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Fine mapping of a major QTL for flag leaf width in rice, qFLW4, which might be caused by alternative splicing of NAL1

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Abstract

Leaf width is an important agricultural trait in rice. QTL mapping in a recombinant inbred line population derived from the cross between the javanica cultivar D50 (narrow-leaved) and the indica cultivar HB277 (wide-leaved) identified five QTLs controlling flag leaf width. Fine mapping of the major QTL qFLW4 narrowed its location to a 74.8 kb interval between the SSR loci RM17483 and RM17486, a region which also contains the gene NAL1 (Narrow leaf 1). There was no difference in the level of NAL1 expression between cvs. D50 and HB277, but an analysis of the NAL1 transcripts showed that while most (if not all) of those produced in cv. D50 were full-length, two-thirds of those in HB277 were non-functional due to either loss or gain of sequence. The inference was that NAL1 is probably synonymous with qFLW4, and that the functional difference between the two alleles was due to alternative splicing. The analysis of expression of other known genes involved in the determination of leaf width provided no evidence of their having any clear functional association with qFLW4/NAL1.

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References

  • Ashikari M, Wu J, Yano M, Sasaki T, Yoshimura A (1999) Rice gibberellin-insensitive dwarf mutant gene Dwarf 1 encodes the alpha-subunit of GTP-binding protein. Proc Natl Acad Sci USA 96:10284–10289

    Article  PubMed  CAS  Google Scholar 

  • Barbazuk WB, Fu Y, McGinnis KM (2008) Genome-wide analyses of alternative splicing in plants: opportunities and challenges. Genome Res 18:1381–1392

    Article  PubMed  CAS  Google Scholar 

  • Buell CR, Campbell MA, Haas BJ, Hamilton JP, Mount SM (2006) Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis. BMC Genomics 7

  • Candela H, Johnston R, Gerhold A, Foster T, Hake S (2008) The milkweed pod1 gene encodes a KANADI protein that is required for abaxial/adaxial patterning in maize leaves. Plant Cell 20:2073–2087

    Article  PubMed  CAS  Google Scholar 

  • Chen S, Yang Y, Shi W, Ji Q, He F, Zhang Z, Cheng Z, Liu X, Xu M (2008) Badh2, encoding betaine aldehyde dehydrogenase, inhibits the biosynthesis of 2-acetyl-1-pyrroline, a major component in rice fragrance. Plant Cell 20:1850–1861

    Article  PubMed  CAS  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, Izhaki A, Baum SF, Floyd SK, Bowman JL (2004) Asymmetric leaf development and blade expansion in Arabidopsis are mediated by KANADI and YABBY activities. Development 131:2997–3006

    Article  PubMed  CAS  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  PubMed  CAS  Google Scholar 

  • Foyer CH (1987) The basis for source–sink interaction in leaves. Plant Physiol Biochem 25:649–657

    CAS  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  PubMed  CAS  Google Scholar 

  • Hirota O, Oka M, Takeda T (1990) Sink activity estimation by sink size and dry matter increase during the ripening stage of barley (Hordeum vulgare) and rice (Oryza sativa). Ann Bot 65:349–354

    Google Scholar 

  • Hu J, Zhu L, Zeng D, Gao Z, Guo L, 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  PubMed  CAS  Google Scholar 

  • Isshiki M, Nakajima M, Satoh H, Shimamoto K (2000) dull: rice mutants with tissue-specific effects on the splicing of the waxy pre-mRNA. Plant J 23:451–460

    Article  PubMed  CAS  Google Scholar 

  • Koo SC, Choi MS, Chun HJ, Park HC, Kang CH, Shim SI, Chung JI, Cheong YH, Lee SY, Yun DJ, Chung WS, Cho MJ, Kim MC (2009) Identification and characterization of alternative promoters of the rice MAP kinase gene OsBWMK1. Mol Cells 27:467–473

    Article  PubMed  CAS  Google Scholar 

  • Krecek P, Skupa P, Libus J, Naramoto S, Tejos R, Friml J, Zazimalova E (2009) The PIN-FORMED (PIN) protein family of auxin transporters. Genome Biol 10:249

    Article  PubMed  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Li M, Xiong G, Li R, Cui J, Tang D, Zhang B, Pauly M, Cheng Z, Zhou Y (2009) Rice cellulose synthase-like D4 is essential for normal cell-wall biosynthesis and plant growth. Plant J 60:1055–1069

