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Genetic dissection and validation of candidate genes for flag leaf size in rice (Oryza sativa L.)

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Abstract

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Two major loci with functional candidate genes were identified and validated affecting flag leaf size, which offer desirable genes to improve leaf architecture and photosynthetic capacity in rice.

Abstract

Leaf size is a major determinant of plant architecture and yield potential in crops. However, the genetic and molecular mechanisms regulating leaf size remain largely elusive. In this study, quantitative trait loci (QTLs) for flag leaf length and flag leaf width in rice were detected with high-density single nucleotide polymorphism genotyping of a chromosomal segment substitution line (CSSL) population, in which each line carries one or a few chromosomal segments from the japonica cultivar Nipponbare in a common background of the indica variety Zhenshan 97. In total, 14 QTLs for flag leaf length and nine QTLs for flag leaf width were identified in the CSSL population. Among them, qFW4-2 for flag leaf width was mapped to a 37-kb interval, with the most likely candidate gene being the previously characterized NAL1. Another major QTL for both flag leaf width and length was delimited by substitution mapping to a small region of 13.5 kb that contains a single gene, Ghd7.1. Mutants of Ghd7.1 generated using CRISPR/CAS9 approach showed reduced leaf size. Allelic variation analyses also validated Ghd7.1 as a functional candidate gene for leaf size, photosynthetic capacity and other yield-related traits. These results provide useful genetic information for the improvement of leaf size and yield in rice breeding programs.

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References

  • Adachi S, Tsuru Y, Nito N, Murata K, Yamamoto T, Ebitani T, Ookawa T, Hirasawa T (2011) Identification and characterization of genomic regions on chromosomes 4 and 8 that control the rate of photosynthesis in rice leaves. J Exp Bot 62:1927–1938

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ali ML, Sanchez PL, Yu S, Lorieux M, Eizenga GC (2010) Chromosome segment substitution lines: a powerful tool for the introgression of valuable genes from Oryza, wild species into cultivated rice (O. sativa). Rice 3:218–234

    Article  Google Scholar 

  • Avramova V, Sprangers K, Beemster GT (2015) The maize leaf: another perspective on growth regulation. Trends Plant Sci 20:787–797

    Article  CAS  PubMed  Google Scholar 

  • Chen Q, Mu J, Zhou H, Yu S (2007) Genetic effect of japonica alleles detected in indica candidate introgression lines. Sci Agric Sin 40:2379–2387

    Google Scholar 

  • Chen M, Luo J, Shao G, Wei X, Tang S, Sheng Z, Song J, Hu P (2012) Fine mapping of a major QTL for flag leaf width in rice, qFLW4, which might be caused by alternative splicing of NAL1. Plant Cell Rep 31:863–872

    Article  CAS  PubMed  Google Scholar 

  • Chen Y, Guo L, Ma H, Chen Y, Zhang H, Ying J, Zhuang J (2014) Fine mapping of qHd1, a minor heading date QTL with pleiotropism for yield traits in rice (Oryza sativa L.). Theor Appl Genet 127:2515–2524

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cho SH, Yoo SC, Zhang H, Pandeya D, Koh HJ, Hwang JY, Kim GT, Paek NC (2013) The rice narrow leaf2 and narrow leaf3 loci encode WUSCHEL-related homeobox 3A (OsWOX3A) and function in leaf, spikelet, tiller and lateral root development. New Phytol 198:1071–1084

    Article  CAS  PubMed  Google Scholar 

  • Digel B, Tavakol E, Verderio G, Tondelli A, Xu X, Cattivelli L, Rossini L, von Korff M (2016) Photoperiod-H1 (Ppd-H1) controls leaf size. Plant Physiol 172:405–415

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ding X, Li X, Xiong L (2011) Evaluation of near-isogenic lines for drought resistance QTL and fine mapping of a locus affecting flag leaf width, spikelet number, and root volume in rice. Theor Appl Genet 123:815–826

