SNP Discovery for QTL Associated with Grazing Distribution in Angus Cattle Using RNA-Seq

Grazing distribution is important for pasture management in beef cattle production systems. In mountainous terrain, abiotic factors such as steep slope and high elevation often yield concentrated grazing near riparian areas and limited livestock use in uplands. While management practices (fencing, water development, and herding) are effective in improving grazing distribution, these practices are costly and labor intensive. Previous research suggests that the traits used in indices to quantify grazing distribution are moderately heritable; therefore, genomic selection could be used to improve grazing distribution. Five QTL and underlying candidate genes (ACN9, FAM48A, GRM5, MAML3, and RUSC2) have been determined to be associated with grazing distribution traits in cattle. The objective of this study was to further examine these candidate genes and identify SNP that may then be incorporated into a previously developed 50-SNP panel used for genotype associations with grazing distribution phenotypes. Sequencing of RNA (RNA-Seq) yielded 30 million reads (single-read) per sample from 6 tissues (aorta, LM muscle, lung, pulmonary artery, and right and left ventricle) collected as part of an altitude tolerance study of Angus cattle. These tissues were from 10 steers with outlying pulmonary arterial pressure observations and unique sires. Sequences were assembled to the annotated bovine reference genome (UMD3.1; release annotation 87) and analyzed using CLC Genomics Workbench (version 8.0). Variant detection was performed using two methods: 1) individual samples and 2) a pool of all samples. No variants were detected in GRM5, MAML3, and RUSC2; however, individual sample analysis identified 30 SNP within ACN9 and FAM48A and pooled sample analysis identified 184 SNP within ACN9 and FAM48A. Twenty-one SNP were identified in both approaches. The Ensemble Variant Effect Predictor was used to determine the functional consequence of each SNP. Of the 21 SNP, 16 were intronic, four were exonic, and one was reported to be a downstream variant and a splice acceptor variant. The SNP discovered using RNA-Seq technology were compared to the exonic SNP in dbSNP within the 5 candidate genes. There were 1,663 exonic SNP in dbSNP in these genes. One synonymous SNP, located within ACN9 (rs382949979), was observed in both data from RNA-Seq and dbSNP. In summary, 21 SNP were discovered in two of the five candidate genes underlying QTL associated with grazing distribution. These SNP will be incorporated in a new genotyping panel to examine associations with the grazing distribution phenotypes.