INTEGRA (Integrated genetic analysis of barley phenotypic data using 2.1M SNPs) is an extension of the AGOUEB project. We have used an approach called Exome Capture Sequencing that allows us to re-sequence the vast majority of the gene containing portion of the barley genome. Over the last year we have completed the sequencing of approaching 1300 barley accessions (wild, cultivated and landrace material). Initial analysis of this dataset has revealed an unprecedented 17,000,000 SNPs across the germplasm. After applying stringent QC and various filtering steps we have ended up with a dataset of approximately 2.1 M highly robust SNPs that are suitable for high level genetic analysis.
The large collection of elite barley germplasm assembled under the highly successful AHDB supported SA LINK project ‘AGOUEB’ (AHDB Project Report 528) have been included in this re-sequencing study. In AGOUEB we assembled a vast collection of new and legacy phenotypic data and conducted preliminary genetic analyses. However, in AGOUEB these studies were necessarily of low resolution (ca. 1000 markers) and as a result lacked the highest level of informativeness. The result is that the majority of the phenotypic data has not yet been analysed optimally and is yet to be published. The result is that the majority of the phenotypic data has not yet been analysed optimally and is yet to be published. In INTEGRA we will use the set of 2.1M filtered SNPs generated from exome capture sequencing of the accessions used in the AGOUEB project. This high density SNP dataset will be combined with the DUS phenotypic data analysed in the AGOUEB project to improve the resolution of the association analysis for these traits. One of the main aims of this project is to discover new molecular diagnostics for use in barley breeding programs by exploiting existing phenotypic data and high density genetic marker data that we have generated over the past year by resequencing the germplasm assembled under AGOUEB.