Whole Genome Resequencing Reveals Genetic Diversity and Selection Signatures of Ethiopian Indigenous Cattle Adapted to Local Environments

Abstract

Cattle are among the most important domesticated bovid species in the world, of which Ethiopia possesses large populations adapted to different agro-ecologies and production systems. Though several molecular population genetic studies have been done on Ethiopian indigenous cattle, genomic diversity and selection signatures pertinent to adaptation to the different local environments have yet to be comprehensively characterized. Here, the whole genome sequences of 151 samples from 14 Ethiopian indigenous cattle populations were analyzed to assess genomic diversity and differentiation as well as signatures of positive selection (using Hp, iHS, FST, and XP-CLR) in comparison to Sudanese zebu, Asian zebu, Ankole, and African and European taurine cattle. High genomic differentiation was observed between Ethiopian and non-Ethiopian cattle populations, while low genomic differentiation and inbreeding were present between and within Ethiopian cattle populations. Sixteen genome regions overlapping with 40 candidate genes were commonly identified by at least three genome scan methods. High frequencies of missense SNPs in ITPR2, CHADL, GNAS, STING1, and KIT genes with high haplotype differentiations were observed in Ethiopian cattle compared to non-Ethiopian cattle. The candidate genes were significantly associated with several biological functions and molecular pathways responsible for nutrient metabolism, skeletal development, immune response, reproduction, water balance, coat color pigmentation, and circulatory homeostasis. Our results provide new insights into the adaptation of the Ethiopian indigenous cattle to the country’s diverse environments.

Genome-wide diversity and admixture of five indigenous cattle populations from the Tigray region of northern Ethiopia

“…However, the number and length of ROH observed in the Tigray cattle were similar to the one reported for other Ethiopian breeds included in our study (Horro, Fogera, Borana, and Afar). It suggests common breeding history among Ethiopian cattle breeds, while PCA and admixture results suggest close genetic relationships among the Ethiopian cattle as recently showed in a genome analysis including 14 Ethiopian indigenous cattle breeds (Terefe et al, 2023).…”

“…However, it should be emphasized that indels have been given so far less attention in cattle genomic analyses ( Stafuzza et al, 2017 ), despite being part of the important drivers of phenotypic and genetic diversity ( Iqbal et al, 2019 ). Most of the whole genome analyses on African cattle breeds were based on SNPs ( Kim et al, 2017 ; Tijjani et al, 2019 ; Kim et al, 2020 ; Jang et al, 2022 ; Mauki et al, 2022 ; Terefe et al, 2022 ; Terefe et al, 2023 ), while our study is the first to report indels for Ethiopian cattle.…”

“…However, it should be noted that polymorphism detection relies on sequence alignment against a single genome of reference, which will still introduce biases in the identification of SNPs following the genome of reference chosen. Recently, a few studies ( Kim et al, 2020 ; Jang et al, 2022 ; Terefe et al, 2022 ; Terefe et al, 2023 ) have reported the whole-genome characterisation of Ethiopian indigenous cattle, making it the African country with the largest number of cattle genome sequences available. However, they are still several main gaps in our knowledge with cattle populations from some geographic areas and cattle populations living in extreme environments yet to be characterised at the whole genome level ( Edea et al, 2013 ; EBI, 2016 ).…”

“…However, they are still several main gaps in our knowledge with cattle populations from some geographic areas and cattle populations living in extreme environments yet to be characterised at the whole genome level ( Edea et al, 2013 ; EBI, 2016 ). For instance, all the previous whole-genome based characterization studies on Ethiopian cattle populations ( Kim et al, 2020 ; Jang et al, 2022 ; Terefe et al, 2022 ) did not include any Tigray cattle, with the exception of one Tigray cattle population (Begait) ( Terefe et al, 2023 ).…”

Genetic Diversity and Selection Signatures in Economically Important Traits of Ethiopian Indigenous Cattle Breed as a Base for Dairy Cattle Genetic Improvement: A Review

“…The candidate genes have different biological processes, cellular and molecular functions and pathways responsible for immune response for disease resistance and adaptation for environmental stress. For example the function of MZB1 gene is related to the endoplasmic reticulum calcium ion homeostasis, cellular signal transduction, B cell activation and T cell proliferation; and STING1 gene is responsible to the innate immune signaling response to protect the host against viral and bacterial infections (Terefe et al, 2023). According to reports, these genes responsible for environmental adaptation, disease resistance and immunity were continuously detected in the genome of the African livestock population due to the retained synonymous and missense mutations creating polymorphism in a single gene and gene segment's (Taye et al, 2017;Terefe et al, 2023;Getinet, 2016;Adebabay, 2018;Edea et al, 2018).…”