ヒヨコマメゲノムの概要配列は形質の改良に必要な資源を提供する

Journal name:
Nature Biotechnology
Volume:
31,
Pages:
240–246
Year published:
DOI:
doi:10.1038/nbt.2491
Received
Accepted
Published online

Abstract

ヒヨコマメ( Cicerarietinum )は大豆に次いで2番目に広く栽培されているマメ科作物であり、ヒトの食餌性窒素摂取量の相当部分を占めるとともに、開発途上国では食糧安全保障上きわめて重要な役割を果たしている。本論文では、ヒヨコマメのカブリ種(大粒種)である「CDCフロンティア」の738 Mbに及ぶ概要全ゲノムショットガン配列を示す。この配列には推定上の遺伝子が28,269個含まれる。10か国から収集した90点の栽培種および野生種の遺伝子型の配列再解読および分析により、育種に関連する遺伝的除去と平衡選択の双方の標的が特定された。病害抵抗性および農業形質の候補遺伝子も明らかにされ、その中には市場で主要な2つのヒヨコマメ栽培種であるデシ(小粒種)とカブリとを識別する形質が含まれていた。今回のデータは、分子育種によるヒヨコマメ改良に有用な資源を含み、ゲノムの多様性および栽培化の双方に関して洞察を与えるものである。

At a glance

Figures

  1. The chickpea genome.
    Figure 1: The chickpea genome.

    Pseudomolecules (A), gene density (red, B); repeat density (blue, C); retrotransposon density (violet, D); transposon density (magenta, E); average pair-wise nucleotide diversity (theta pi) across 17 desi chickpea varieties (green, F), 12 kabuli chickpea varieties (orange, G) and 29 leading chickpea varieties (black, H).

  2. Comparison of chickpea, legume and other dicotyledonous genomes.
    Figure 2: Comparison of chickpea, legume and other dicotyledonous genomes.

    (a) Age distribution of 4DTV for genes from three legume species (chickpea, M. truncatula and L. japonicus) genomes. (b) Synteny blocks shared between chickpea and other sequenced legume genomes, including M. truncatula, L. japonicus, soybean and pigeonpea. (c) Shared and unique gene families in legume species chickpea, M. truncatula, L. japonicus, soybean, pigeonpea; in millettioid and galegoids, and in legumes, A. thaliana and grape. (d) Phylogenetic tree of seven species.

  3. Diversity in elite desi and kabuli chickpea varieties.
    Figure 3: Diversity in elite desi and kabuli chickpea varieties.

    Diversity metrics, presented as average pair-wise nucleotide diversity (current [θπ] and historical [θw]) and Tajima's D, are shown across all eight pseudomolecules in 29 elite (17 desi and 12 kabuli) chickpea varieties. #, six regions with increased Tajima's D and high FST are present on pseudomolecules Ca2, Ca3 and Ca4. +, pseudomolecule Ca4 has a region with reduced Tajima's D (–2.32) that conatins 11 genes including 3MATE transporter TT12 orthologs. *, NBS-LRR disease resistance genes are associated with regions of elevated Tajima's D on five pesudomolecules namely Ca1, Ca2, Ca4, Ca7 and Ca8.

  4. Population structure and diversity in elite varieties and germplasm.
    Figure 4: Population structure and diversity in elite varieties and germplasm.

    (a) Structure analysis of 29 elite varieties (19 desi and 10 kabuli) based on whole-genome resequencing data. (b) Principle component analysis (PCA) of 90 chickpea genotypes including 29 elite varieties and 61 germplasm lines using 1.96 million SNPs as datapoints. (c) Neighbor-joining (NJ) tree analysis of 90 genotypes based on 1.96 million SNPs.

Accession codes

Referenced accessions

BioProject

NCBI Reference Sequence

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Author information

Affiliations

  1. International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Andhra Pradesh, India.

    • Rajeev K Varshney,
    • Rachit K Saxena,
    • Sarwar Azam,
    • Pooran M Gaur,
    • Hari D Upadhyaya,
    • Mahendar Thudi &
    • C L L Gowda
  2. CGIAR Generation Challenge Programme, Texcoco, Mexico.

    • Rajeev K Varshney
  3. Beijing Genomics Institute (BGI) - Shenzhen, China.

    • Chi Song,
    • Sheng Yu,
    • Xudong Zhang,
    • Ying Wang,
    • Chunyan Xu,
    • Weiming He,
    • Shancen Zhao,
    • Xun Xu,
    • Gengyun Zhang &
    • Jun Wang
  4. National Research Council Canada (NRC-CNRC), Canada.

    • Andrew G Sharpe,
    • Larissa D Ramsay,
    • Janet A Condie &
    • Krishna K Gali
  5. USDA-ARS, Iowa State University, Ames, Iowa, USA.

    • Steven Cannon
  6. Department of Plant Pathology, University of California, Davis, Davis, California, USA.

    • Jongmin Baek,
    • Benjamin D Rosen,
    • R Varma Penmetsa,
    • Noelia Carrasquilla-Garcia,
    • Ming-Cheng Luo &
    • Douglas R Cook
  7. Crop Development Centre, Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.

