Tropically adapted cattle of Africa: perspectives on potential role of copy number variations

Wang, M. D.; Dzama, K.; Rees, D. J. G.; Muchadeyi, Farai C.

doi:10.1111/age.12391

Cited by 13 publications

(10 citation statements)

References 96 publications

(167 reference statements)

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“…; Wang et al . ; Pitt et al . ), we found a number of differentially methylated genes between Creole and Spanish groups implicated in several biological processes, such as immunity, nervous system processes, energy management, heat resistance and skin and coat attributes, which are key for survival in harsh environments (Table ).…”

Section: Discussionmentioning

confidence: 99%

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Genome‐wide differential DNA methylation in tropically adapted Creole cattle and their Iberian ancestors

2018

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Enhancing climate resilience and sustainable production for animals in harsh environments are important goals for the livestock industry given the predicted impacts of climate change. Rapid adaptation to extreme climatic conditions has already been imposed on livestock species, including those exported after Columbus's arrival in the Americas. We compared the methylomes of two Creole cattle breeds living in tropical environments with their putative Spanish ancestors to understand the epigenetic mechanisms underlying rapid adaptation of a domestic species to a new and more physiologically challenging environment. Reduced representation bisulfite sequencing was used to assess differences in methylation in Creole and Spanish samples and revealed 334 differentially methylated regions using high stringency parameters (P-value <0.01, ≥4 CpGs within a distance of 200 bp, mean methylation difference >25%) annotated to 263 unique features. Gene ontology analysis revealed candidate genes involved in tropical adaptation processes, including genes differentially hyper-or hypomethylated above 80% in Creole samples displaying biological functions related to immune response (IRF6, PTGDR, FAM19A5, PGLYRP1), nervous system (GBX2, NKX2-8, RPGR), energy management (BTD), heat resistance (CYB561) and skin and coat attributes (LGR6). Our results entail that major environmental changes imposed on Creole cattle have had an impact on their methylomes measurable today, which affects genes implicated in important pathways for adaptation. Although further work is needed, this first characterization of methylation patterns driven by profound environmental change provides a valuable pointer for the identification of biomarkers of resilience for improved cattle performance and welfare under predicted climatic change models.

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Section: Discussionmentioning

confidence: 99%

“…; Wang et al . ; Pitt et al . ), we lack understanding of relevant epigenetic function (see Varriale for a review).…”

Section: Introductionmentioning

confidence: 99%

Genome‐wide differential DNA methylation in tropically adapted Creole cattle and their Iberian ancestors

2018

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“…Gifford‐Gonzalez & Hanotte, ; Linseele, ). In addition, breed diversification has been a major factor in the zoogeography of African livestock, enabling domesticates to live in a wide variety of modern ecological zones (Bahbahani et al, ; Murray & Trail, ; Mwai, Hanotte, Kwon, & Cho, ; Wang, Dzama, Rees, & Muchadeyi, ). Thus, the broadening of the animal production climatic niche is associated with evolutionary trends, and it is highly likely that these were the mechanism for expansion of the climatic land use niche for domestic animals that we observed.…”

Section: Discussionmentioning

confidence: 99%

Reconstructing the climatic niche breadth of land use for animal production during the African Holocene

Phelps

Broennimann

Manning

et al. 2019

Global Ecol Biogeogr

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Aim: Domestic animals first appeared in the archaeological record in northern Africac. 9000 years before present and subsequently spread southwards throughout the continent. This geographic expansion is well studied and can broadly be explained in terms of the movement of pastoralist populations due to climate change. However, no studies have explicitly evaluated changes in the climatic niche of these domesticates. A priori, one cannot assume a relationship between the geographic spread of animal production and changes in climatic niche breadth because their relationship is highly variable. Therefore, we investigated Holocene changes in the climatic niche of domestic animals (animal production) and compared these to changes in the climatic niche of hunted terrestrial ungulates. Location: The African continent.Time period: 9000-500 BP.Major taxa studied: Domestic animals, hunted (wild) terrestrial ungulates.Methods: For the first time, we applied methods from environmental niche dynamics to archaeological data to reconstruct and quantify changes in the climatic niche breadth of animal production during the African Holocene. We used faunal remains from archaeological assemblages and associated radiocarbon dates to estimate the proportion of the African climate space used for animal production and hunting at 500-year intervals. Results:We found that the climatic niche of domestic species broadened significantly with the geographic spread, most notably during the termination of the African Humid Period, whilst no such broadening occurred for the climatic niche of hunted species. Main conclusions:Our results provide a quantitative measure of the extent to which humans have constructed and adapted the climatic niche of animal production to manage their domestic animals across increasingly diverse ecological conditions. By incorporating ecological analysis into estimations of past land use, our methods have

