Abstract
Molecular understanding of morphological agronomic traits is very important to improve grain yield and quality. According to the literature information summarized in Overview of Functionally Characterized Genes in Rice online database, 430 genes related to these traits have been functionally characterized in rice, while the functions of other genes remain to be elucidated. Gene indexed mutants are available for at least half of the genes identified in the rice genome, and are very useful resources to study gene function. To suggest candidate genes for functional studies associated with morphological agronomic traits, we identified genes with tissue/organ-preferred expression patterns through meta-analysis of microarray data, and identified 781 genes for roots, 1,084 for leaves, 1,029 for calluses, 927 for anthers, 241 for embryos, and 343 for endosperms. Additionally, 4,243 genes expressed in all tissue types were allocated to a ubiquitously-expressed gene group (‘housekeeping’ genes). The estimated tissue/organ-preferred and housekeeping genes accounted for 40% of the characterized genes associated with morphological agronomic traits, indicating that identification of tissue/organ-preferred genes is an effective way to provide putative gene function. In this study, we reported the information of gene-indexed mutants for 84% of the identified candidate genes. Our candidate genes and relating indexed mutant resources can potentially be used to improve morphological agronomic traits in rice.
Similar content being viewed by others
References
Aya K, Ueguchi-Tanaka M, Kondo M, Hamada K, Yano K, Nishimura M, Matsuoka M (2009) Gibberellin modulates anther development in rice via the transcriptional regulation of GAMYB. Plant Cell 21:1453–1472
Banerjee J, Maiti MK (2010) Functional role of rice germin-like protein1 in regulation of plant height and disease resistance. Biochem Biophys Res Commun 394:178–183
Cao P, Jung KH, Choi D, Hwang D, Ronald PC (2012) The Rice Oligonucleotide Array Database: an atlas of rice gene expression. Rice 5:17
Chandran AKN, Jung KH (2014) Resources for systems biology in rice. J Plant Biol 57:80–82
Chandran AKN, Lee GS, Yoo YH, Yoon UH, Ahn BO, Yun DW, Kim JH, Choi HK, An G, Kim TH, Jung KH (2016) Functional classification of rice flanking sequence tagged genes using MapMan terms and global understanding on metabolic and regulatory pathways affected by dxr mutant having defects in light response. Rice 9:17
Cui R, Han J, Zhao S, Su K, Wu F, Du X, Xu Q, Chong K, Theissen G, Meng Z (2010) Functional conservation and diversification of class E floral homeotic genes in rice (Oryza sativa). Plant J 61:767–781
Dreni L, Jacchia S, Fornara F, Fornari M, Ouwerkerk PB, An G, Colombo L, Kater MM (2007) The D-lineage MADS-box gene OsMADS13 controls ovule identity in rice. Plant J 52:690–699
Edgar R, Domrachev M, Lash AE (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30:207–210
Ge L, Chen H, Jiang JF, Zhao Y, Xu ML, Xu YY, Tan KH, Xu ZH, Chong K (2004) Overexpression of OsRAA1 causes pleiotropic phenotypes in transgenic rice plants, including altered leaf, flower, and root development and root response to gravity. Plant Physiol 135:1502–1513
Guo S, Xu Y, Liu H, Mao Z, Zhang C, Ma Y, Zhang Q, Meng Z, Chong K (2013) The interaction between OsMADS57 and OsTB1 modulates rice tillering via DWARF14. Nat Commun 4:1566
Hudson D, Guevara DR, Hand AJ, Xu Z, Hao L, Chen X, Zhu T, Bi YM, Rothstein SJ (2013) Rice cytokinin GATA transcription Factor1 regulates chloroplast development and plant architecture. Plant Physiol 162:132–144
IRGSP (2005) The map-based sequence of the rice genome. Nature 436:793–800
Jeon JS, Lee S, Jung KH, Jun SH, Jeong DH, Lee J, Kim C, Jang S, Lee S, An G (2000) T-DNA insertional mutagenesis for functional genomics in rice. Plant J 22:561–570
Jeong HJ, Jung KH (2015) Rice tissue-specific promoters and conditiondependent promoters for effective translational application. J Integr Plant Biol 57:913–924
Jung KH, Kim SR, Giong HK, Nguyen MX, Koh HJ, An G (2015) Genome-wide identification and functional analysis of genes expressed ubiquitously in rice. Mol Plant 8:276–89
Kim CM, Park SH, Je BI, Park SH, Park SJ, Piao HL, Eun MY, Dolan L, Han CD (2007) OsCSLD1, a Cellulose Synthase-Like D1 Gene, Is Required for Root Hair Morphogenesis in Rice. Plant Physiol 43:1220–1230
