Open AccessTargeted re‐sequencing of the allohexaploid wheat exome
Author(s) -
Winfield Mark O.,
Wilkinson Paul A.,
Allen Alexandra M.,
Barker Gary L. A.,
Coghill Jane A.,
Burridge Amanda,
Hall Anthony,
Brenchley Rachael C.,
D’Amore Rosalinda,
Hall Neil,
Bevan Michael W.,
Richmond Todd,
Gerhardt Daniel J.,
Jeddeloh Jeffrey A.,
Edwards Keith J.
Publication year - 2012
Publication title -
plant biotechnology journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.525
H-Index - 115
eISSN - 1467-7652
pISSN - 1467-7644
DOI - 10.1111/j.1467-7652.2012.00713.x
Subject(s) - biology , genome , polyploid , genetics , exome sequencing , single nucleotide polymorphism , whole genome sequencing , dna sequencing , common wheat , genomics , computational biology , gene , genotype , mutation , chromosome
Summary 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 characterize 56.5 Mb of genomic DNA with sequence similarity to over 100 000 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 (SNPs). While 80% of these were variants between the homoeologous genomes, A, B and D, a significant number (20%) were putative varietal SNPs 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 SNPs identified should be of considerable use to the wider wheat community.