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United States Department of Agriculture

Agricultural Research Service

Research Project: DEVELOPMENT OF GENOMIC TOOLS TO STUDY RUMINANT RESISTANCE TO GASTROINTESTINAL NEMATODES

Location: Animal Genomics and Improvement Laboratory

Title: Identification of single nucleotide polymorphisms (SNPs)associated to Red Maasai x Dorper resistance to gastrointestinal parasite infections

Authors
item Benavides, Magda -
item SONSTEGARD, TAD
item Kemp, Steve -
item Mugambi, Jm -
item Gibson, John -
item Baker, Rl -
item VAN TASSELL, CURTIS

Submitted to: BARC Poster Day
Publication Type: Abstract Only
Publication Acceptance Date: March 14, 2013
Publication Date: April 15, 2013
Citation: Benavides, M., Sonstegard, T.S., Kemp, S., Mugambi, J., Gibson, J., Baker, R., Van Tassell, C.P. 2013. Identification of single nucleotide polymorphisms (SNPs)associated to Red Maasai x Dorper resistance to gastrointestinal parasite infections. BARC Poster Day. BARC {oster Day 2013 Abstract #3.

Technical Abstract: Gastrointestinal (GI) parasitic infection is a main health constraint that affects small ruminant production. Anthelmintic drugs are used to control parasites, however long-term use led to selection pressure, resulting in parasite resistance against all current chemical interventions available in the market. The aim of this study is to identify polymorphisms strongly associated with sheep host resistance against gastrointestinal parasite infections. A double backcross population of Red Maasai and Dorper sheep from the International Livestock Research Institute (ILRI) was genotyped with the OvineSNP50K BeadChip. Data for average fecal egg counts (AVFEC), packed cell volume (AVPCV), and live weight (AVLWT) were adjusted for fixed effects prior to setting the threshold for the tails of the distributions (10% most resistant and 10% most susceptible lambs). Single nucleotide markers (SNPs) were filtered for minor allele frequency, call rates per marker, and Hardy-Weinberg equilibrium criteria using PLink. Genome-wide significance threshold were defined after 100,000 permutations on EMMAX. Association analyses were calculated using QxPak v5.05 and significant SNPs with -log10 p-values >=4 were observed on 6, 7, and 7 chromosomes and 7, 9, and 8 chromosomic regions were detected for AVPCV, AVLWT, and AVFEC, respectively. No SNP was relevant for more than one trait. A set of 7, 10 and 9 SNPs explained 28.6%, 19.4% and 21.8% of the phenotypic variation of those traits. As a practical result, a panel with such markers could be used in Red Maasai x Dorper breeding programs to select for more resistant sheep. However, to determine the causal mutations that define more resistant Red Maasai x Dorper sheep, further studies will focus on 4, 3, and 3 SNPs that explained 21.8%, 11.2% and 13.4% of the phenotypic variation for AVPCV, AVLWT, and AVFEC, respectively, after a classification tree was used to calculate the best haplotype combination among most significant SNPs.

Last Modified: 9/10/2014