Wheat exome capture and targeted resequencing
Wheat exome capture and targeted resequencing
Bread wheat, Triticum aestivum, is an allohexaploid composed of the three   distinct ancestral genomes, A, B and D.  The polyploid nature of the wheat   genome together with its large size has limited our ability to generate the   significant amount of sequence data required for whole genome studies.   Even with the advent of next generation sequencing technology, it is still   relatively expensive to generate whole genome sequences for more than a few   wheat genomes at any one time.  To overcome this problem, we have developed   a targeted-capture re-sequencing protocol based upon NimbleGen array   technology to capture and characterise 56.5 Mb of genomic DNA with sequence   similarity to over one hundred thousand transcripts from eight different UK   allohexaploid wheat varieties.  Using this procedure in conjunction with a   carefully designed bioinformatic procedure, we have identified more than   500,000 putative single nucleotide polymorphisms.  While 80% of these were   variants between the homoeologous genomes, A, B and D, a significant number   (20%) were putative varietal single nucleotide polymorphisms between the   eight varieties studied.  A small number of these latter polymorphisms were   experimentally validated using KASPar technology and 94% proved to be   genuine.  The procedures described here to sequence a large proportion of   the wheat genome and the various single nucleotide polymorphisms identified   should be of considerable use to the wider wheat community