Search for Selection Signatures Related to Trypanosomosis Tolerance in African Goats

Serranito, Bruno; Taurisson-Mouret, Dominique; Harkat, Sahraoui; Laoun, Abbas; Ouchene-Khelifi, N. A.; Pompanon, François; Benjelloun, Badr; Cecchi, Giuliano; Thévenon, Sophie; Lenstra, Johannes A.; Silva, Anne Da

doi:10.3389/fgene.2021.715732

Cited by 9 publications

(6 citation statements)

References 102 publications

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“…In addition, our study demonstrates that climate can indirectly impact the regulation of autoimmune responses in various goat breeds through its influence on their habitats [ 65 , 66 ]. Several novel genes ( LPP , DNAJC16 , SUGT1 , STARD10 , STX2 , CCR9 , and BANK1 ) have been identified as being associated with disease resistance and immune response for goat populations.…”

Section: Discussionmentioning

confidence: 99%

Selection signatures and landscape genomics analysis to reveal climate adaptation of goat breeds

Peng,

Zhang,

Gao

et al. 2024

BMC Genomics

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Goats have achieved global prominence as essential livestock since their initial domestication, primarily owing to their remarkable adaptability to diverse environmental and production systems. Differential selection pressures influenced by climate have led to variations in their physical attributes, leaving genetic imprints within the genomes of goat breeds raised in diverse agroecological settings. In light of this, our study pursued a comprehensive analysis, merging environmental data with single nucleotide polymorphism (SNP) variations, to unearth indications of selection shaped by climate-mediated forces in goats. Through the examination of 43,300 SNPs from 51 indigenous goat breeds adapting to different climatic conditions using four analytical methods: latent factor mixed models (LFMM), F-statistics (Fst), Extended haplotype homozygosity across populations (XPEHH), and spatial analysis method (SAM), A total of 74 genes were revealed to display clear signs of selection, which are believed to be influenced by climatic conditions. Among these genes, 32 were consistently identified by at least two of the applied methods, and three genes (DENND1A, PLCB1, and ITPR2) were confirmed by all four approaches. Moreover, our investigation yielded 148 Gene Ontology (GO) terms based on these 74 genes, underlining pivotal biological pathways crucial for environmental adaptation. These pathways encompass functions like vascular smooth muscle contraction, cellular response to heat, GTPase regulator activity, rhythmic processes, and responses to temperature stimuli. Of significance, GO terms about endocrine regulation and energy metabolic responses, key for local adaptation were also uncovered, including biological processes, such as cell differentiation, regulation of peptide hormone secretion, and lipid metabolism. These findings contribute to our knowledge of the genetic structure of climate-triggered adaptation across the goat genome and have practical implications for marker-assisted breeding in goats.

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Section: Discussionmentioning

confidence: 99%

Selection signatures and landscape genomics analysis to reveal climate adaptation of goat breeds

Peng,

Zhang,

Gao

et al. 2024

BMC Genomics

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“…In North Africa, Ouchene-Khelifi et al ( 2018 ), showed a genetic homogenization of the goat stock, probably due to anarchic crossbreeding of breeders subjected to increasing economic pressure. In East Africa, Serranito et al ( 2021b ) highlighted very pronounced levels of admixture for goat breeds of Uganda, Tanzania and Kenya. The authors drew attention to the potentially decisive causal role of various structures involving religious organizations, government institutions, non-governmental organization, such as Heifer International, British Farm-Africa, National Livestock Production Development Programs, German-GTZ, etc.…”

