Frequency and pattern of structural variation in the cultivated and non-cultivated gene-pool of barley as revealed by Comparative Genomic Hybridization

There is an increased interest in the plant genomics community in studying the extent of intraspecific structural variation. In particular, the levels of copy number variation (CNV) and presence-absence variation (PAV) are of primary interest. In recent years, several studies have tried to identify this type of genomic structural variation in crops such as maize, soybean and wheat. However, the levels of CNV and PAV have not yet been examined in barley. In this study, we used a barley CGH 2.1M custom array representing ~ 50 Mbp of capture space to evaluate structural variation in the barley genome. Whole-genome shotgun sequence from the reference genotype “Morex” was used by Roche Nimblegen to create the barley CGH array. To validate the array, we conducted a pilot experiment using a 3HL wheat-barley addition line. We are currently using the CGH array to examine the structural variation in various modern cultivars and wild accessions. Most of the array hybridizations have been performed and data have been extracted from the scanned images. We are in the process of data analysis, which will show the extent of structural diversity within and between cultivated and wild barleys. Preliminary results indicate substantial structural variation among cultivated barleys.