    Article  PubMed  Google Scholar 

  • Eshed Y, Zamir D (1995) An introgression line population of Lycopersicon pennellii in the cultivated tomato enables the identification and fine mapping of yield-associated QTL. Genetics 141:1147–1162

    CAS  PubMed  PubMed Central  Google Scholar 

  • Fabre D, Adriani DE, Dingkuhn M, Ishimaru T, Punzalan B, Lafarge T, Clément-Vidal A, Luquet D (2016) The qTSN4 effect on flag leaf size, photosynthesis and panicle size, benefits to plant grain production in rice, depending on light availability. Front Plant Sci 7:623

    Article  PubMed  PubMed Central  Google Scholar 

  • Farooq M, Tagle AG, Santos RE, Ebron LA, Fujita D, Kobayashi N (2010) Quantitative trait loci mapping for leaf length and leaf width in rice cv. IR64 derived lines. J Integr Plant Biol 52:578–584

    Article  CAS  PubMed  Google Scholar 

  • Flood PJ, Harbinson J, Aarts MGM (2011) Natural genetic variation in plant photosynthesis. Trends Plant Sci 16:327–335

    Article  CAS  PubMed  Google Scholar 

  • Fujino K, Matsuda Y, Ozawa K, Nishimura T, Koshiba T, Fraaije MW, Sekiguchi H (2008) NARROW LEAF 7 controls leaf shape mediated by auxin in rice. Mol Genet Genomics 279:499–507

    Article  CAS  PubMed  Google Scholar 

  • Fujita D, Trijatmiko KR, Tagle AG, Sapasap MV, Koide Y, Sasaki K, Tsakirpaloglou N, Gannaban RB, Nishimura T, Yanagihara S, Fukuta Y, Koshiba T, Slamet-Loedin IH, Ishimaru T, Kobayashi N (2013) NAL1 allele from a rice landrace greatly increases yield in modern indica cultivars. Proc Natl Acad Sci USA 110:20431–20436

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gao H, Jin M, Zheng X, Chen J, Yuan D, Xin Y, Wang M, Huang D, Zhang Z, Zhou K, Sheng P, Ma J, Ma W, Deng H, Jiang L, Liu S, Wang H, Wu C, Yuan L, Wan J (2014) Days to heading 7, a major quantitative locus determining photoperiod sensitivity and regional adaptation in rice. Proc Natl Acad Sci USA 111:16337–16342

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Giuliani R, Koteyeva N, Voznesenskaya E, Evans MA, Cousins AB, Edwards GE (2013) Coordination of leaf photosynthesis, transpiration, and structural traits in rice and wild relatives (Genus Oryza). Plant Physiol 162:1632–1651

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gu J, Yin X, Struik PC, Stomph TJ, Wang H (2012) Using chromosome introgression lines to map quantitative trait loci for photosynthesis parameters in rice (Oryza sativa L.) leaves under drought and well watered field conditions. J Exp Bot 63:455–469

    Article  CAS  PubMed  Google Scholar 

  • Hiei Y, Ohta S, Komari T, Kumashiro T (1994) Efficient transformation of rice (Oryza sativa L.) mediated by Agrobacterium and sequence analysis of the boundaries of the T-DNA. Plant J 6:271–282

    Article  CAS  PubMed  Google Scholar 

  • Hu J, Zhu L, Zeng D, Gao Z, Guo B, Fang Y, Zhang G, Dong G, Yan M, Liu J, Qian Q (2010) Identification and characterization of NARROW AND ROLLED LEAF 1, a novel gene regulating leaf morphology and plant architecture in rice. Plant Mol Biol 73:283–292

    Article  CAS  PubMed  Google Scholar 

  • Ishiwata A, Ozawa M, Nagasaki H, Kato M, Noda Y, Yamaguchi T, Nosaka M, Shimizu-Sato S, Nagasaki A, Maekawa M, Hirano HY, Sato Y (2013) Two WUSCHEL-related homeobox genes, narrow leaf2 and narrow leaf3, control leaf width in rice. Plant Cell Physiol 54:779–792

