From Exome Sequencing to Variant Discovery in Barley

Barley (Hordeum vulgare) being a member of the grass family is one of the most important cereals and a close relative of wheat with a complex diploid genome of 5.1 Gbp. Genome-assisted research is aided with the availability of the Morex cultivar whole genome shotgun assembly (International Barley Genome Sequencing, Mayer et al. 2012). Exome targeted sequencing helps to bring down the cost of sequencing and analysis by targeting only the coding portion of the genome.

In our study we estimate the mutation frequency in 24 lines from saturated barley EMS (Ethyl methanesulfonate) Optic mutant population. Here we have used a Nimblegen array capture design that has been enriched for 61.6 Mbp coding sequence targets that include predicted genes from the cultivar Morex genome assembly, publicly available full length cDNAs and de novo assembled RNAseq consensus sequence contigs (Mascher, Richmond et al. 2013). We used Bowtie2 (Langmead and Salzberg 2012) to map the reads onto the Morex reference followed by a post-filtering of uniquely mapped, properly paired and duplicate removed reads. We show that variant calling on the captured reads along with threshold filtering helps in understanding the EMS behavior on the Optic population.