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The pangenome of an agronomically important crop plant Brassica oleracea

Author

Listed:
  • Agnieszka A. Golicz

    (School of Agriculture and Food Sciences, The University of Queensland)

  • Philipp E. Bayer

    (School of Plant Biology, The University of Western Australia)

  • Guy C. Barker

    (School of Life Sciences, The University of Warwick)

  • Patrick P. Edger

    (Michigan State University)

  • HyeRan Kim

    (Korea Research Institute of Bioscience & Biotechnology)

  • Paula A. Martinez

    (School of Agriculture and Food Sciences, The University of Queensland)

  • Chon Kit Kenneth Chan

    (School of Plant Biology, The University of Western Australia)

  • Anita Severn-Ellis

    (School of Plant Biology, The University of Western Australia)

  • W. Richard McCombie

    (Cold Spring Harbor Laboratory)

  • Isobel A. P. Parkin

    (Agriculture and Agri-Food Canada)

  • Andrew H. Paterson

    (Plant Genome Mapping Laboratory, University of Georgia)

  • J. Chris Pires

    (Bond Life Sciences Center, University of Missouri)

  • Andrew G. Sharpe

    (National Research Council Canada)

  • Haibao Tang

    (Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University)

  • Graham R. Teakle

    (School of Life Sciences, The University of Warwick)

  • Christopher D. Town

    (J. Craig Venter Institute)

  • Jacqueline Batley

    (School of Plant Biology, The University of Western Australia)

  • David Edwards

    (School of Plant Biology, The University of Western Australia)

Abstract

There is an increasing awareness that as a result of structural variation, a reference sequence representing a genome of a single individual is unable to capture all of the gene repertoire found in the species. A large number of genes affected by presence/absence and copy number variation suggest that it may contribute to phenotypic and agronomic trait diversity. Here we show by analysis of the Brassica oleracea pangenome that nearly 20% of genes are affected by presence/absence variation. Several genes displaying presence/absence variation are annotated with functions related to major agronomic traits, including disease resistance, flowering time, glucosinolate metabolism and vitamin biosynthesis.

Suggested Citation

  • Agnieszka A. Golicz & Philipp E. Bayer & Guy C. Barker & Patrick P. Edger & HyeRan Kim & Paula A. Martinez & Chon Kit Kenneth Chan & Anita Severn-Ellis & W. Richard McCombie & Isobel A. P. Parkin & An, 2016. "The pangenome of an agronomically important crop plant Brassica oleracea," Nature Communications, Nature, vol. 7(1), pages 1-8, December.
    • Handle: RePEc:nat:natcom:v:7:y:2016:i:1:d:10.1038_ncomms13390
    DOI: 10.1038/ncomms13390
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    Citations

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    Cited by:

    1. Zhengcao Li & Henner Simianer, 2020. "Pan-genomic open reading frames: A potential supplement of single nucleotide polymorphisms in estimation of heritability and genomic prediction," PLOS Genetics, Public Library of Science, vol. 16(8), pages 1-19, August.
    2. Xiaoling Tong & Min-Jin Han & Kunpeng Lu & Shuaishuai Tai & Shubo Liang & Yucheng Liu & Hai Hu & Jianghong Shen & Anxing Long & Chengyu Zhan & Xin Ding & Shuo Liu & Qiang Gao & Bili Zhang & Linli Zhou, 2022. "High-resolution silkworm pan-genome provides genetic insights into artificial selection and ecological adaptation," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    3. Daiqi Wang & Hongru Wang & Xiaomei Xu & Man Wang & Yahuan Wang & Hong Chen & Fei Ping & Huanhuan Zhong & Zhengkun Mu & Wantong Xie & Xiangyu Li & Jingbin Feng & Milan Zhang & Zhilan Fan & Tifeng Yang , 2023. "Two complementary genes in a presence-absence variation contribute to indica-japonica reproductive isolation in rice," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    4. Cristian Groza & Xun Chen & Travis J. Wheeler & Guillaume Bourque & Clément Goubert, 2024. "A unified framework to analyze transposable element insertion polymorphisms using graph genomes," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    5. Eltohamy A A Yousef & Thomas Müller & Andreas Börner & Karl J Schmid, 2018. "Comparative analysis of genetic diversity and differentiation of cauliflower (Brassica oleracea var. botrytis) accessions from two ex situ genebanks," PLOS ONE, Public Library of Science, vol. 13(2), pages 1-19, February.
    6. Neik, T. X. & Siddique, K. H. M. & Mayes, S. & Edwards, D. & Batley, J. & Mabhaudhi, Tafadzwanashe & Song, B. K. & Massawe, F., 2023. "Diversifying agrifood systems to ensure global food security following the Russia–Ukraine crisis," Papers published in Journals (Open Access), International Water Management Institute, pages 1-7:1124640.

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