    Article  CAS  PubMed  Google Scholar 

  • Jiang D, Fang JJ, Lou LM, Zhao JF, Yuan SJ, Yin L, Sun W, Peng LX, Guo BT, Li XY (2015) Characterization of a null allelic mutant of the rice NAL1 gene reveals its role in regulating cell division. PLoS One 10:e0119169

    Article  Google Scholar 

  • Koo BH, Yoo SC, Park JW, Kwon CT, Lee BD, An G, Zhang Z, Li J, Li Z, Paek NC (2013) Natural variation in OsPRR37 regulates heading date and contributes to rice cultivation at a wide range of latitudes. Mol Plant 6:1877–1888

    Article  CAS  PubMed  Google Scholar 

  • Li ZK, Pinson SR, Stansel JW, Paterson AH (1998) Genetic dissection of the source-sink relationship affecting fecundity and yield in rice (Oryza sativa L.). Mol Breeding 4:419–426

    Article  CAS  Google Scholar 

  • Li M, Sun P, Zhou H, Chen S, Yu S (2011) Identification of quantitative trait loci associated with germination using chromosome segment substitution lines of rice (Oryza sativa L.). Theor Appl Genet 123:411–420

    Article  PubMed  Google Scholar 

  • Lu L, Yan WH, Xue W, Shao D, Xing Y (2012) Evolution and association analysis of Ghd7 in rice. PLoS One 7:e34021

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • McCouch SR (2008) Gene nomenclature system for rice. Rice 1:72–84

    Article  Google Scholar 

  • Mei H, Li Z, Shu QY, Guo L, Wang Y, Yu X, Ying C, Luo L (2005) Gene actions of QTLs affecting several agronomic traits resolved in a recombinant inbred rice population and two backcross populations. Theor Appl Genet 110:649–659

    Article  CAS  PubMed  Google Scholar 

  • Murray MG, Thompson WF (1980) Rapid isolation of high molecular-weight plant DNA. Nucl Acid Res 8:4321

    Article  CAS  Google Scholar 

  • Panaud O, Chen X, Mccouch SR (1996) Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.). Mol Gen Genet 252:597–607

    CAS  PubMed  Google Scholar 

  • Qi J, Qian Q, Bu Q, Li S, Chen Q, Sun J, Liang W, Zhou Y, Chu C, Li X, Ren F, Palme K, Zhao B, Chen J, Chen M, Li C (2008) Mutation of the rice Narrow leaf1 gene, which encodes a novel protein, affects vein patterning and polar auxin transport. Plant Physiol 147:1947–1959

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shen B, Yu W, Du J, Fan Y, Wu J, Zhuang J (2011) Validation and dissection of quantitative trait loci for leaf traits in interval RM4923-RM402 on the short arm of rice chromosome 6. J Genet 90:39–44

    Article  PubMed  Google Scholar 

  • Shibaya T, Hori K, Ogiso-Tanaka E, Yamanouchi U, Shu K, Kitazawa N, Shomura A, Ando T, Ebana K, Wu J, Yamazaki T, Yano M (2016) Hd18, encoding histone acetylase related to Arabidopsis FLOWERING LOCUS D, is involved in the control of flowering time in rice. Plant Cell Physiol 57:1828–1838

    Article  CAS  PubMed  Google Scholar 

  • Sun W, Zhou Q, Yao Y, Qiu X, Xie K, Yu S (2015) Identification of genomic regions and the isoamylase gene for reduced grain chalkiness in rice. PLoS One 10:e0122013

    Article  PubMed  PubMed Central  Google Scholar 

  • Sun Y, Zhang X, Wu C, He Y, Ma Y, Hou H, Guo X, Du W, Zhao Y, Xia L (2016) Engineering herbicide-resistant rice plants through CRISPR/Cas9-mediated homologous recombination of acetolactate synthase. Mol Plant 9:628–631

