Sequencing and Array Options for Genotyping in Buffalo

The ability to collect vast amounts of high quality sequencing data for low cost has facilitated assembly and SNP discovery in the buffalo genome.  Simultaneous with throughput advances in sequencing, are lower costs and higher flexibility in SNP genotyping technology both via arrays and via sequence-based methods.  The goal to develop SNP screening panels for genomic and marker-assisted selection requires a cost benefit analysis to determine risk to experimental design for missing data (e.g., sequence-based genotyping) and false positives.  Benefits and considerations of sequence-based versus array methods for genotyping will be discussed.   Data on a pilot project using sequence-based multiplex genotyping of 48 buffalo samples to detect approximately 50,000 SNPs on the HiSeq2500 will also be presented.  We anticipate that a community based Consortium approach to build common tools for genotyping in buffalo will revolutionize the breeding paradigm for this important livestock species group.