Copy number variant-based genome wide association study reveals immune-related genes associated with parasite resistance in a heritage sheep breed from the United States

Abstract

Florida Native is a heritage sheep breed in the United States and expresses superior ability to regulate gastrointestinal nematodes. The objective of the present study was to investigate the importance of copy number variants (CNVs) on resistance to natural Haemonchus contortus infections. A total of 300 Florida Native sheep were evaluated. Phenotypic records included fecal egg count (FEC, eggs/gram), FAMACHA© score, percentage cell volume (PCV, %), body condition score (BCS) and average daily gain (ADG, kg). Sheep were genotyped using the GGP Ovine 50K single nucleotide polymorphism (SNP) chip. Log ratios from 45.2 k SNP markers spanning the entire genome were utilized for CNV detection. After quality control, 261 animals with CNVs and phenotypic records were used for the association testing. Association tests were carried out using correlation-trend test and principal component analysis correction to identify CNVs associated with FEC, FAMACHA©, PCV, BCS and ADG. Significant CNVs were detected when their adjusted p-value was