Genome-wide identification and analysis of rice genes to elucidate morphological agronomic traits
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.
KeywordsGene-indexed mutant Meta-expression analysis Morphological agronomic traits Rice Tissue/organ-preferred genes
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- 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 9:17CrossRefPubMedPubMedCentralGoogle Scholar
- 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 135:1502–1513CrossRefPubMedPubMedCentralGoogle Scholar
- 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 26:2486–2504CrossRefPubMedPubMedCentralGoogle Scholar
- 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 24:1848–1859CrossRefPubMedPubMedCentralGoogle Scholar
- 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 191:234–250CrossRefPubMedGoogle Scholar
- 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 109:15947–15952CrossRefPubMedPubMedCentralGoogle Scholar
- 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 24:4407–4421CrossRefPubMedPubMedCentralGoogle Scholar