Characterizing homologues of crop domestication genes in poorly described wild relatives by high-throughput sequencing of whole genomes
Article first published online: 15 JUL 2011
© 2011 The Authors. Plant Biotechnology Journal © 2011 Society for Experimental Biology, Association of Applied Biologists and Blackwell Publishing Ltd
Plant Biotechnology Journal
Volume 9, Issue 9, pages 1131–1140, December 2011
How to Cite
Malory, S., Shapter, F. M., Elphinstone, M. S., Chivers, I. H. and Henry, R. J. (2011), Characterizing homologues of crop domestication genes in poorly described wild relatives by high-throughput sequencing of whole genomes. Plant Biotechnology Journal, 9: 1131–1140. doi: 10.1111/j.1467-7652.2011.00640.x
- Issue published online: 9 NOV 2011
- Article first published online: 15 JUL 2011
- Received 30 March 2011; revised 31 May 2011; accepted 4 June 2011.
- wild relatives;
- high-throughput sequencing;
- gene homologues;
- massively parallel sequencing;
- poorly described genomes
Wild crop relatives represent a source of novel alleles for crop genetic improvement. Screening biodiversity for useful or diverse gene homologues has often been based upon the amplification of targeted genes using available sequence information to design primers that amplify the target gene region across species. The crucial requirement of this approach is the presence of sequences with sufficient conservation across species to allow for the design of universal primers. This approach is often not successful with diverse organisms or highly variable genes. Massively parallel sequencing (MPS) can quickly produce large amounts of sequence data and provides a viable option for characterizing homologues of known genes in poorly described genomes. MPS of genomic DNA was used to obtain species-specific sequence information for 18 rice genes related to domestication characteristics in a wild relative of rice, Microlaena stipoides. Species-specific primers were available for 16 genes compared with 12 genes using the universal primer method. The use of species-specific primers had the potential to cover 92% of the sequence of these genes, while traditional universal primers could only be designed to cover 80%. A total of 24 species-specific primer pairs were used to amplify gene homologues, and 11 primer pairs were successful in capturing six gene homologues. The 23 million, 36-base pair (bp) paired end reads, equated to an average of 2X genome coverage, facilitated the successful amplification and sequencing of six target gene homologues, illustrating an important approach to the discovery of useful genes in wild crop relatives.