Location: Genetics and Animal Breeding
2018 Annual Report
Accomplishments
1. Genetic factors are associated with myoglobin concentration of porcine longissimus muscle. A recent increase in consumer complaints about light colored pork muscles is a growing concern to the pork industry. Consumers prefer a redder-colored lean, especially consumers in Asian export markets. As myoglobin is the primary red pigmentation in porcine muscles, ARS scientists at Clay Center, Nebraska conducted a genome-wide association analysis to identify genetic markers associated with this important trait. Results indicate there are at least two major regions of the genome affecting myoglobin concentration as well as several other regions with minor effects. These results indicate a primary factor associated with myoglobin concentration is the percentage of different fiber types represented in the lean tissue, which contradicts a common belief that fiber type distribution within muscles is similar across animals within a species. With our enhanced knowledge of myoglobin concentration in muscles, selection methods can now be developed to improve pork color which may subsequently improve muscle pH as well as other quality attributes, and improve overall pork quality and subsequent consumer demand.
2. Copy number variation (CNV) of genomic DNA segregating in commercial pigs was quantified. Genome-wide association studies have made thousands of connections between single nucleotide polymorphisms (SNP) and phenotypes, but this type of variation only represents a portion of the total heritable genetic variation. Hence, determining other types of DNA variation that may make substantial contributions to variation in complex traits is a meaningful goal. Copy number variations (CNV) are gains and losses of large regions of genomic sequence between individuals of a species (ranging from thousands to nearly a million bases) and have been associated with phenotypic differences in humans and mouse. CNV can disrupt genes or enhance the amount of gene product if a complete gene is within a CNV region, and has been duplicated one or more times. Utilizing 240 sequenced genomes of commercial pigs, ARS scientists at Clay Center, Nebraska, identified 2,920 CNV covering approximately 1.8% of the swine genome. A larger than expected number of genes overlapped by CNV were found to be involved in the neurophysiological processing of environmental stimuli. Additionally, CNV were shown to overlap several known regions of DNA that correlate with variation in economically relevant swine phenotypes. The focus of future work will be to discover the extent to which CNV affect traits of economic interest and how to incorporate them into genomic selection systems.
Review Publications
Oliver, W.T., Keel, B.N., Lindholm-Perry, A.K., Horodyska, J., Foote, A.P. 2018. The effects of Capn1 gene inactivation on the differential expression of genes in skeletal muscle. Gene. 668:54-58. https://doi.org/10.1016/j.gene.2018.05.040.
Keel, B.N., Deng, B., Moriyama, E.N. 2018. MOCASSIN-prot: A multi-objective clustering approach for protein similarity networks. Bioinformatics. 34(8):1270-1277. https://doi.org/10.1093/bioinformatics/btx755.
Cross, A.J., Keel, B.N., Brown-Brandl, T.M., Cassady, J.P., Rohrer, G.A. 2018. Genome-wide association of changes in swine feeding behaviour due to heat stress. Genetics Selection Evolution. 50:11. https://doi.org/10.1186/s12711-018-0382-1.
Keel, B.N., Zarek, C.M., Keele, J.W., Kuehn, L.A., Snelling, W.M., Oliver, W.T., Freetly, H.C., Lindholm-Perry, A.K. 2018. RNA-seq meta-analysis identifies genes in skeletal muscle associated with gain and intake across a multi-season study of crossbred beef steers. BMC Genomics. 19:430. https://doi.org/10.1186/s12864-018-4769-8.
Keel, B.N., Snelling, W.M. 2018. Comparison of Burrows-Wheeler transform-based mapping algorithms used in high-throughput whole-genome sequencing: application to Illumina data for livestock genomes. Frontiers in Genetics. 9:35. https://doi.org/10.3389/fgene.2018.00035.
Cross, A.J., King, D.A., Shackelford, S.D., Wheeler, T.L., Nonneman, D.J., Keel, B.N., Rohrer, G.A. 2018. Genome-wide association of myoglobin concentrations in pork loins. Meat and Muscle Biology. 2(1):189-196. https://doi.org/10.22175/mmb2017.08.0042.