    Article  PubMed  CAS  Google Scholar 

  • Matsukura S, Mizoi J, Yoshida T, Todaka D, Ito Y, Maruyama K, Shinozaki K, Yamaguchi-Shinozaki K (2010) Comprehensive analysis of rice DREB2-type genes that encode transcription factors involved in the expression of abiotic stress-responsive genes. Mol Genet Genomics 283:185–196

    Article  PubMed  CAS  Google Scholar 

  • Mei HW, Luo LJ, Ying CS, Wang YP, Yu XQ, Guo LB, Paterson AH, Li ZK (2003) Gene actions of QTLs affecting several agronomic traits resolved in a recombinant inbred rice population and two testcross populations. Theor Appl Genet 107:89–101

    PubMed  CAS  Google Scholar 

  • Mei HW, Li ZK, Shu QY, Guo LB, Wang YP, Yu XQ, Ying CS, Luo LJ (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  PubMed  CAS  Google Scholar 

  • Ner-Gaon H, Leviatan N, Rubin E, Fluhr R (2007) Comparative cross-species alternative splicing in plants. Plant Physiol 144:1632–1641

    Article  PubMed  CAS  Google Scholar 

  • Niu X, Zheng W, Lu BR, Ren G, Huang W, Wang S, Liu J, Tang Z, Luo D, Wang Y, Liu Y (2007) An unusual posttranscriptional processing in two betaine aldehyde dehydrogenase loci of cereal crops directed by short, direct repeats in response to stress conditions. Plant Physiol 143:1929–1942

    Article  PubMed  CAS  Google Scholar 

  • Oki K, Inaba N, Kitano H, Takahashi S, Fujisawa Y, Kato H, Iwasaki Y (2009) Study of novel d1 alleles, defective mutants of the alpha subunit of heterotrimeric G-protein in rice. Genes Genet Syst 84:35–42

    Article  PubMed  CAS  Google Scholar 

  • Overvoorde P, Fukaki H, Beeckman T (2010) Auxin control of root development. Cold Spring Harb Perspect Biol 2:a001537

    Article  PubMed  Google Scholar 

  • Prathepha P (2007) Identification of variant transcripts of waxy gene in non-glutinous rice (O. sativa L.) with different amylose content. Pak J Biol Sci 10:2500–2504

    Article  PubMed  CAS  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  PubMed  CAS  Google Scholar 

  • Qian Q, He P, Zheng X, Chen Y, Zhu L (2000) Genetic analysis of morphological index and its related taxonomic traits for classification of indica/japonica rice. Sci China C Life Sci 43:113–119

    Article  PubMed  CAS  Google Scholar 

  • Reddy ASN (2007) Alternative splicing of pre-messenger RNAs in plants in the genomic era. Annu Rev Plant Biol 58:267–294

    Article  PubMed  CAS  Google Scholar 

  • Sakamoto T, Morinaka Y, Ohnishi T, Sunohara H, Fujioka S, Ueguchi-Tanaka M, Mizutani M, Sakata K, Takatsuto S, Yoshida S, Tanaka H, Kitano H, Matsuoka M (2006) Erect leaves caused by brassinosteroid deficiency increase biomass production and grain yield in rice. Nat Biotechnol 24:105–109

    Article  PubMed  CAS  Google Scholar 

  • Sasaki A, Itoh H, Gomi K, Ueguchi-Tanaka M, Ishiyama K, Kobayashi M, Jeong DH, An G, Kitano H, Ashikari M, Matsuoka M (2003) Accumulation of phosphorylated repressor for gibberellin signaling in an F-box mutant. Science 299:1896–1898

    Article  PubMed  CAS  Google Scholar 

  • Sazuka T, Kamiya N, Nishimura T, Ohmae K, Sato Y, Imamura K, Nagato Y, Koshiba T, Nagamura Y, Ashikari M, Kitano H, Matsuoka M (2009) A rice tryptophan deficient dwarf mutant, tdd1, contains a reduced level of indole acetic acid and develops abnormal flowers and organless embryos. Plant J 60:227–241

    Article  PubMed  CAS  Google Scholar 

  • Shi XR, Li Q, He ZH (2005) Stress-induced Rim2/Hipa pseudogene of rice exhibits alternative tailing and splicing during transcription. Zhi Wu Sheng Li Yu Fen Zi Sheng Wu Xue Xue Bao 31:607–614

