Location: Bovine Functional Genomics
2013 Annual Report
Objective 2. Characterize genetic variation in small ruminants to develop selection tools for host resistance to parasites and their pathogenic effects. Genes and QTL in small ruminant genomes that influence host resistance to gastrointestinal nematodes will be identified.
Objective 3. Investigate the ruminant host transcriptome and immune responses to identify similarities and differences in response to parasitic infection across ruminants. Inter- and intra-species and breed differences in parasite-induced changes in the host transcriptome will be analyzed, and biological pathways underlying host resistance and their regulatory processes will be characterized.
A double backcross population of Red Maasai and Dorper sheep was genotyped using an OvineSNP50K BeadChip. Sophisticated statistical methods were developed and employed to ensure valid inference of the results from this study. Specifically, permutation testing was used to guard against deviations from normally distributed trait data. Data for three parasitological parameters (average fecal egg counts, packed cell volume, and animal live weight), were adjusted for fixed effects prior to setting the threshold for the tails of the distributions. Genome-wide significance threshold were defined after 100,000 permutations. Association analyses were calculated and statistically significant SNP markers were observed. Chromosomal regions were detected for association with parasite parameters. A set of 7, 10, and 9 SNP explained approximately 29, 19, and 22% of the phenotypic variation of those traits, respectively. As a practical result, a panel with such genetic markers could be used in Red Maasai x Dorper breeding programs to select for sheep with greater parasite resistance.
The transcriptome characterization of two breeds of sheep endemic to the Canary Islands, the Canaria Hair Breed and the Canaria sheep, was partially completed. The Canaria Hair Breed displays a greater resistance to barber's pole worm (Haemonchus contortus) infection than Canaria sheep, as manifested by reduced counts of fecal eggs and adult worm counts, as well as increased female worm stunting. Bioinformatics analysis of obtained sequence reads is in progress. However, a complete ovine transcriptome characterization, including transcript abundance estimation and detection of RNA editing and alternative splicing events, is hampered by the lack of a well-annotated ovine genome. A NIFA grant proposal was submitted to seek funding to improve genome annotation and to develop and integrate bioinformatics tools and methods needed for RNA sequencing analysis.
Parasite-naïve dairy goats of the Alpine breed were obtained at birth and thirty were orally infected with barber's pole worm larvae. The remaining six goat kids were not infected and will serve as controls. The experimental infection is expected to be completed by mid-July and will be used to study correlations between parasitological variables and transcriptomics parameters during the next year.
Van, M., Van, C., Borloo, J., Rinaldi, M., Li, R.W., Chiers, K., Van Den Broeck, W., Vercruysse, J., Claerebout, E., Geldhof, P. 2013. Granule-exocytosis of granulysin and granzyme B as a potential key mechanism in vaccine-induced immunity in cattle against the nematode ostertagia ostertagi. Infection and Immunity. 81(15):1798-1809.
Dreesen, L., Rinaldi, M., Chiers, K., Li, R.W., Geurden, T., Van Den Broeck, W., Goddeeris, B., Vercruysse, J., Claerebout, E., Geldhof, P. 2012. Micro array analysis of the intestinal host response in Giardia duodenalis assemblage E infected cattle. PLoS One. 7(7):e40985.
Li, R.W., Choudhary, R.K., Capuco, A.V., Urban, Jr., J.F. 2012. Exploring the host transcriptome for mechanisms underlying protective immunity and resistance to helminth infection in ruminants. Veterinary Parasitology. 190(1-2):1-11.
Leski, T., Bangura, U., Jimmy, D.H., Ansumana, R., Lizewski, S.E., Li, R.W., Stenger, D.A., Taitt, C.R., Vora, G. 2013. Identification of blaOXA-51, blaOXA-58, blaDIM-1 and blaVIM carbapenemase genes in hospital enterobacteriaceae isolates from Sierra Leone. Journal of Clinical Microbiology. 51:2435-2438.
Li, R.W., Sperling, A.K. 2013. The IGF2 Locus. Journal of Clinical Microbiology. 51(7):2435-2438.
Marshall, K., Nagda, S., Gibson, J.P., Sonstegard, T.S., Hanotte, O., Silva, M.V., Baker, L., Van Tassell, C.P. 2013. Quantitative trait loci for resistance to Haemonchus contortus under artificial challenge in Red Maasai and Dorper sheep of East Africa. Animal Genetics. 44(3):285-295.