    Article  CAS  PubMed  Google Scholar 

  • Sun B, Zhan X, Lin Z, Wu W, Yu P, Zhang Y, Sun L, Cao L, Cheng S (2017) Fine mapping and candidate gene analysis of qHD5, a novel major QTL with pleiotropism for yield-related traits in rice (Oryza sativa L.). Theor Appl Genet 130:247–258

    Article  CAS  PubMed  Google Scholar 

  • Taguchi-Shiobara F, Ota T, Ebana K, Ookawa T, Yamasaki M, Tanabata T, Yamanouchi U, Wu J, Ono N, Nonoue Y, Nagata K, Fukuoka S, Hirabayashi H, Yamamoto T, Yano M (2015) Natural variation in the flag leaf morphology of rice due to a mutation of the NARROW LEAF 1 gene in Oryza sativa L. Genetics 201:795–808

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Takai T, Adachi S, Taguchi-Shiobara F, Sanoh-Arai Y, Iwasawa N, Yoshinaga S, Hirose S, Taniguchi Y, Yamanouchi U, Wu JZ, Matsumoto T, Sugimoto K, Kondo K, Ikka T, Ando T, Kono I, Ito S, Shomura A, Ookawa T, Hirasawa T, Yano M, Kondo M, Yamamoto T (2013) A natural variant of NAL1, selected in high-yield rice breeding programs, pleiotropically increases photosynthesis rate. Sci Rep 3:2149

    Article  PubMed  PubMed Central  Google Scholar 

  • Tian F, Li D, Fu Q, Zhu Z, Fu Y, Wang X, Sun C (2006) Construction of introgression lines carrying wild rice (Oryza rufipogon Griff.) segments in cultivated rice (Oryza sativa L.) background and characterization of introgressed segments associated with yield-related traits. Theor Appl Genet 112:570–580

    Article  CAS  PubMed  Google Scholar 

  • Tian F, Bradbury PJ, Brown PJ, Hung H, Sun Q, Flint-Garcia S, Rocheford TR, McMullen MD, Holland JB, Buckler ES (2011) Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat Genet 43:159–162

    Article  CAS  PubMed  Google Scholar 

  • Tsukaya H (2005) Leaf shape: genetic controls and environmental factors. Int J Dev Biol 49:547–555

    Article  PubMed  Google Scholar 

  • Wang P, Zhou G, Yu H, Yu S (2011) Fine mapping a major QTL for flag leaf size and yield-related traits in rice. Theor Appl Genet 123:1319–1330

    Article  CAS  PubMed  Google Scholar 

  • Wang P, Zhou G, Cui K, Li Z, Yu S (2012) Clustered QTL for source leaf size and yield traits in rice (Oryza sativa L.). Mol Breeding 29:99–113

    Article  CAS  Google Scholar 

  • Wang Q, Xie W, Xing H, Yan J, Meng X, Li X, Fu X, Xu J, Lian X, Yu S, Xing Y, Wang G (2015) Genetic architecture of natural variation in rice chlorophyll content revealed by a genome-wide association study. Mol Plant 8:946–957

    Article  CAS  PubMed  Google Scholar 

  • Weng X, Wang L, Wang J, Hu Y, Du H, Xu C, Xing Y, Li X, Xiao J, Zhang Q (2014) Grain number, plant height, and heading date 7 is a central regulator of growth, development, and stress response. Plant Physiol 164:735–747

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xue W, Xing Y, Weng X, Zhao Y, Tang W, Wang L, Zhou H, Yu S, Xu C, Li X, Zhang Q (2008) Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nat Genet 40:761–767

    Article  CAS  PubMed  Google Scholar 

  • Yamamoto T, Kuboki Y, Lin S, Sasaki T, Yano M (1998) Fine mapping of quantitative trait loci Hd-1, Hd-2 and Hd-3, controlling heading date of rice, as single Mendelian factors. Theor Appl Genet 97:37–44