    Google Scholar 

  • To KY, Suen DF, Chen SC (1999) Molecular characterization of ribulose-1,5-bisphosphate carboxylase/oxygenase activase in rice leaves. Planta 209:66–76

    Article  PubMed  CAS  Google Scholar 

  • Ueguchi-Tanaka M, Fujisawa Y, Kobayashi M, Ashikari M, Iwasaki Y, Kitano H, Matsuoka M (2000) Rice dwarf mutant d1, which is defective in the alpha subunit of the heterotrimeric G protein, affects gibberellin signal transduction. Proc Natl Acad Sci USA 97:11638–11643

    Article  PubMed  CAS  Google Scholar 

  • Ueguchi-Tanaka M, Hirano K, Hasegawa Y, Kitano H, Matsuoka M (2008) Release of the repressive activity of rice DELLA protein SLR1 by gibberellin does not require SLR1 degradation in the gid2 mutant. Plant Cell 20:2437–2446

    Article  PubMed  CAS  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

    Google Scholar 

  • Werneke JM, Chatfield JM, Ogren WL (1989) Alternative mRNA splicing generates the two ribulosebisphosphate carboxylase/oxygenase activase polypeptides in spinach and Arabidopsis. Plant Cell 1:815–825

    Article  PubMed  CAS  Google Scholar 

  • Woo YM, Park HJ, Su’udi M, Yang JI, Park JJ, Back K, Park YM, An G (2007) Constitutively wilted 1, a member of the rice YUCCA gene family, is required for maintaining water homeostasis and an appropriate root to shoot ratio. Plant Mol Biol 65:125–136

    Article  PubMed  CAS  Google Scholar 

  • Wu C, Fu Y, Hu G, Si H, Cheng S, Liu W (2010) Isolation and characterization of a rice mutant with narrow and rolled leaves. Planta 232:313–324

    Article  PubMed  CAS  Google Scholar 

  • Xu M, Zhu L, Shou H, Wu P (2005) A PIN1 family gene, OsPIN1, involved in auxin-dependent adventitious root emergence and tillering in rice. Plant Cell Physiol 46:1674–1681

    Article  PubMed  CAS  Google Scholar 

  • Yan S, Yan CJ, Zeng XH, Yang YC, Fang YW, Tian CY, Sun YW, Cheng ZK, Gu MH (2008) ROLLED LEAF 9, encoding a GARP protein, regulates the leaf abaxial cell fate in rice. Plant Mol Biol 68:239–250

    Article  PubMed  CAS  Google Scholar 

  • Yuan L (1997) Hybrid rice breeding for super high yield. Hybrid Rice 12:1–6

    Google Scholar 

  • Yuan L (2008) Research progress on hybrid rice breeding in china. Chin Rice 1:1–13

    Article  Google Scholar 

  • Yue B, Xue WY, Luo LJ, Xing YZ (2006) QTL analysis for flag leaf characteristics and their relationships with yield and yield traits in rice. Yi Chuan Xue Bao 33:824–832

    PubMed  CAS  Google Scholar 

  • Zhang GH, Xu Q, Zhu XD, Qian Q, Xue HW (2009) SHALLOT-LIKE1 is a KANADI transcription factor that modulates rice leaf rolling by regulating leaf abaxial cell development. Plant Cell 21:719–735

    Article  PubMed  Google Scholar 

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Acknowledgments

This work was supported by grants of ‘863’ programs of China (grant no. 2009AA101101), Natural Science Foundation of China (grant no. 31161140348), Innovation Foundation of JiangXi Academy of Agricultural Science (grant no. 2009CDS003), and Science and Technology Project of Zhejiang province (grant no. 2010C32061).

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Authors and Affiliations

  1. State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China

    Mingliang Chen, Ju Luo, Gaoneng Shao, Xiangjin Wei, Shaoqing Tang, Zhonghua Sheng, Jian Song & Peisong Hu

  2. JiangXi Rice Research Institute, JiangXi Academy of Agricultural Science, Nanchang, 330200, China

    Mingliang Chen

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  1. Mingliang Chen
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Correspondence to Peisong Hu.

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Communicated by H. Judelson.

M. Chen and J. Luo contributed equally.

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Chen, M., Luo, J., Shao, G. et al. 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 (2012). https://doi.org/10.1007/s00299-011-1207-7

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  • DOI: https://doi.org/10.1007/s00299-011-1207-7

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