Genomic signatures for drylands adaptation at gene-rich regions in African zebu cattle

Tijjani, Abdulfatai; Salim, Bashir; Silva, Marcos Vinicius Barbosa da; Eltahir, Hamza A; Musa, Taha Hussein; Marshall, Karen; Hanotte, Olivier; Musa, Hassan Hussein

doi:10.1016/j.ygeno.2022.110423

Cited by 9 publications

(17 citation statements)

References 94 publications

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“…Illumina BovineSNP50 and BovineHD Bead-Chip) were used (Flori et al, 2014;Gautier et al, 2009). However, today, a growing number of studies are using high-throughput whole genome sequencing technologies and information (Table 1; Kim et al, 2020;Kim, Hanotte, et al, 2017;Taye, Lee, Caetano-Anolles, et al, 2017;Tijjani et al, 2019Tijjani et al, , 2022. Whole genome sequences of indigenous African humpless (taurine) and humped (zebu/ sanga) cattle were first reported and characterised by Kim, Hanotte, et al (2017) (Bioproject accession number PRJNA312138).…”

Section: T H E Con T R I Bu T Ion Of Ge Nom E -W I De Poly Mor Ph I S...mentioning

confidence: 99%

“…Interestingly, we found in African indicine a signature of selection ( XP‐EHH ) on BTA3 in a region intersecting with the prolactin‐releasing hormone gene ( PRLH ), which harbours a highly conserved missense variant at exon 2 (Kim, Hanotte, et al, 2017; Tijjani et al, 2022). This variant might be involved in the regulation of the expression and stimulation of the prolactin hormone (PRL) and its receptor (PRLR) (Kim, Hanotte, et al, 2017).…”

Section: Genomic Footprints Of Natural Selectionmentioning

confidence: 99%

“…Another region putatively associated with heat tolerance is found on BTA5. It harbours the homeobox genes, HOXC12 and HOXC13 , which have roles in determining skin thickness and the number of hair follicles (Makina et al, 2014; Taye, Lee, Caetano‐Anolles, et al, 2017; Tijjani et al, 2022). Besides environmental selection, it may also be argued that these footprints of selection involving coat colour and coat structural properties might have been directly influenced by aesthetic and social‐cultural preferences.…”

Section: Genomic Footprints Of Natural Selectionmentioning

confidence: 99%

“…FTO , IGF‐1 , ATRN , PRKCZ , ACLY, GHR and NFATC2 ) (Bahbahani et al, 2015; Taye, Lee, Caetano‐Anolles, et al, 2017). Contributing to the regulation of metabolic heat production, these genes may represent an adaptive response of African cattle to high‐temperature environments (Taye, Lee, Caetano‐Anolles, et al, 2017; Tijjani et al, 2022). Of particular interest are the candidate IGF‐1, ACLY and PRKCZ proteins, which are involved in insulin metabolism, carbohydrate regulation and lipid metabolic processes that are essential for the body's energy balance (Bahbahani et al, 2015; Taye, Lee, Caetano‐Anolles, et al, 2017; Tijjani et al, 2022).…”

Section: Genomic Footprints Of Natural Selectionmentioning

confidence: 99%

“…Indigenous African cattle genomes have now been extensively studied by researchers aiming to understand the genetic basis of their unique diversity, environmental adaptation, and to a lesser extent, production traits. More particularly, several studies have sought to unravel the genomic footprints of positive selection (Bahbahani et al, 2017;Bahbahani, Afana, et al, 2018;Bovine HapMap Consortium, 2009;Kim et al, 2020;Kim, Hanotte, et al, 2017;Mekonnen et al, 2019;Taye et al, 2018;Tijjani et al, 2019Tijjani et al, , 2022.…”

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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: T H E Con T R I Bu T Ion Of Ge Nom E -W I De Poly Mor Ph I S...mentioning

confidence: 99%

Section: Genomic Footprints Of Natural Selectionmentioning

confidence: 99%

Section: Genomic Footprints Of Natural Selectionmentioning

confidence: 99%

Section: Genomic Footprints Of Natural Selectionmentioning

confidence: 99%

mentioning

confidence: 99%

See 3 more Smart Citations

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

Kambal,

Tijjani,

Ibrahim

et al. 2023

Animal Genetics

Self Cite

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Signatures of positive selection for local adaptation of African native cattle populations: A review

AYALEW

Tarekegn

et al. 2023

Journal of Integrative Agriculture

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Whole genome sequences of 70 indigenous Ethiopian cattle

Ayalew,

Xiaoyun,

Tarekegn

et al. 2024

Sci Data

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Indigenous animal genetic resources play a crucial role in preserving global genetic diversity and supporting the livelihoods of millions of people. In Ethiopia, the majority of the cattle population consists of indigenous breeds. Understanding the genetic architecture of these cattle breeds is essential for effective management and conservation efforts. In this study, we sequenced DNA samples from 70 animals from seven indigenous cattle breeds, generating about two terabytes of pair-end reads with an average coverage of 14X. The sequencing data were pre-processed and mapped to the cattle reference genome (ARS-UCD1.2) with an alignment rate of 99.2%. Finally, the variant calling process produced approximately 35 million high-quality SNPs. These data provide a deeper understanding of the genetic landscape, facilitate the identification of causal mutations, and enable the exploration of evolutionary patterns to assist cattle improvement and sustainable utilization, particularly in the face of unpredictable climate changes.

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Genomic signatures for drylands adaptation at gene-rich regions in African zebu cattle

Cited by 9 publications

References 94 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

Signatures of positive selection for local adaptation of African native cattle populations: A review

Whole genome sequences of 70 indigenous Ethiopian cattle

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