SNP Discovery in RNA-Seq Across Breeds of Cattle in Puberty-Related Candidate Genes (i.e., Network Hubs)

Fertility traits are economically important in cattle production systems and used in genetic selection programs. In an earlier study of Brangus (3/8 Brahman x 5/8 Angus) heifers, various omics data were used in co-expression gene network analyses to identify gene-hubs indicative of puberty. The current study aimed to discover SNP in RNA-sequence in 62 of these candidate gene-hubs and determine their presence in other breeds. These genes were primarily transcription factors with conserved sequences. RNA-seq reads from Brangus and Nellore (Bos indicus) and Angus and Holstein (Bos taurus) cattle were assembled to the bovine reference genome and analyzed using CLC Genomics Workbench (variant detection module). The RNA from Brangus heifers were from reproductive and metabolic tissues, whereas the RNA from Nellore, Angus, and Holstein cattle were from tissues derived from studies of metabolism and health. Two SNP detection approaches were executed with the Brangus data: 1) samples were pooled and variant detection performed, and 2) SNP discovery was performed on each individual sample (8 heifers and 8 tissues). The two approaches revealed 1,157 SNP in the 62 genes. These SNP were then compared with those identified in the pooled samples of the other breeds. We observed 177 SNP that existed in RNA of Brangus and the other breeds. The shared SNP were within 15 genes with an average of 11.8 ± 2.0 SNP/gene. This approach identified SNP that may be useful in multi-breed genotyping strategies; however, the number of SNP detected in RNA across various tissues and breeds was minimal.