Hereditary Genetics: Current Research

Landscape Genomics and Signature Selection to Understand the Genetic Adaptation of Indigenous Cattle

8^th World Congress on Epigenetics and Chromosome

August 17, 2021 | Webinar

Goitom S, Mathew G, Francis K and Kiplangat N

Department of Animal Sciences, Jomo Kenyatta University of Agriculture & Technology, Kenya.
Department of Animal Sciences, Egerton University, Kenya

Posters & Accepted Abstracts: Hereditary Genet

Abstract:

Results: Signature analysis is one of the techniques which reveals genetic information in relation to adaptive and productive characteristics of cattle populations. Previous studies showed that indigenous cattle populations of Eritrea adapted to different ecological conditions, and have high morphological diversity with medium to high genetic diversity. Therefore, this study aimed to produce additional information of variability of indigenous cattle by selecting signatures in different Agro- Ecological Zones (AEZs). Blood samples were collected from 188 animals (59, 63 and 66 mature cows from western lowlands, highlands and eastern lowlands AEZs respectively) from 27 cattle populations. 1,027,008 autosomal Single Nucleotide Polymorphisms (SNPs) for cattle populations in specific AEZ were produced after filtered for call rate >98%, Minor Allele Frequency (MAF) >5%, pruning for Linkage Disequilibrium (LD) with 50 5 2 and HWE (P >0.001). Signature analysis was based on mean FST values. A threshold cutting of the upper 1% was used to delineate extreme values to determine candidate regions. Monomorphic SNPs (MAF <0.05) were produced 0.157, 0.163 and 0.150 for highland, western lowland and eastern lowlands respectively. Expected heterozygosity (HE) 0.261, 0.264 and 0.268 were for cattle populations in highland, western lowland and eastern lowland respectively. Isolation by Distance (IBD) was evaluated based on two geographical distances and barriers among cattle population found in different AEZs. 25.1% (R2) of the variation is explained by the barrier of western escarpment found between highland and western lowland AEZs while only 2.8% is explained by the barrier of eastern escarpment which is found between highland and eastern lowland of cattle populations. 122 genomic regions with elevated FST were found and it overlapped with nine genes associated with missense variants (IFNAR2, IFNAR2, CASR, AHSG, ATP1B3, AIRE, ROBO2, SCHIP1 and PARS2). Genes were annotated for Gene Ontology (GO). These genes have function on mineral homeostasis, energy metabolism, and immune responses. Specifically, SCHIP1 gene has a function on head and facial morphology, locomotion, and skeletal and muscle system development with deleterious effect. The associations have relationships with characterization ICPs and need to consider in setting breeding program and adaptation.