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Journal of Integrative Agriculture  2016, Vol. 15 Issue (12): 2688-2702    DOI: 10.1016/S2095-3119(16)61427-2
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Genetic dissection of the developmental behavior of plant height in rice under different water supply conditions
WANG Jiang-xu*, SUN Jian*, LI Cheng-xin, LIU Hua-long, WANG Jing-guo, ZHAO Hong-wei, ZOU De-tang
College of Agriculture, Northeast Agricultural University, Harbin 150030, P.R.China
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Abstract      Plant height (PH) is one of the most important agronomic traits of rice, as it directly affects the lodging resistance and the high yield potential. Meanwhile, PH is often constrained by water supply over the entire growth period. In this study, a recombinant inbred line (RIL) derived from Xiaobaijingzi and Kongyu 131 strains grown under drought stress and with normal irrigation over 2 yr (2013 and 2014), respectively (regarded as four environments), was used to dissect the genetic basis of PH by developmental dynamics QTL analysis combined with QTL×environment interactions. QTLs with net effects excluding the accumulated effects were detected to explore the relationship between gene×gene interactions and gene×environment interactions in specific growth period. A total of 26 additive QTLs (A-QTLs) and 37 epistatic QTLs (E-QTLs) associated with PH were detected by unconditional and conditional mapping over seven growth periods. qPH-2-3, qPH-4-3, qPH-6-1, qPH-7-1, and qPH-12-5 could be detected by both unconditional and conditional analyses. qPH-4-3 and qPH-7-5 were detected in four stages (periods) to be sequentially expressed QTLs controlling PH continuous variation. QTLs with additive effects (A-QTLs) were mostly expressed in the period S3|S2 (the time interval from stages 2 to 3), and QTL×environment interactions performed actively in the first three stages (periods) which could be an important developmental period for rice to undergo external morphogenesis during drought stress. Several QTLs showed high adaptability for drought stress and many QTLs were closely related to the environments such as qPH-3-5, qPH-2-2 and qPH-6-1. 72.5% of the QTLs with a and aa effects detected by conditional analysis were under drought stress, and the PVE of QTLs detected by conditional analysis under drought stress were also much higher than that under normal irrigation. We infer that environments would influence the detection results and sequential expression of genes was highly influenced by environments as well. Many QTLs (qPH-1-2, qPH-3-5, qPH-4-1, qPH-2-3) coincident with previously identified drought resistance genes. The result of this study is helpful to elucidating the genetic mechanism and regulatory network underlying the development of PH in rice and providing references to marker assisted selection.
Keywords:  rice        plant height        drought stress        QTL        developmental behavior        environment interactions  
Received: 07 December 2015   Accepted:

This work was supported by the National Key Technologies R&D Program of China during the 12th Five-Year Plan period (2013BAD20B04).

Corresponding Authors:  ZOU De-tang, Tel: +86-451-55190292, E-mail:   
About author:  WANG Jiang-xu, Mobile: +86-13946190937, Tel: +86-451-55190292, E-mail:; SUN Jian, E-mail:;

Cite this article: 

WANG Jiang-xu, SUN Jian, LI Cheng-xin, LIU Hua-long, WANG Jing-guo, ZHAO Hong-wei, ZOU De-tang. 2016. Genetic dissection of the developmental behavior of plant height in rice under different water supply conditions. Journal of Integrative Agriculture, 15(12): 2688-2702.

Babu R C, Nguyen B D, Chamarerk V. 2003. Genetic analysis of drought resistance in rice by molecular markers. Crop Science, 43, 1457–1469.

Cao G, Zhu J, He C, Gao Y, Yan J, Wu P. 2001. Impact of epistasis and QTL×environment interaction on the developmental behavior of plant height in rice (Oryza sativa L.). Theoretical and Applied Genetics, 103, 153–160.

Chen Y, Park B, Han K. 2010. Qualitative reasoning of dynamic gene regulatory interactions from gene expression data.

BMC Genomics, 11, S14.

Doyl J J, Doyle J L. 1990. Isolation of plant DNA from fresh tissue. Focus, 12, 13–15.

Gu J, Yin X, Zhang C. 2014. Linking ecophysiological modelling with quantitative genetics to support marker-assisted crop design for improved yields of rice (Oryza sativa) under drought stress. Annals of Botany, 114, 499–511.

