Genome-wide local ancestry and evidence for mitonuclear coadaptation in African hybrid cattle populations

Ward, James A.; McHugo, Gillian P.; Dover, Michael J.; Hall, Thomas J.; Ng'ang'a, Said I; Sonstegard, Tad S.; Bradley, Daniel G.; Frantz, Laurent; Salter‐Townshend, Michael; MacHugh, David E.

doi:10.1016/j.isci.2022.104672

Cited by 18 publications

(24 citation statements)

References 85 publications

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“…However, hybridisation comes at a cost and beyond F1 unselected hybrids may have reduced fitness (Adavoudi & Pilot, 2021). Of relevance here, two recent studies have reported in African hybrid cattle populations signatures of positive selection in genome regions including genes involved in nuclear‐mitochondrial DNA interactions and reproduction (Kwon et al, 2022; Ward et al, 2022).…”

Section: Discussionmentioning

confidence: 93%

“…Moving to West Africa, a close relationship was found between the zebu breeds in Cameroon and Nigeria, with a higher proportion of zebu genetic background in these populations compared with the zebu introgressed West African taurine (Ibeagha‐Awemu et al, 2019). Recent studies have also explored maternal and/or paternal DNA markers to trace the demography of African cattle (Bradley et al, 1994; Kambal et al, 2021; Kwon et al, 2022; Mauki et al, 2021; Pérez‐Pardal et al, 2010; Ward et al, 2022). All these studies support the fact that the genetic backgrounds of different ancestral origins, admixed and selected over time in different proportions according to the geography and environment of the continent, are at the roots of the success of African cattle pastoralism.…”

Section: The Contribution Of Genome‐wide Polymorphism Studies To the ...mentioning

confidence: 99%

“…A dominant zebu genome influence is now visible in nearly all indigenous African cattle populations with the exception of taurine populations living deep within the tsetse belt in West Africa. Also, all African cattle have retained their maternal mitochondrial taurine ancestry and it has recently been shown that the ancestral incompatibility between the mitochondrial DNA and the autosomal genome has contributed to the shaping of the autosomal genome of African cattle (Kwon et al, 2022; Ward et al, 2022).…”

Section: Domestication Admixture and Introgressions Have Shaped The G...mentioning

confidence: 99%

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Candidate signatures of positive selection for environmental adaptation in indigenous African cattle: A review

Kambal,

Tijjani,

Ibrahim

et al. 2023

Animal Genetics

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Environmental adaptation traits of indigenous African cattle are increasingly being investigated to respond to the need for sustainable livestock production in the context of unpredictable climatic changes. Several studies have highlighted genomic regions under positive selection probably associated with adaptation to environmental challenges (e.g. heat stress, trypanosomiasis, tick and tick‐borne diseases). However, little attention has focused on pinpointing the candidate causative variant(s) controlling the traits. This review compiled information from 22 studies on signatures of positive selection in indigenous African cattle breeds to identify regions under positive selection. We highlight some key candidate genome regions and genes of relevance to the challenges of living in extreme environments (high temperature, high altitude, high infectious disease prevalence). They include candidate genes involved in biological pathways relating to innate and adaptive immunity (e.g. BoLAs, SPAG11, IL1RL2 and GFI1B), heat stress (e.g. HSPs, SOD1 and PRLH) and hypoxia responses (e.g. BDNF and INPP4A). Notably, the highest numbers of candidate regions are found on BTA3, BTA5 and BTA7. They overlap with genes playing roles in several biological functions and pathways. These include but are not limited to growth and feed intake, cell stability, protein stability and sweat gland development. This review may further guide targeted genome studies aiming to assess the importance of candidate causative mutations, within regulatory and protein‐coding genome regions, to further understand the biological mechanisms underlying African cattle's unique adaption.

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Section: Discussionmentioning

confidence: 93%

Section: The Contribution Of Genome‐wide Polymorphism Studies To the ...mentioning

confidence: 99%

Section: Domestication Admixture and Introgressions Have Shaped The G...mentioning

confidence: 99%

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Candidate signatures of positive selection for environmental adaptation in indigenous African cattle: A review

Kambal,

Tijjani,

Ibrahim

et al. 2023

Animal Genetics

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“…Asian and American indicine cattle representing four breeds [29,30], 45 Iberian cattle representing 13 breeds [31], and 31 African taurine cattle representing two breeds [29,32]. In addition, 12 Criollo cattle representing the Senepol breed were obtained from the WIDDE database [33].…”

Section: Bovinehd 777k Array Datamentioning

confidence: 99%

“…While there is no question on whether zebu cattle have been directly imported from South Asia, it is unclear whether this accounts for all of the zebu ancestry evident in South and Central American cattle [14]. In Africa a gradient of zebu ancestry is present, escalating across the continent from West to East Africa [16][17][18][19][20], Therefore, it is plausible that some of the zebu ancestry for certain Criollo breeds could be attributed to historical African cattle importation [15].…”

Section: Introductionmentioning

confidence: 99%

Genomic Insights into the Population History and Adaptive Traits of Latin American Criollo Cattle

Ward,

Ng’ang’a,

Randhawa

et al. 2023

Preprint

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Criollo cattle, descendants of animals brought by Iberian colonists to the Americas, have been subject to centuries of natural and human-mediated selection in novel tropical agroecological zones. Consequently, these breeds have evolved distinct characteristics such as resistance to disease and exceptional heat tolerance. In addition to European taurine (Bos taurus) ancestry, it has been proposed that gene flow from African taurine and Asian zebu (Bos indicus) cattle has shaped the ancestry of Criollo cattle. In this study, we analysed Criollo breeds from Colombia and Venezuela using whole genome sequencing data to examine population structure and admixture at very high resolution. We did not detect evidence of African taurine admixture in Criollo cattle; however, there was evidence of longstanding zebu ancestry in one breed (Hartón del Valle). In addition, we detected selection signatures associated with a myriad of adaptive traits, revealing genes linked to thermotolerance, reproduction, fertility, immunity, and distinct coat and skin coloration traits. This study underscores the remarkable adaptability of Criollo cattle and highlights the genetic richness and potential of these breeds in the face of climate change, habitat flux, and disease challenges. Further research is warranted to leverage these findings for more effective and sustainable cattle breeding programmes.

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Assessment of Genomic Diversity and Selective Pressures in Crossbred Dairy Cattle of Pakistan

Nisa,

Naqvi,

Arshad

et al. 2024

Biochem Genet

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Genome-wide local ancestry and evidence for mitonuclear coadaptation in African hybrid cattle populations

Cited by 18 publications

References 85 publications

Candidate signatures of positive selection for environmental adaptation in indigenous African cattle: A review

Candidate signatures of positive selection for environmental adaptation in indigenous African cattle: A review

Genomic Insights into the Population History and Adaptive Traits of Latin American Criollo Cattle

Assessment of Genomic Diversity and Selective Pressures in Crossbred Dairy Cattle of Pakistan

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