Cervus elaphus Genome sequencing and SNP discovery

The use of whole generation sequencing in combination with an existing and near-complete bovine reference genome has enabled the deer genome to be assembled sufficiently for large-scale SNP discovery. In total, 28 Gbp of sequence data were generated from seven Cervus elaphus (European red deer and Canadian elk) individuals. After repeat-masking, a procedure involving BLAST-based positioning to the bovine reference genome build UMD 3.0 enabled the binning of reads into 1 Mbp groups; the reads within these bins were then melded to produce chromosomal scaffolds with an average contig length of 1.1 kb, which were subsequently analysed for SNPs. Additionally, 213 markers located on the published red x Pere David deer linkage map were aligned to both UMD3.0 and the newly formed deer chromosomal scaffolds via BLAST searching. This enabled deer linkage groups to be assigned to deer chromosomal scaffolds, although the mapping locations remain based on bovine order. Based on previous experience with our SNP pipeline in sheep, we expected that around 48% of putative SNPs would yield usable marker assays on an Illumina SNP chip. Subsequent genotyping of 270 SNPs on a Sequenom MS system showed that 88% of the SNPs could be amplified in multiplexes without optimisation of reaction conditions for each multiplex. Also, inheritance patterns showed no evidence of departure from Hardy-Weinberg equilibrium. However, 23 (9%) of the autosomal SNP calls were homozygous. Given that the original sequenced animals were included in the genotyping assessment this could be due to false SNP identification at the sequence level. However, >99% of the non-repetitive fraction of the bovine genome was covered by deer chromosomal scaffolds containing 1.8 million SNPs that met their technical design threshold of 0.80 indicating that these SNPs would be suitable for incorporating into a cervine Illumina InfiniumII SNPchip.