Study : Exome sequencing of diverse collection of wheat landraces, cultivars and breeding lines


Exome sequencing of diverse collection of wheat landraces, cultivars and breeding lines
The exome sequenced hexaploid wheat accessions were selected from a worldwide population of landraces and cultivars obtained from the USDA National Small Grains Collection and the Australian Grains Genebank (formally the Australian Winter Cereal Collection). The worldwide population comprised 3990 accessions from 106 countries that were genotyped using the Infinium iSelect 90K SNP wheat bead chip array. The MCG method was used to select accessions for exome sequencing. This method uses a genetic relationship matrix calculated from genotype data to iteratively chose and arbitrary number of accessions (in the case of this study 20% of the accessions) that collectively explain the largest proportion of variance in genetic relationships among the whole set. Genomic DNA was extracted from leaf tissue for each accession using the Agencourt DNAdvance Genomic DNA Isolation Kit (Beckman Coulter) and subjected to sequence capture using the NimbleGen SeqCap EZ wheat whole genome assay. In brief, 1 µg of DNA was fragmented with the Covaris S2 instrument to obtain an average fragment length of 300 bp. Shorter fragments were removed using Agencourt AMPure XP beads (Beckman Coulter). The KAPA Library Preparation Kit (Kapa Biosystems) and adapters supplied in the NimbleGen SeqCap EZ Reagent Kit Plus v2 (Roche) were used to prepare sample libraries for the capture assay, according to the KAPA protocol but excluding steps 8.1-8.22. The quality and yield of each sample library was assessed using an Agilent 2200 TapeStation (Agilent Technologies) before proceeding to the sequence capture assay following the Roche protocol. Each target capture sequence enriched sample library was sequenced on an Illumina HiSeq2000 instrument (Illumina) to generate about 30 million reads per accession. The project leaders are Matthew Hayden (Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia; La Trobe University, Bundoora, Victoria, Australia) and Eduard Akhunov (Kansas State University, USA). More information can be found on our project website at
Data files


Accession number Name Taxon
AVS:29636 Triticum aestivum Aus29636/2*Annuello*2 / Aus29636/2*Annuello*3 / Aus29636/2*Annuello*7 / spring wheat
AVS:34278 Triticum aestivum Aus34278/correll*29 / Aus34278/correll*32 / Aus34278/correll*46 / spring wheat
AVS:34434 Triticum aestivum Aus34434/annuello*16 / Aus34434/annuello*3 / Aus34434/annuello*39 / Aus34434/annuello*51 / spring wheat
AWCC:102307 Triticum aestivum DUTOIT / F
AWCC:103416 Triticum turgidum subsp. durum SWONSKA
AWCC:106256 Triticum aestivum BROVKI
AWCC:114940 Triticum aestivum ERYTHROSPERMUM 917
AWCC:114997 Triticum aestivum NW59A / winter wheat
AWCC:119805 Triticum aestivum EKA NOWA
AWCC:120077 Triticum aestivum NEUZUCHT
AWCC:121758 Triticum aestivum Hill 81 / winter wheat
AWCC:131089 Triticum aestivum CRETE 3 / spring wheat
AWCC:131533 Triticum aestivum AUSTRALIA CCI W270 / spring wheat
AWCC:131590 Triticum aestivum CHINA 19 / spring wheat
AWCC:131628 Triticum aestivum CHINA Sh208 / spring wheat
AWCC:131888 Triticum aestivum PORTUGAL 39 / spring wheat
AWCC:131944 Triticum aestivum UKRAINE W94508
AWCC:131980 Triticum aestivum INDIA 114 / spring wheat
AWCC:140592 Triticum aestivum ERYT977.89 / winter wheat
AWCC:167578 Triticum aestivum Espada / spring wheat