativa japonica cultivar Hwaseongbyeo. Theor Appl Genet, 2006, 112: 1052–1062
[10] Yue B, Xue W Y, Luo L J, Xing Y Z. QTL analysis for flag leaf characteristics and their relationships with yield and yield traits in rice. Acta Genet Sin, 2006, 33: 824–832
[11] Tong H H, Mei H W, Xing Y Z, Cao Y P, Yu X Q, Zhang S Q, Luo L J. QTL analysis for morphological and physiological characteristics of flag leaf at the late developmental stage in rice. Chin J Rice Sci, 2007, 21: 493–499
[12] Wang P, Zhou G L, Yu H H, Yu S B. Fine mapping a major QTL for flag leaf size and yield-related traits in rice. Theor Appl Genet, 2011, 123: 1319–1330
[13] Zhu J Y, Niu Y C, Tao Y J, Wang J, Tai S S, Li J, Yang J, Zhong W G, Zhou Y, Liang G H. Construction of high-throughput genotyped chromosome segment substitution lines in rice (Oryaza sativa L.) and QTL mapping for heading date. Plant Breed, 2015, 134: 156–163
[14] Young D, Tankseley S D. Restriction fragment length polymorphism maps and the concept of graphical genotypes. Theor Appl Genet, 1989, 77: 95–101
[15] McCouch S R, Doerge R W. QTL mapping in rice. Trends Genet, 1995, 11: 482-487
[16] Eshed Y, Zamir D. An introgression line population of Lycopersicon pennellii in the cultivater tomato enables the identification and fine mapping of yield-associated QTL. Genetics, 1995, 141: 1147–1162
[17] Paterson A H, Deverna J W, Lanini B. Fine mapping of quantitative trait loci using selected overlapping recombinant chromosome in an interspecies cross of tomato. Genetics, 1990, 124: 735–742
[18] Li Z K, Pinson S R, Stansel J W, Paterson A H. Genetic dissection of the source-sink relationship affecting fecundity and yield in rice (Oryza sativa L.). Mol Breed, 1998, 4: 419–426
[19] 周丽慧, 赵春芳, 赵凌, 张亚东, 朱镇, 陈涛, 赵庆勇, 姚姝, 于新, 王才林. 利用染色体片段置换系群体检测水稻叶片形态QTL. 中国水稻科学, 2013, 27: 26–34
    Zhou L H, Zhao C F, Zhao L, Zhang Y D, Zhu Z, Chen T, Zhao Q Y, Yao S, Yu X, Wang C L. QTL detection for leaf morphology of rice using chromosome segment substation lines. Chin J Rice Sci, 2013, 27: 26–34 (in Chinese with English abstract)
[20] 徐建军, 赵强, 赵元凤, 朱磊, 徐辰武, 顾铭洪, 韩斌, 梁国华. 利用重测序的水稻染色体片段代换系群体定位剑叶形态QTL. 中国水稻科学, 2011, 25: 483–487
Xu J J, Zhao Q, Zhao Y F, Zhu L, Xu C W, Gu M H, Han B, Liang G H. Mapping of QTLs for flag leaf shape using whole-genome re-sequenced chromosome segment substitution lines in rice. Chin J Rice Sci, 2011, 25: 483–487 (in Chinese with English abstract)
[21] 王智权, 刘喜, 江玲, 杨超, 刘世家, 陈亮明, 翟虎渠, 万建民. 利用染色体片段置换系(CSSLs)群体检测水稻剑叶形态性状QTL. 南京农业大学学报, 2010, 33(6): 1–6
    Wang Z Q, Liu X, Jiang L, Yang C, Liu S J, Chen L M, Zhai H Q, Wan J M. QTL detection for flag leaf morphological traits of rice in a population of chromosome segment substitution lines. J Nanjing Agric Univ, 2010, 33(6): 1–6 (in Chinese with English abstract)
[22] Cai J, Zhang M, Guo LB, Li X M, Bao JS, Ma L Y. QTLs for rice flag leaf traits in doubled haploid populations in different environments. Genet Mol Res, 2015, 14: 6786–6795
[23] Ujiie K, Yamamoto T, Yano M, Ishimaru K. Genetic factors determining varietal differences in characters affecting yield between two rice (Oryza sativa L.) varieties, Koshihikari and IR64. Genet Resour Crop Evol, 2016, 63: 97–123
[24] 李睿, 赵姝丽, 毛艇, 徐正进, 陈温福. 水稻剑叶形态性状QTL分析. 作物杂志, 2010, (3): 26–29
    Li R, Zhao S L, Mao T, Xu Z J, Chen W F. QTL analysis for rice flag leaf. Crops, 2010, (3): 26–29 (in Chinese)
[25] Fujita D, Trijatmiko K R, Tagle A G, Sapasap M V, Koide Y, Sasaki K, Tsakirpaloglou N, Gannaban RB, Nishimura T, Yanagihara S, Fukuta Y, Koshiba T, Slamet-Loedin I H, Ishimaru T, Kobayashi N. NAL1 allele from a rice landrace greatly increases yield in modern indica cultivars. Proc Natl Acad Sci USA, 2013, 110: 20431–20436
[26] Zhang G H, Li S Y, Wang L, Ye W J, Zeng D L, Rao Y C, Peng Y L, Hu J, Yang Y L, Xu J, Rem D Y, Gao Z Y, Zhu L, Dong G J, Hu X M, Yan M X, Guo L B, Li C Y, Qian Q. LSCHL4 from japonica cultivar, which is allelic to NAL1, increases yield of indica super rice 93-11. Mol Plant, 2014, 7: 1350–1364
[27] Cho S H, Yoo S C, Zhang H, Pandeya D, Koh H J, Hwang J Y, Kim G T, Paek N C. The rice narrow leaf 2 and narrow leaf 3 loci encode WUSCHEL-related homeobox 3A (OsWOX3A) and function in leaf, spikelet, tiller and lateral root development. New Phytol, 2013, 198: 1071–1084
[28] Cho S H, Kang K, Lee S H, Lee I J, Paek N C. OsWOX3A is involved in negative feedback regulation of the gibberellic acid biosynthetic pathway in rice (Oryza sativa). J Exp Bot, 2016, 67: 1677–1687
[29] Ding Z Q, Lin Z F, Li Q, Wu M, Xiang C Y, Wang J F. DNL1, encodes cellulose synthase-like D4, is a major QTL for plant height and leaf width in rice (Oryza sativa L.). Biochem Biophys Res Commun, 2015, 457: 133–140
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