Genetic improvement in livestock, particularly dairy cattle, has been a priority for both industry and researchers for nearly a century. While the animal itself is the foundation for improvement, our research and the implementation of improvement has progressed with developing technologies and priorities. In terms of genetics, we have evolved from basic measures of heritability to identifying specific mutations and their biological role affecting a trait. My research focuses on population structure and trait association in domestic animals using high-density genome-wide single-nucleotide polymorphism (SNP) array data and fine-mapping sequence data. My end goal is to conduct research that will assist in the genetic improvement of domestic animals through an increased understanding of the genetic mechanisms controlling biological pathways and the development of genomic tools for implementation.
Two such projects in my lab include the African Goat Improvement Project (AGIN) and thermo-tolerance in tropical cattle. AGIN is a highly collaborative effort between international and local researchers working towards the improvement of African goat populations for small-holder farmers. Here, I lead the genetic analysis of indigenous goat populations to lay the foundation for future selection and conservation programs. I utilize genetic data to identify distinct breeds, degrees of admixture, and relationship to adaptive traits of body size and climate resiliency. Preliminary data of body measurements and genotype show breed variation. Genetic population structure reflects breed and country of origin and a possible manifestation of selection between European and African goats. There are also potential regions of the genome distinguishing modernized breeds of European ancestry as opposed to indigenous African breeds. Future work includes the establishment of community based breeding programs and more in-depth trait phenotyping of specific populations.
Similarly, I have investigated tropical cattle breeds demonstrating thermo-tolerance due to their unique “slick” hair coat. This short, fine, sleek hair coat is an adaptive mechanism for tropical cattle to manage the hot, humid temperatures while maintaining optimal levels of milk production and reproductive function. A thorough understanding of population structure, including ancestral breed relationship to the tropical cattle was integral for designing a genome-wide association study (GWAS) for the SLICK phenotype. Typically, the tropical breeds show the SLICK phenotype making it impractical to do a within breed GWAS. However, by utilizing the ancestral breeds of their origin as non-SLICK control animals, population structure was minimized when focusing on the SLICK phenotype in the GWAS. In addition, runs of homozygosity, signatures of selection, and haplotype analysis all confirmed an associated 0.5Mb region of interest on chromosome 20 highlighting the SKP2, SPEF2, and PRLR genes as candidates for SLICK. Current research is investigating the specific causal mutations within the different tropical cattle breeds.
This research is a snapshot of the genomic investigation of livestock being conducted in my lab. Each species, breed, and trait offers a unique challenge in designing the population or trait association projects underway, but allows us to build upon an ever growing foundation of knowledge in how to design and manage effective projects that assist in the genetic improvement of livestock.