    Article  CAS  Google Scholar 

  • Yan J, Zhu J, He C, Benmoussa M, Wu P (1999) Molecular marker-assisted dissection of genotype × environment interaction for plant type traits in rice (Oryza sativa L.). Crop Sci 39:538–544

    Article  Google Scholar 

  • Yan W, Liu H, Zhou X, Li Q, Zhang J, Lu L, Liu T, Liu H, Zhang C, Zhang Z, Shen G, Yao W, Chen HX, Yu S, Xie W, Xing Y (2013) Natural variation in Ghd7.1 plays an important role in grain yield and adaptation in rice. Cell Res 23:969–971

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yang W, Guo Z, Huang C, Wang K, Jiang N, Feng H, Chen G, Liu Q, Xiong L (2015) Genome-wide association study of rice (Oryza sativa L.) leaf traits with a high-throughput leaf scorer. J Exp Bot 66:5605–5615

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yano M, Katayose Y, Ashikari M, Yamanouchi U, Monna L, Fuse T, Baba T, Yamamoto K, Umehara Y, Nagamura Y, Sasaki T (2000) Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS. Plant Cell 12:2473–2484

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yu H, Xie W, Li J, Zhou F, Zhang Q (2014) A whole-genome SNP array (RICE6K) for genomic breeding in rice. Plant Biotechnol J 12:28–37

    Article  CAS  PubMed  Google Scholar 

  • Yuan L (2008) Research progress on hybrid rice breeding in China. Chin Rice 1:1–130

    Article  Google Scholar 

  • Zhang G, Li S, Wang L, Ye W, Zeng D, Rao Y, Peng Y, Hu J, Yang Y, Xu J, Ren D, Gao Z, Zhu L, Dong G, Hu X, Yan M, Guo L, Li C, Qian Q (2014) LSCHL4 from Japonica cultivar, which is allelic to NAL1, increases yield of Indica super rice 93-11. Mol Plant 7:1350–1364

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang B, Ye W, Ren D, Tian P, Peng Y, Gao Y, Ruan B, Wang L, Zhang G, Guo L, Qian Q, Gao Z (2015) Genetic analysis of flag leaf size and candidate genes determination of a major QTL for flag leaf width in rice. Rice 8:2

    Article  PubMed Central  Google Scholar 

  • Zhao K, Tung CW, Eizenga GC, Wright MH, Ali ML, Price AH, Norton GJ, Islam MR, Reynolds A, Mezey J, McClung AM, Bustamante CD, McCouch SR (2011) Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nat Commun 2:467

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhao H, Yao W, Ouyang Y, Yang W, Wang G, Lian X, Xing Y, Chen L, Xie W (2015) Rice Var Map: a comprehensive database of rice genomic variations. Nucl Acid Res 43:D1018–D1022

    Article  CAS  Google Scholar 

  • Zhou P, Tan Y, He Y, Xu C, Zhang Q (2003) Simultaneous improvement for four quality traits of Zhenshan 97, an elite parent of hybrid rice, by molecular marker-assisted selection. Theor Appl Genet 106:326–331

    Article  CAS  PubMed  Google Scholar 

  • Zhu X, Song Q, Ort DR (2012) Elements of a dynamic systems model of canopy photosynthesis. Curr Opin Plant Biol 15:237–244

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

This work was supported by Grants from the National Natural Science Foundation of China (nos. 31671656; 31261140369), and the National High Technology Research and Development of China (no. 2014AA10A604).

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SY designed and conceived research; XT and RG performed population development and fine mapping; WS and CZ analyzed data; XT conducted transgenic experiments; XT and SY wrote the paper. All authors read and approved the final manuscript.

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Correspondence to Sibin Yu.

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Tang, X., Gong, R., Sun, W. et al. Genetic dissection and validation of candidate genes for flag leaf size in rice (Oryza sativa L.). Theor Appl Genet 131, 801–815 (2018). https://doi.org/10.1007/s00122-017-3036-8

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  • DOI: https://doi.org/10.1007/s00122-017-3036-8

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