Molecular Breeding

, 39:165 | Cite as

Towards a deeper integrated multi-omics approach in the root system to develop climate-resilient rice

  • Kanami Yoshino
  • Yuko Numajiri
  • Shota Teramoto
  • Naoki Kawachi
  • Takanari Tanabata
  • Tsuyoshi Tanaka
  • Takeshi Hayashi
  • Taiji KawakatsuEmail author
  • Yusaku UgaEmail author
Part of the following topical collections:
  1. Topical Collection on Rice Functional Genomics


Roots are the only organ system to uptake water and nutrients from the soil. The root system is crucial for plants to survive and adapt to environmental stresses. Therefore, the root system architecture (RSA) is an important breeding target for developing climate-resilient rice. Since the rice genome has been completely sequenced, many genes for root development have been cloned and characterized. In addition, with the advances in technologies related to omics analysis, such as high-throughput sequencing, transcriptome analysis of roots has also progressed. In contrast, high-throughput root phenotyping has not been established not only in rice but also in whole plants because roots are hidden underground. This deficiency represents a bottleneck for utilizing an integrated multi-omics approach for molecular breeding of RSA. We first summarized previous transcriptome analyses for root development under various abiotic stresses such as drought, salinity, and heat, and assessed the current status of root phenotyping technology and modeling in rice. This knowledge allowed us to contemplate the possibility of applying an integrated multi-omics dataset from RSA to molecular breeding of climate-resilient rice.


Image analysis Phenomics ROOTomics Root morphology Transcriptomics X-ray computed tomography 



We thank the staff of the technical support center of the National Agriculture and Food Research Organization for their field management and experimental support

Funding information

This work was financially supported by JST CREST Grant Number JPMJCR17O1, Japan.

Compliance with ethical standards

Conflicts of interest

The authors declare that they have no conflict of interest.


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© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Institute of Agrobiological SciencesNational Agriculture and Food Research OrganizationTsukubaJapan
  2. 2.Institute of Crop ScienceNational Agriculture and Food Research OrganizationTsukubaJapan
  3. 3.Takasaki Advanced Radiation Research InstituteNational Institutes for Quantum and Radiological Science and TechnologyTakasakiJapan
  4. 4.Department of Frontier Research and DevelopmentKazusa DNA Research InstituteKisarazuJapan

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