Accessing complex crop genomes with next-generation sequencing

Edwards, David, Batley, Jacqueline and Snowdon, Rod J. (2013) Accessing complex crop genomes with next-generation sequencing. Theoretical and Applied Genetics, 126 1: 1-11. doi:10.1007/s00122-012-1964-x


Author Edwards, David
Batley, Jacqueline
Snowdon, Rod J.
Title Accessing complex crop genomes with next-generation sequencing
Journal name Theoretical and Applied Genetics   Check publisher's open access policy
ISSN 0040-5752
1432-2242
Publication date 2013-01
Year available 2012
Sub-type Critical review of research, literature review, critical commentary
DOI 10.1007/s00122-012-1964-x
Volume 126
Issue 1
Start page 1
End page 11
Total pages 11
Place of publication Heidelberg, Germany
Publisher Springer
Collection year 2013
Language eng
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.
Keyword Polyploidisation events
Next-generation sequencing
Data analysis techniques
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ
Additional Notes Published online: 5 September 2012.

Document type: Journal Article
Sub-type: Critical review of research, literature review, critical commentary
Collections: School of Agriculture and Food Sciences
Official 2013 Collection
 
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