Characterizing homologues of crop domestication genes in poorly described wild relatives by high-throughput sequencing of whole genomes

Malory, Sylvia, Shapter, Frances M., Elphinstone, Martin S., Chivers, Ian H. and Henry, Robert J. (2011) Characterizing homologues of crop domestication genes in poorly described wild relatives by high-throughput sequencing of whole genomes. Plant Biotechnology Journal, 9 9: 1131-1140. doi:10.1111/j.1467-7652.2011.00640.x


 
Related Publications and Datasets
 
Author Malory, Sylvia
Shapter, Frances M.
Elphinstone, Martin S.
Chivers, Ian H.
Henry, Robert J.
Title Characterizing homologues of crop domestication genes in poorly described wild relatives by high-throughput sequencing of whole genomes
Journal name Plant Biotechnology Journal   Check publisher's open access policy
ISSN 1467-7644
1467-7652
Publication date 2011-12
Sub-type Article (original research)
DOI 10.1111/j.1467-7652.2011.00640.x
Volume 9
Issue 9
Start page 1131
End page 1140
Total pages 10
Place of publication Oxford, United Kingdom
Publisher Wiley-Blackwell
Collection year 2012
Language eng
Formatted abstract
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.
Keyword Wild relatives
High-throughput sequencing
Gene homologues
Massively parallel sequencing
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2012 Collection
Queensland Alliance for Agriculture and Food Innovation
 
Versions
Version Filter Type
Citation counts: TR Web of Science Citation Count  Cited 13 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 20 times in Scopus Article | Citations
Google Scholar Search Google Scholar
Created: Sat, 04 Feb 2012, 17:42:51 EST by System User on behalf of Qld Alliance for Agriculture and Food Innovation