Can we use 770 K Illumina bovine chip or we should go for whole genome sequencing and develop a new chip or we should use GBS approach?
Which approach could be most economical?
If we use 770 K chip and have traning population of 1000 lactating cow of one lactation records, could it be the starting point?
It is hard to beat the existing SNP chips. Developing a new chip would be expensive for a moderate-sized project of 1000 cows. You could do GBS and assay fewer loci, but for an unstructured population you are less able to impute data and getting high read depth on hundreds of thousands of loci will be expensive.
If you have poor and unreliable records, none of these methods would be beneficial. You MUST have accurate phenotypic records and then chose one of these methods. If your phenotypes are accurate, then I would choose 770k. Hope that helps!
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