Genetic variance explanation of Residual Feed Intake (RFI) by SNPs discovered on transcriptome of Holstein cows

In recent years, Single Nucleotide Polymorphisms (SNPs) has been the most important and efficient tool in animal breeding. Genome-wide Association Studies (GWAS) and Genome-enabled predictions (genomic selection) are two major applications of SNPs in animal genetics and breeding that both relay on genotyping a lot of SNPs. Some high dense (HD) SNP arrays have been applied particularly in dairy cattle for this purpose. Since transcriptome is resulted only from transcription of coding genomic regions and finally expressed into a protein, the SNPs located on transcriptome may estimate breeding values well. Based on this hypothesis, SNP discovery was done on a transcriptome assembled from aligning and mapping of RNA-Seq reads on bovine reference genome for an US Holstein cow population by samtools package. Then, the contribution of the discovered SNPs in explanation of genetic variance for Residual Feed Intake (RFI) trait in Australian Holstein was evaluated based on variance components analysis. It was discovered 53478 SNPs that the most weren’t on the current Illumina bovine SNP arrays. Only 6336 discovered SNPs were shared with Illumina bovine HD array. This reduced SNP panel was low dense and therefore could not capture genetic variance of RFI larger than Illumina bovine high dense SNP Chip. It's suggested to applying the discovered SNPs on transcritome in genomic predictions based on whole genome sequencing with no limitations for the number of shred loci with the current Illumina SNP arrays.