Han Y, Jiang J, Liu H, Ma W, Xu Y, Xu Z. 2005. Overexpression of OsSIN, encoding a novel small protein, causes short internodes in Oryza sativa. Plant Science, 169, 487–495.

Hittalmani S, Huang N, Courtois B, Venuprasad R, Shashidhar H E, Zhuang, J Y, Khush G S. 2003. Identification of QTL for growth-and grain yield-related traits in rice across nine locations of Asia. Theoretical and Applied Genetics, 107, 679–690.

Hong Z, Ueguchi-Tanaka M, Umemura K, Kazuto U, Sakurako U, Shozo F, Suguru T, Shigeo Y, Motoyuki A. 2003. A rice brassinosteroid-deficient mutant, ebisu dwarf (d2), is caused by a loss of function of a new member of cytochrome P450. The Plant Cell, 15, 2900–2910.

Hu H, Dai M, Yao J, Xiao B Z, Li X H, Zhang Q F. 2006. Overexpressing a NAM, ATAF, and CUC (NAC) transcription factor enhances drought resistance and salt tolerance in rice. Proceedings of the National Academy of Sciences of the United States of America, 103, 12987–12992.

Huang N, Courtois B, Khush G S. 1996. Association of quantitative trait loci for plant height with major dwarfing genes in rice. Heredity, 77, 130–137.

Ito Y, Kurata N. 2008. Disruption of KNOX gene suppression in leaf by introducing its cDNA in rice. Plant Science, 174, 357–365.

Jiang C, Pan X, Gu M. 1994. The use of mixture models to detect effects of major genes on quantitative characters in a plant breeding experiment. Genetics, 136, 383–394.

Kato Y, Hirotsu S, Nemoto K, Yamagishi J. 2008. Identification of QTLs controlling rice drought tolerance at seedling stage in hydroponic culture. Euphytica, 160, 423–430.

Kumar R, Venuprasad R, Atlin G N. 2007. Genetic analysis of rainfed lowland rice drought tolerance under naturally-occurring stress in eastern India: Heritability and QTL effects. Field Crops Research, 103, 42–52.

Lanceras J C, Pantuwan G, Jongdee B. 2004. Quantitative trait loci associated with drought tolerance at reproductive stage in rice. Plant Physiology, 135, 384–399.

Lander E S, Green P, Abrahamson J, Barlow A, Daly M J, Lincoln S E, Newberg L. 1987. MAPMAKER, an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics, 1, 174–181.

Lark K, Chase K, Adler F, Mansur L, Orf J. 1995. Interactions between quantitative trait loci in soybean in which trait variation at one locus is conditional upon a specific allele at another. Proceedings of the National Academy of Sciences of the United States of America, 92, 4656–4660.

Lee S, Jia M H, Jia Y, Liu G. 2014. Tagging quantitative trait loci for heading date and plant height in important breeding parents of rice (Oryza sativa). Euphytica, 197, 191–200.

Li S, Wang C, Chang X, Jing R. 2012. Genetic dissection of developmental behavior of grain weight in wheat under diverse temperature and water regimes. Genetica, 140, 393–405.

Li X P, Han Y P, Teng W L, Zang S Z, Yu K F, Vaino P. 2010. Pyramided QTL underlying tolerance to phytophthora root rot in mega-environments from soybean cultivars ‘Conrad’ and ‘Hefeng 25’. Theoretical and Applied Genetics, 121, 651–658.

Li Z K, Yu S B, Lafitte H R, Huang N, Courtois B, Hittalmani S, Khush G S. 2003. QTL×environment interactions in rice. I. Heading date and plant height. Theoretical and Applied Genetics, 108, 141–153.

Machado S, Bynum E D, Archer T L, Lascano R J, Wilson L T, Bordovosky J, Segarra E, Bronson K, Nesmith D M, Xu W. 2002. Spatial and temporal variability of corn growth and grain yield, implications for site-specific farming. Crop Science, 42, 1564–1576.

Madoka A, Takahiro K, Mikiko K. 2002. Gibberellin biosynthesis and signal transduction is essential for internode elongation in deepwater rice. Plant Cell & Environment, 37, 2313–2324.

McCouch S R, Cho Y G, Yano M. 1997. Report on QTL nomenclature. Rice Genet Newsletter, 14, 11–13.

