Disease & heat resistance

Runs of homozygosity in sheep selected for gastrointestinal nematode resistance

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Abstract

This study aimed to identify and characterize runs of homozygosity (ROH) patterns to identify regions potentially associated with gastrointestinal nematode (GIN) resistance in Santa Ines sheep. The phenotypic data encompassed 5,529 records from 1,703 naturally infected animals. A total of 571 animals were genotyped with the Ovine SNP50 Genotyping BeadChip (Illumina, Inc.), which were classified according to their response to parasitic infection as susceptible (n=248), resilient (n=217), and resistant (n=106), considering resistance phenotypes based on packed cell volume, fecal egg counts, and ocular conjunctiva coloration. ROH analyses were performed separately for each phenotypic group (susceptible, resilient, and resistant). The genotype quality control included only SNPs located on autosomes (Oar_v3.1), SNPs with MAF > 5%, call rate > 95%, and those in Hardy-Weinberg equilibrium (p 95% were retained for analysis. ROH were identified using PLINK software and ROH hotspots were identified by considering the top 1% of SNPs distribution within a ROH. The distribution of ROH by length revealed that the Santa Ines genome exhibits a high frequency of small (2-4 Mb) and medium (4-8 Mb) ROH segments, comprising 74% of all ROH observed. A total of 468, 390 and 417 SNPs from the top 1% SNP distribution were identified for the susceptible, resilient and resistant groups, respectively. All the phenotypic groups shared a total of 112 SNPs distributed on OAR16 (n=70), OAR6 (n=23), and OAR14 (n=19), suggesting the presence of common variants related to basal defense mechanisms against parasites. A total of 35, 41 and 31 genes were identified in ROH hotspots from susceptive, resilient, and resistant groups. The ANKH, KCNIP4, SLIT2, CDH8, CDH18, and MYO10 genes were described for all groups. Resilient and resistant groups shared the DOCK5 gene, susceptible and resistant groups shared the MARCHF11, TRIO, and OTULINL genes, whereas susceptible and resilient groups shared the PROC, ZNF622, ADGRA3, ZCCHC4, PPARGC1A, ANAPC4, UGGT1, DHX15, TBC1D19, IWS1, and SAP130 genes. The functional enrichment analysis by DAVID tool revealed significant Gene Ontology terms related to cell adhesion, ion metabolism, vascular endothelial growth factor, response to estrogen, aminoglycan metabolism, and proteoglycan metabolism. The ROH hotspots identified in the current study provide an insight into the variation in response to the GIN infection in Santa Inês sheep.

Keywords: 2026

How to Cite:

Castro, V., Freitas, L., Paz, C., Pereira, L., Peripolli, E., Rodrigues, J. & Stafuzza, N., (2026) “Runs of homozygosity in sheep selected for gastrointestinal nematode resistance”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2280600. doi: https://doi.org/10.31274/wcgalp.23450

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