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Crop Biotech Update

New Sequencing Techniques for Fine Mapping Wheat Genes

April 27, 2012

Dr. Martin Trick and Dr. Cristobal Uauy of the John Innes Centre (JIC) have recently published a study that applies next generation sequencing techniques to wheat. These can help hasten and more efficiently fine map of genes to the level that the plant breeding community needs.

Because of the wheat's huge genome, which has been duplicated twice for durum wheat and thrice in bread wheat during domestication, identifying the genes functions or knowing which genes are responsible for certain traits have been difficult, time consuming, and costly.

To accelerate fine mapping in wheat, as well as to address the problem with gene markers not being close enough to the genes needed in commercial plant breeding programmes, Dr. Uauy and his team at JIC used a newly-developed next generation sequencing techniques to try mapping a previously defined wheat gene. These methods focus on the sequencing of mRNA transcribed from the DNA. Also, these methods identify single nucleotide polymorphisms (SNPs) which can be mapped into the genome. Furthermore, these SNPs could be developed into useful markers.

The study tests the use of next generation sequencing and SNP detection in mapping a gene that influences grain protein content. Together with The Genome Analysis Centre, the team is able to identify 3, 500 potential SNPs that represent the differences between wheat genes of the two lines of genetically identical (isogenic) that the team crossed. The resulting plants are then sorted into two groups, according to grain protein content. Through segregant analysis, a technique that examines the frequency of each SNP in the two groups and shows which are the closest to the gene, the team is able to fine map the gene to a very small interval in a much shorter time.

Read more about how these next generation sequencing techniques and segregant analysis can help in fine mapping genes in wheat and other plants with non-sequenced genome at http://www.tgac.ac.uk/news/27/68/Fine-mapping-wheat-genes/.