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“…Our findings reveal a close connection between genomic regions associated with morphometric traits and adaptive traits. For instance, two of the identified variants detected for morphometric traits in this study are directly linked to immune response, while several potential candidate genes have functional annotations for, e.g., signal transduction, metabolism, and immune response adaptation [134]. The comparison with previous studies confirms associations of the identified genes with selection signatures as well as immunity or resistance to diseases, feed efficiency and adaptation to harsh environments (heat stress, high altitude), addressing the main components of adaptation [4].…”

Section: Genomic Regions Associated With Morphometric and Adaptation mentioning

confidence: 96%

A multi-breed GWAS for morphometric traits in four Beninese indigenous cattle breeds reveals loci associated with conformation, carcass and adaptive traits

et al. 2020

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Background Specific adaptive features including disease resistance and growth abilities in harsh environments are attributed to indigenous cattle breeds of Benin, but these breeds are endangered due to crossbreeding. So far, there is a lack of systematic trait recording, being the basis for breed characterizations, and for structured breeding program designs aiming on conservation. Bridging this gap, own phenotyping for morphological traits considered measurements for height at withers (HAW), sacrum height (SH), heart girth (HG), hip width (HW), body length (BL) and ear length (EL), including 449 cattle from the four indigenous Benin breeds Lagune, Somba, Borgou and Pabli. In order to utilize recent genomic tools for breed characterizations and genetic evaluations, phenotypes for novel traits were merged with high-density SNP marker data. Multi-breed genetic parameter estimations and genome-wide association studies (GWAS) for the six morphometric traits were carried out. Continuatively, we aimed on inferring genomic regions and functional loci potentially associated with conformation, carcass and adaptive traits. Results SNP-based heritability estimates for the morphometric traits ranged between 0.46 ± 0.14 (HG) and 0.74 ± 0.13 (HW). Phenotypic and genetic correlations ranged from 0.25 ± 0.05 (HW-BL) to 0.89 ± 0.01 (HAW-SH), and from 0.14 ± 0.10 (HW-BL) to 0.85 ± 0.02 (HAW-SH), respectively. Three genome-wide and 25 chromosome-wide significant SNP positioned on different chromosomes were detected, located in very close chromosomal distance (±25 kb) to 15 genes (or located within the genes). The genes PIK3R6 and PIK3R1 showed direct functional associations with height and body size. We inferred the potential candidate genes VEPH1, CNTNAP5, GYPC for conformation, growth and carcass traits including body weight and body fat deposition. According to their functional annotations, detected potential candidate genes were associated with stress or immune response (genes PTAFR, PBRM1, ADAMTS12) and with feed efficiency (genes MEGF11 SLC16A4, CCDC117). Conclusions Accurate measurements contributed to large SNP heritabilities for some morphological traits, even for a small mixed-breed sample size. Multi-breed GWAS detected different loci associated with conformation or carcass traits. The identified potential candidate genes for immune response or feed efficiency indicators reflect the evolutionary development and adaptability features of the breeds.

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Tropically adapted cattle of Africa: perspectives on potential role of copy number variations

Cited by 13 publications

References 96 publications

Genome‐wide differential DNA methylation in tropically adapted Creole cattle and their Iberian ancestors

Genome‐wide differential DNA methylation in tropically adapted Creole cattle and their Iberian ancestors

Reconstructing the climatic niche breadth of land use for animal production during the African Holocene

A multi-breed GWAS for morphometric traits in four Beninese indigenous cattle breeds reveals loci associated with conformation, carcass and adaptive traits

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