Journal of Plant Biology

, Volume 59, Issue 6, pp 639–647 | Cite as

Genome-wide identification and analysis of rice genes to elucidate morphological agronomic traits

  • Anil Kumar Nalini Chandran
  • Nikita Bhatnagar
  • Bumki Kim
  • Ki-Hong Jung
Original Article


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.


Gene-indexed mutant Meta-expression analysis Morphological agronomic traits Rice Tissue/organ-preferred genes 


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Supplementary material

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Copyright information

© Korean Society of Plant Biologists and Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  • Anil Kumar Nalini Chandran
    • 1
  • Nikita Bhatnagar
    • 1
    • 2
  • Bumki Kim
    • 2
  • Ki-Hong Jung
    • 1
  1. 1.Graduate School of Biotechnology & Crop Biotech InstituteKyung Hee UniversityYonginKorea
  2. 2.Molecular Breeding Division, National Academy of Agricultural ScienceRDAJeonjuKorea

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