    • Bunyamin Tar'an
  8. Departamento de Genetica, University of Cordoba, Cordoba, Spain.

    • Teresa Millan,
    • Josefa Rubio &
    • Juan Gil
  9. Centers for Applied Genetic Technologies, University of Georgia, Athens, Georgia, USA.

    • Aiko Iwata &
    • Scott A Jackson
  10. University of Arizona, Tucson, Arizona, USA.

    • William Nelson &
    • Carol Soderlund
  11. National Center for Genome Resources (NCGR), Santa Fe, New Mexico, USA.

    • Andrew D Farmer &
    • Arvind K Bharti
  12. GenXPro GmbH, Frankfurt am Main, Germany.

    • Peter Winter
  13. Commonwealth Scientific and Industrial Research Organization (CSIRO), Australia.

    • James K Hane &
    • Karam B Singh
  14. All India Coordinated Research Project on Chickpea (AICRP), Indian Council of Agricultural Research (ICAR), New Delhi, India.

    • Narendra P Singh
  15. Environment and Agriculture, Curtin University, Bentley, Australia.

    • Judith Lichtenzveig
  16. Indian Institute of Pulses Research (IIPR), Indian Council of Agricultural Research (ICAR), Kanpur, India.

    • N Nadarajan
  17. Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic.

    • Jaroslav Dolezel
  18. National Bureau of Plant Genetic Resources (NBPGR), Indian Council of Agricultural Research (ICAR), New Delhi, India.

    • Kailash C Bansal
  19. ACPFG and The University of Queensland, St. Lucia, Queensland, Australia.

    • David Edwards
  20. Johann Wolfgang Goethe - University, Frankfurt am Main, Germany.

    • Guenter Kahl
  21. The University of Western Australia Institute of Agriculture, The University of Western Australia, Crawley, Australia.

    • Karam B Singh
  22. Division of Crop Sciences, Indian Council of Agricultural Research (ICAR), New Delhi, India.

    • Swapan K Datta
  23. Department of Biology, University of Copenhagen, Copenhagen, Denmark.

    • Jun Wang

Contributions

R.K.V., C. Song, R.K.S., S.A., S.Y., A.G.S., J.B., B.T., T.M., L.D.R., R.V.P., P.W., N.C.-G., J.A.C., M.T., M.-C.L., K.K.G., J.D., X.X., G.Z., G.K., K.B.S., J.W. and D.R.C. contributed to generation of genome sequence, transcriptome sequence, BAC-end sequencing, genetic mapping and physical mapping data; B.T., T.M., P.M.G., H.D.U., C.L.L.G., N.P.S., J.R., N.N., K.C.B., J.G. and S.K.D. contributed genetic material, C. Song, S.A., S.Y., A.G.S., S.C., X.Z., J.B., Y.W., C.X. and W.H. worked on genome assembly; C. Song, S.Y., R.K.S., A.I., S.Z. and W.N., contributed to genome annotation and gene function analysis; R.K.V., C. Song, S.A., S.Y., B.D.R., W.N., C. Sodurland, S.Z., J.K.H., M.-C.L., J.L., J.D., X.X., D.E., G.Z., G.K., K.B.S., S.A.J., J.W. and D.R.C. worked on genome analysis and comparative genomics; R.K.V., R.K.S., S.Y., B.T., T.M., Y.W., A.D.F., P.M.G., C.X., A.K.B., W.H., P.W., S.Z., H.D.U., C.L.L.G., N.P.S., J.L., J.R., N.N., K.C.B., G.K., J.G., K.B.S., S.K.D., J.W. and D.R.C. worked on germplasm diversity analysis; and R.K.V., D.R.C. and J.W., together with S.A.J., K.B.S., S.K.D., G.Z., T.M., B.T., D.E., S.C., A.G.S., R.K.S., S.A. and C. Song wrote and finalized the manuscript; R.K.V. and D.R.C. conceived and directed the project.

Competing financial interests

P.W. is employed by GenXPro.

Corresponding authors

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Author details

Supplementary information

PDF files

  1. Supplementary Text and Figures (647 KB)

    Supplementary Tables 1–20 and Supplementary Figures 1–8

  2. Supplementary Figure 5 (635 KB)

    Maximum likelihood phylogram comparing NBS domains of the non-TIR resistance gene homologs from chickpea (Ca) with Medicago (Mt).

  3. Supplementary Figure 6 (492 KB)

    Maximum likelihood phylogram comparing NBS domains of the TIR resistance gene homologs from chickpea (Ca) with Medicago truncatula (Mt).

Excel files

  1. Supplementary Table 1 (53 KB)

    Details on 90 Cicer accessions used for re-sequencing (29 cultivars) and RAD genotyping (61 accessions including cultivars/breeding lines, land races and wild relatives)

  2. Supplementary Table 6 (1 MB)

    Details on the repeat regions and masking

  3. Supplementary Table 13 (279 KB)

    Synteny blocks of the chickpea genome conserved with genomes of four legume (Medicago truncatula, Lotus japonicus, soybean, and pigeonpea) and two non-legume dicot (Arabidopsis thailiana and grape) genomes

  4. Supplementary Table 17 (10 MB)

    Primer sequences for SSR markers

Additional data