Mei H W, Luo L J, Ying C S. 2003. Gene actions of QTLs affecting several agronomic traits resolved in a recombinant inbred rice population and two testcross populations. Theoretical and Applied Genetics, 107, 89–101.

Monna L, Kitazawa N, Yoshino R, Suzuki J, Masuda H, Maehara Y, Tanji M, Sato M, Nasu S, Minobe Y. 2002. Positional cloning of rice semidwarfing gene, sd-1: Rice “green revolution gene” encodes a mutant enzyme involved in gibberellin synthesis. DNA Research, 9, 11–17.

Njiti V, Meksem K, Iqbal M J, Johnson J E, Kassem M A, Zobrist K F, Kilo V Y, Lightfoot D A. 2002. Common loci underlie field resistance to soybean sudden death syndrome in Forrest, Pyramid, Essex, and Douglas. Theoretical and Applied Genetics, 104, 294–300.

Pantuwan G, Fukai S, Cooper M, Rajatasereekul S, O’Toole J C. 2002. Yield response of rice (Oryza sativa L.) genotypes to different types of drought under rainfed lowlands: Part 1. Grain yield and yield components. Field Crops Research, 73, 153–168.

Peng S, Khush G S, Cassman K G. 1994. Evolution of the new plant ideotype for increased yield potential breaking the yield barrier. In: Proceedings of a Workshop on Rice Yield Potential in Favourable Environments. International Rice Research Institute, Philippines. pp. 5–20.

Prince S J, Beena R, Gomez S M. 2015. Mapping consistent rice (Oryza sativa L.) yield QTLs under drought stress in target rainfed environments. Rice, 8, 1–13.

Saikumar S, Gouda P K, Saiharini A, Varma C M K, Vineesha C, Padmavathi G. 2014. Major QTL for enhancing rice grain yield under lowland reproductive drought stress identified using an O. sativa/O. glaberrima introgression line. Field Crops Research, 163, 119–131.

Saikumar S, Saiharini A, Patil V. 2015. Contrasting rice backcross inbred lines (BILs) for grain yield and heading under lowland reproductive stage moisture stress. European Journal of Agronomy, 70, 85–97.

Spielmeyer W, Ellis M H, Chandler P M. 2002. Semidwarf (sd-1),

“green revolution” rice, contains a defective gibberellin 20-oxidase gene. Proceedings of the National Academy of Sciences of the United States of America, 99, 9043–9048.

Sandhu N, Singh A, Dixit S, Cruz M T S, Maturan P C, Jain R K, Kumar A. 2014. Identification and mapping of stable QTL with main and epistasis effect on rice grain yield under upland drought stress. BMC Genetics, 15, 63.

Sellamuthu R, Liu G F, Ranganathan C B, Serraj R. 2011. Genetic analysis and validation of quantitative trait loci associated with reproductive-growth traits and grain yield under drought stress in a doubled haploid line population of rice (Oryza sativa L.). Field Crops Research, 124, 46–58.

Septiningsih E M, Prasetiyono J, Lubis E. 2003. Identification of quantitative trait loci for yield and yield components in an advanced backcross population derived from the Oryza sativa variety IR64 and the wild relative O. rufipogon. Theoretical and Applied Genetics, 107, 1419–1432.

Setter T L, Laureles E V, Mazaredo A M. 1997. Lodging reduces yield of rice by self-shading and reductions in canopy photosynthesis. Field Crops Research, 49, 95–106.

Shinozaki K, Yamaguchi-Shinozaki K. 2007. Gene networks involved under drought stress response and tolerance. Journal of Experimental Botany, 58, 221–227.

Tanabe S, Ashikari M, Fujioka S. 2005. A novel cytochrome P450 is implicated in brassinosteroid biosynthesis via the characterization of a rice dwarf mutant, dwarf11, with reduced seed length. The Plant Cell, 17, 776–790.

Trigiano R N, Caetano-Anolles G. 1998. Laboratory exercises on DNA amplification fingerprinting for evaluating the molecular diversity of horticultural species. HortTechnology, 8, 413–423.

Trijatmiko K R, Prasetiyono J, Thomson M J, Cruz C M V, Moeljopawiro S, Pereira A. 2014. Meta-analysis of quantitative trait loci for grain yield and component traits under reproductive-stage drought stress in an upland rice population. Molecular Breeding, 34, 283–295.

