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Genome sequencing reveals agronomically important loci in rice using MutMap

Nature Biotechnology volume 30, pages 174–178 (2012)Cite this article

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Abstract

The majority of agronomic traits are controlled by multiple genes that cause minor phenotypic effects, making the identification of these genes difficult. Here we introduce MutMap, a method based on whole-genome resequencing of pooled DNA from a segregating population of plants that show a useful phenotype. In MutMap, a mutant is crossed directly to the original wild-type line and then selfed, allowing unequivocal segregation in second filial generation (F2) progeny of subtle phenotypic differences. This approach is particularly amenable to crop species because it minimizes the number of genetic crosses (n = 1 or 0) and mutant F2 progeny that are required. We applied MutMap to seven mutants of a Japanese elite rice cultivar and identified the unique genomic positions most probable to harbor mutations causing pale green leaves and semidwarfism, an agronomically relevant trait. These results show that MutMap can accelerate the genetic improvement of rice and other crop plants.

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Figure 1: Simplified scheme for application of MutMap to rice.
Figure 2: Identification of genomic regions harboring causal mutations for two pale green leaf mutants, Hit1917-pl1 and Hit0813-pl2, using MutMap.
Figure 3: Genetic complementation of Hit1917-pl1 pale green leaf mutant with OsCAO1.
Figure 4: Identification of genomic regions possibly harboring causal mutations for five agronomically useful rice mutants using MutMap.

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Acknowledgements

This study was supported by the Program for Promotion of Basic Research Activities for Innovative Biosciences, to R.T., H.I. and A.A. Ministry of Agriculture, Forestry and Fisheries of Japan (Genomics for Agricultural Innovation PMI-0010), Ministry of Education, Culture, Sports, Science and Technology of Japan (Grant-in-Aid for Scientific Research on Innovative Areas 23113009) to R.T. and a Daiwa Adrian Prize to S. Kamoun and R.T. L.C. and S. Kamoun were supported by the Gatsby Charitable Foundation. We thank S. Kuroda for general support and M.J. Terry, B. Wulff and K. Tsunewaki for suggestions to improve the paper.

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  1. Akira Abe and Shunichi Kosugi: These authors contributed equally to this work.

Authors and Affiliations

  1. Iwate Agricultural Research Center, Kitakami, Japan

    Akira Abe

  2. United Graduate School of Agricultural Sciences, Iwate University, Morioka, Japan

    Akira Abe & Hiroki Takagi

  3. Iwate Biotechnology Research Center, Kitakami, Japan

    Shunichi Kosugi, Kentaro Yoshida, Satoshi Natsume, Hiroki Takagi, Hiroyuki Kanzaki, Hideo Matsumura, Kakoto Yoshida, Chikako Mitsuoka, Muluneh Tamiru & Ryohei Terauchi

  4. Gene Research Center, Shinshu University, Ueda, Japan

    Hideo Matsumura

  5. Graduate University for Advanced Studies, Hayama, Japan

    Hideki Innan

  6. The Sainsbury Laboratory, Norwich Research Park, Norwich, UK

    Liliana Cano & Sophien Kamoun

Authors
  1. Akira Abe
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  2. Shunichi Kosugi
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  14. Ryohei Terauchi
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Contributions

A.A. conceived the idea and carried out rice crossing and phenotyping; S. Kosugi developed a bioinformatics pipeline to perform MutMap; K.Y., S.N. and L.C. carried out genome analysis; H.T. and K.Y. carried out rice transformation; H.K., H.M. and M.T. performed mutagenesis; C.M. carried out sequencing; H.I. performed theoretical analysis; S. Kamoun and R.T. conceived the idea, supervised the work and wrote the manuscript.

Corresponding author

Correspondence to Ryohei Terauchi.

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The authors declare no competing financial interests.

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Supplementary Tables 1–7, Supplementary Data and Supplementary Figures 1–4 (PDF 5781 kb)

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Abe, A., Kosugi, S., Yoshida, K. et al. Genome sequencing reveals agronomically important loci in rice using MutMap. Nat Biotechnol 30, 174–178 (2012). https://doi.org/10.1038/nbt.2095

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