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Accessing complex crop genomes with next-generation sequencing

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Abstract

Many important crop species have genomes originating from ancestral or recent polyploidisation events. Multiple homoeologous gene copies, chromosomal rearrangements and amplification of repetitive DNA within large and complex crop genomes can considerably complicate genome analysis and gene discovery by conventional, forward genetics approaches. On the other hand, ongoing technological advances in molecular genetics and genomics today offer unprecedented opportunities to analyse and access even more recalcitrant genomes. In this review, we describe next-generation sequencing and data analysis techniques that vastly improve our ability to dissect and mine genomes for causal genes underlying key traits and allelic variation of interest to breeders. We focus primarily on wheat and oilseed rape, two leading examples of major polyploid crop genomes whose size or complexity present different, significant challenges. In both cases, the latest DNA sequencing technologies, applied using quite different approaches, have enabled considerable progress towards unravelling the respective genomes. Our ability to discover the extent and distribution of genetic diversity in crop gene pools, and its relationship to yield and quality-related traits, is swiftly gathering momentum as DNA sequencing and the bioinformatic tools to deal with growing quantities of genomic data continue to develop. In the coming decade, genomic and transcriptomic sequencing, discovery and high-throughput screening of single nucleotide polymorphisms, presence–absence variations and other structural chromosomal variants in diverse germplasm collections will give detailed insight into the origins, domestication and available trait-relevant variation of polyploid crops, in the process facilitating novel approaches and possibilities for genomics-assisted breeding.

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Acknowledgments

DE and JB acknowledge funding support from the Grains Research and Development Corporation (Project DAN00117) and the Australian Research Council (Projects LP0882095, LP0883462, LP110100200 and DP0985953), along with further support from the Australian Genome Research Facility (AGRF) and the Queensland Cyber Infrastructure Foundation (QCIF). RS was supported by a fellowship from the OECD Cooperative Research Programme “Biological Resource Management for Sustainable Agricultural Systems” and by DFG grants SN14/11-1 and SN14/12-1.

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Authors and Affiliations

  1. Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, 4072, Australia

    David Edwards

  2. Centre of Excellence for Integrative Legume Research, School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, 4072, Australia

    Jacqueline Batley

  3. Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany

    Rod J. Snowdon

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  1. David Edwards
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  2. Jacqueline Batley
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  3. Rod J. Snowdon
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Correspondence to Jacqueline Batley.

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Communicated by R. Varshney.

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Edwards, D., Batley, J. & Snowdon, R.J. Accessing complex crop genomes with next-generation sequencing. Theor Appl Genet 126, 1–11 (2013). https://doi.org/10.1007/s00122-012-1964-x

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