Section: Discussionmentioning

confidence: 99%

IBD sharing patterns as intra-breed admixture indicators in small ruminants

Blondeau Da Silva,

Mwacharo,

et al. 2023

Heredity

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In this study, we investigated how IBD patterns shared between individuals of the same breed could be informative of its admixture level, with the underlying assumption that the most admixed breeds, i.e. the least genetically isolated, should have a much more fragmented genome. We considered 111 goat breeds (i.e. 2501 individuals) and 156 sheep breeds (i.e. 3304 individuals) from Europe, Africa and Asia, for which beadchip SNP genotypes had been performed. We inferred the breed’s level of admixture from: (i) the proportion of the genome shared by breed’s members (i.e. “genetic integrity level” assessed from ADMIXTURE software analyses), and (ii) the “AV index” (calculated from Reynolds’ genetic distances), used as a proxy for the “genetic distinctiveness”. In both goat and sheep datasets, the statistical analyses (comparison of means, Spearman correlations, LM and GAM models) revealed that the most genetically isolated breeds, also showed IBD profiles made up of more shared IBD segments, which were also longer. These results pave the way for further research that could lead to the development of admixture indicators, based on the characterization of intra-breed shared IBD segments, particularly effective as they would be independent of the knowledge of the whole genetic landscape in which the breeds evolve. Finally, by highlighting the fragmentation experienced by the genomes subjected to crossbreeding carried out over the last few generations, the study reminds us of the need to preserve local breeds and the integrity of their adaptive architectures that have been shaped over the centuries.

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“…Although they may not be commercially valuable, they are endowed with unique abilities to survive in a particular environment or disease ( 8 ). The detection of signatures of selection in sheep populations originating from different geographical origins may detect potential candidate genes associated with different ecological adaptations ( 9 ). To date, several genome-wide SNP studies identified the genomic basis of adaptation of NA local sheep breeds to semi-arid ( 7 , 10 ), hot desert conditions ( 11 , 12 ), tolerance to environmental diseases ( 13–16 ), and signatures of domestication ( 1 ).…”

Section: Introductionmentioning

confidence: 99%

Refining the genomic profiles of North African sheep breeds through meta-analysis of worldwide genomic SNP data

Baazaoui,

Bedhiaf-Romdhani,

Mastrangelo

et al. 2024

Front. Vet. Sci.

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IntroductionThe development of reproducible tools for the rapid genotyping of thousands of genetic markers (SNPs) has promoted cross border collaboration in the study of sheep genetic diversity on a global scale.MethodsIn this study, we collected a comprehensive dataset of 239 African and Eurasian sheep breeds genotyped at 37,638 filtered SNP markers, with the aim of understanding the genetic structure of 22 North African (NA) sheep breeds within a global context.Results and discussionWe revealed asubstantial enrichment of the gene pool between the north and south shores of the Mediterranean Sea, which corroborates the importance of the maritime route in the history of livestock. The genetic structure of North African breeds mirrors the differential composition of genetic backgrounds following the breed history. Indeed, Maghrebin sheep stocks constitute a geographically and historically coherent unit with any breed-level genetic distinctness among them due to considerable gene flow. We detected a broad east–west pattern describing the most important trend in NA fat-tailed populations, exhibited by the genetic closeness of Egyptian and Libyan fat-tailed sheep to Middle Eastern breeds rather than Maghrebin ones. A Bayesian FST scan analysis revealed a set of genes with potentially key adaptive roles in lipid metabolism (BMP2, PDGFD VEGFA, TBX15, and WARS2), coat pigmentation (SOX10, PICK1, PDGFRA, MC1R, and MTIF) and horn morphology RXFP2) in Tunisian sheep. The local ancestry method detected a Merino signature in Tunisian Noire de Thibar sheep near the SULF1gene introgressed by Merino’s European breeds. This study will contribute to the general picture of worldwide sheep genetic diversity.

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Search for Selection Signatures Related to Trypanosomosis Tolerance in African Goats

Cited by 9 publications

References 102 publications

Selection signatures and landscape genomics analysis to reveal climate adaptation of goat breeds

Selection signatures and landscape genomics analysis to reveal climate adaptation of goat breeds

IBD sharing patterns as intra-breed admixture indicators in small ruminants

Refining the genomic profiles of North African sheep breeds through meta-analysis of worldwide genomic SNP data

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