Ko SS, Li MJ, Sun-Ben Ku M, Ho YC, Lin YJ, Chuang MH, Hsing HX, Lien YC, Yang HT, Chang HC, Chan MT (2014) The bHLH142 Transcription Factor Coordinates with TDR1 to Modulate the Expression of EAT1 and Regulate Pollen Development in Rice. Plant Cell 26:2486–2504
Kobayashi K, Yasuno N, Sato Y, Yoda M, Yamazaki R, Kimizu M, Yoshida H, Nagamura Y, Kyozuka J (2012) Inflorescence meristem identity in rice is specified by overlapping functions of three AP1/FUL-like MADS box genes and PAP2, a SEPALLATA MADS box gene. Plant Cell 24:1848–1859
Lazzarotto F, Teixeira FK, Rosa SB, Dunand C, Fernandes CL, Fontenele Ade V, Silveira JA, Verli H, Margis R (2011) Ascorbate peroxidase-related (APx-R) is a new hemecontaining protein functionally associated with ascorbate peroxidase but evolutionarily divergent. New Phytol 191:234–250
Li P, Wang Y, Qian Q, Fu Z, Wang M, Zeng D, Li B, Wang X, Li J (2007) LAZY1 controls rice shoot gravitropism through regulating polar auxin transport. Cell Res 17:402–410
Li Y, Fan C, Xing Y, Yun P, Luo L, Yan B, Peng B, Xie W, Wang G, Li X, Xiao J, Xu C, He Y (2014) Chalk5 encodes a vacuolar H+-translocating pyrophosphatase influencing grain chalkiness in rice. Nat Genet 46:398–404
Ma N, Wang Y, Qiu S, Kang Z, Che S, Wang G, Huang J (2013) Overexpression of OsEXPA8, a root-specific gene, improves rice growth and root system architecture by facilitating cell extension. PLoS One 8:e75997
Ouyang S, Zhu W, Hamilton J, Lin H, Campbell M, Childs K, Thibaud-Nissen F, Malek RL, Lee Y, Zheng L, Orvis J, Haas B, Wortman J, Buell CR (2007) The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Res 35 (Database issue): D883–887
Pérez-Rodríguez P, Riaño-Pachón DM, Corrêa LG, Rensing SA, Kersten B, Mueller-Roeber B (2010) PlnTFDB: updated content and new features of the plant transcription factor database. Nucleic Acids Res 38(Database issue):D822–827
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13:2498–504
Sharma A, Komatsu S (2002) Involvement of a Ca2+-dependent protein kinase component downstream to the gibberellin-binding phosphoprotein, RuBisCO activase, in rice. Biochem Biophys Res Commun 290:690–695
Todaka D, Nakashima K, Maruyama K, Kidokoro S, Osakabe Y, Ito Y, Matsukura S, Fujita Y, Yoshiwara K, Ohme-Takagi M, Kojima M, Sakakibara H, Shinozaki K, Yamaguchi-Shinozaki K (2012) Rice phytochrome-interacting factor-like protein OsPIL1 functions as a key regulator of internode elongation and induces a morphological response to drought stress. Proc Natl Acad Sci USA 109:15947–15952
Wang L, Xie W, Chen Y, Tang W, Yang J, Ye R, Liu L, Lin Y, Xu C, Xiao J, Zhang Q (2010) A dynamic gene expression atlas covering the entire life cycle of rice. Plant J 61:752–766
Wang JC, Xu H, Zhu Y, Liu QQ, Cai XL (2013) OsbZIP58, a basic leucine zipper transcription factor, regulates starch biosynthesis in rice endosperm. J Exp Bot 64:3453–3466
Yamamoto E, Yonemaru J-I, Yamamoto T, Yano M (2012) OGRO: The Overview of functionally characterized Genes in Rice online database. Rice 5:1–10
Zhang JW, Xu L, Wu YR, Chen XA, Liu Y, Zhu SH, Ding WN, Wu P, Yi KK (2012a) OsGLU3, a putative membrane-bound endo-1,4-beta-glucanase, is required for root cell elongation and division in rice (Oryza sativa L.). Mol Plant 5:176–186
Zhang L, Cheng Z, Qin R, Qiu Y, Wang JL, Cui X, Gu L, Zhang X, Guo X, Wang D, Jiang L, Wu CY, Wang H, Cao X, Wan J (2012b) Identification and characterization of an epi-allele of FIE1 reveals a regulatory linkage between two epigenetic marks in rice. Plant Cell 24:4407–4421
Zimmermann P, Laule O, Schmitz J, Hruz T, Bleuler S, Gruissem W (2008) Genevestigator transcriptome meta-analysis and biomarker search using rice and barley gene expression databases. Mol Plant 1:851–857
Author information
Authors and Affiliations
Corresponding author
Additional information
These authors contributed equally.
Electronic supplementary material
Rights and permissions
About this article
Cite this article
Chandran, A.K.N., Bhatnagar, N., Kim, B. et al. Genome-wide identification and analysis of rice genes to elucidate morphological agronomic traits. J. Plant Biol. 59, 639–647 (2016). https://doi.org/10.1007/s12374-016-0407-7
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12374-016-0407-7