Theoretical and Applied Genetics

, Volume 126, Issue 1, pp 1–11

Accessing complex crop genomes with next-generation sequencing

  • David Edwards
  • Jacqueline Batley
  • Rod J. Snowdon

DOI: 10.1007/s00122-012-1964-x

Cite this article as:
Edwards, D., Batley, J. & Snowdon, R.J. Theor Appl Genet (2013) 126: 1. doi:10.1007/s00122-012-1964-x


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.

Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  • David Edwards
    • 1
  • Jacqueline Batley
    • 2
  • Rod J. Snowdon
    • 3
  1. 1.Australian Centre for Plant Functional Genomics, School of Agriculture and Food SciencesUniversity of QueenslandBrisbaneAustralia
  2. 2.Centre of Excellence for Integrative Legume Research, School of Agriculture and Food SciencesUniversity of QueenslandBrisbaneAustralia
  3. 3.Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and NutritionJustus Liebig UniversityGiessenGermany

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