Venuprasad R, Dalid C O, Del Valle M, Zhao D, Espiritu M, Cruz M S, Atlin G N. 2009. 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, 120, 177–190.

Vikram P, Swamy B P M, Dixit S. 2011. qDTY1.1, a major QTL for rice grain yield under reproductive-stage drought stress with a consistent effect in multiple elite genetic backgrounds. BMC Genetics, 12, 89.

Wang D L, Zhu J, Li Z K, Paterson A H. 1999. Mapping QTLs with epistatic effects and QTL×environment interactions by mixed linear model approaches. Theoretical and Applied Genetics, 99, 1255–1264.

Wei X, Xu J, Guo H. 2010. DTH8 suppresses flowering in rice, influencing plant height and yield potential simultaneously. Plant Physiology, 153, 1747–1758.

Wu W, Li W, Tang D, Lu H, Worland A J. 1999. Time related mapping of quantitative trait loci underlying tiller number in rice. Genetics, 151, 297–303.

Wu X, Wang Z, Chang X, Jing R. 2010. Genetic dissection of the developmental behaviours of plant height in wheat under diverse water regimes. Journal of Experimental Botany, 61, 2923–2937.

Xing W, Zhao H W, Zou D T. 2014. Detection of main-effect and epistatic QTL for yield-related traits in rice under drought stress and normal conditions. Canadian Journal of Plant Pathology, 94, 633–641.

Xu J L, Lafitte H R, Gao Y M. 2005. QTLs for drought escape and tolerance identified in a set of random introgression lines of rice. Theoretical and Applied Genetics, 111, 1642–1650.

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. 2008. Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nature Genetics, 40, 761–767.

Yan J, Zhu J, He C, Benmoussa M, Wu P. 1998a. Molecular dissection of developmental behavior of plant height in rice (Oryza sativa L.). Genetics, 150, 1257–1265.

Yan J, Zhu J, He C, Benmoussa M, Wu P. 1998b. Quantitative trait loci analysis for the developmental behavior of tiller number in rice (Oryza sativa L.). Theoretical and Applied Genetics, 97, 267–274.

Yang G, Xing Y, Li S, Ding J, Yue B, Deng K, Li Y, Zhu Y. 2006. Molecular dissection of developmental behavior of tiller number and plant height and their relationship in rice (Oryza sativa L.). Hereditas, 143, 236–245.

Yang J, Hu C, Hu H, Yu R, Xia Z, Ye X, Zhu J. 2008. QTLNetwork: Mapping and visualizing genetic architecture of complex traits in experimental populations. Bioinformatics, 24, 721–723.

Yasuno N, Yasui Y, Takamure I, Kato K. 2007. Genetic interaction between 2 tillering genes, reduced culm number 1 (rcn1) and tillering dwarf gene d3, in rice. Journal of Heredity, 98, 169–172.

Zhang K, Tian J, Zhao L. 2008. Mapping QTLs with epistatic effects and QTL×environment interactions for plant height using a doubled haploid population in cultivated wheat. Journal of Genetics and Genomics, 35, 119–127.

Zhao J, Wang T, Wang M, Liu Y, Yuan S, Gao Y, Wan J. 2014. DWARF3 participates in an SCF complex and associates with DWARF14 to suppress rice shoot branching. Plant and Cell Physiology, 55, 1096–1109.

Zhu G, Ye N, Zhang J. 2009. Glucose-induced delay of seed germination in rice is mediated by the suppression of ABA catabolism rather than an enhancement of ABA biosynthesis. Plant and Cell Physiology, 50, 644–651.

Zhu J. 1995. Analysis of conditional genetic effects and variance components in developmental genetics. Genetics, 141, 1633–1639.

Zhu X, Liang W, Cui X, Chen M, Yin C, Luo Z, Zhu J, Lucas W J,

    Wang Z, Zhang D. 2015. Brassinosteroids promote development of rice pollen grains and seeds by triggering expression of Carbon Starved Anther, a MYB domain protein. The Plant Journal, 82, 570–581.

Zhuang J Y, Lin H X, Lu J. 1997. Analysis of QTL×environment interaction for yield components and plant height in rice. Theoretical and Applied Genetics, 95, 799–808.
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