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Genome wide association study reveals new candidate genes for resistance to nematodes in Creole goat

Silva, F.F., Bambou, J.C., Oliveira, J.A., Barbier, C., Fleury, J., Machado, T., Mandonnet, N.
Small ruminant research 2018 v.166 pp. 109-114
Nematoda, breeding programs, chromosomes, gastrointestinal nematodes, genes, genetic improvement, genome-wide association study, genotyping, goat diseases, goats, hemorrhage, immune response, inflammation, intestines, introgression, marker-assisted selection, muscles, quality control, quantitative trait loci, resistance mechanisms, single nucleotide polymorphism, statistical models, Guadeloupe
An alternative control for gastrointestinal nematode (GIN) infection in goats can be achieved by genetic improvement of the host resistance through identification of genes controlling the resistance mechanisms and their use in breeding programs under a marker-assisted selection or gene introgression frameworks. In this context, we aimed to develop genome wide association studies (GWAS) for resistance to H. contortus in Creole goats from Guadeloupe to identify possible candidate genes associated with GIN resistance in this population. Resistance was characterized by the fecal egg counting (FEC). A total of 182 Creole goats were phenotyped for FEC and genotyped through Illumina Goat SNP50 BeadChip. After SNP quality control analysis, 46,643 SNP markers were used for GWAS. The significant associations were identified by fitting a linear mixed model. A total of seven QTL (on the chromosomes 4, 6, 11, and 17) associated to FEC were reported and candidate genes recording was performed at these positions. The identified genes were related to the intestine damage (PROM1), inflammation process (FGFBP1), immune response (LIMCH1), hemorrhage control (ADAMTS3), and muscle weakness (SUCLG1). Network analysis provided annotation results linking all identified candidate genes, which are biologically related to resistance mechanisms approaching H. contortus infections.