Genomic footprints of dryland stress adaptation in Egyptian fat-tail sheep and their divergence from East African and western Asia cohorts

Mwacharo, Joram M.; Kim, Eui-Soo; Elbeltagy, Ahmed R.; Aboul-Naga, Adel; Rischkowsky, Barbara; Rothschild, Max F.

doi:10.1038/s41598-017-17775-3

Cited by 57 publications

(56 citation statements)

References 78 publications

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“…). Intriguingly, CMPK1 has been identified as being under selection in Egyptian sheep populations adapted to hot dryland (Mwacharo ). The other candidate gene worth noting, identified on BTA24 (0.93–1.19 Mb) and linked to apoptosis, was NFATC1 ( NFAT ).…”

Section: Resultsmentioning

confidence: 99%

Genome‐wide scan reveals divergent selection among taurine and zebu cattle populations from different regions

Edea

Dadi

Dessie³

et al. 2018

Animal Genetics

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In this study, to identify genomic signatures of divergent selection, we genotyped 10 cattle breeds/populations (n = 275), representing eight Ethiopian cattle populations (n = 229) and two zebu populations (n = 46) adapted to tropical and sub-tropical environments, using the high-density single-nucleotide polymorphisms (SNPs) derived mainly from Bos indicus breeds, and using five reference taurine breeds (n = 212). Population genetic differentiation (F ST ) values across sliding windows were estimated between zebu and reference combined taurine breeds. The most differentiated regions (F ST ≥ 0.53), representing the top 1% smoothed F ST values, were considered to represent regions under diversifying selection. In total, 285 and 317 genes were identified in the comparisons of Ethiopian cattle with taurine and Asian zebu with taurine respectively. Some of these genes are involved in stress responses/thermo-tolerance and DNA damage repair (HSPA4, HSF1, CMPK1 and EIF2AK4), pigmentation (ERBB3 and MYO1A), reproduction/fertility (UBE2D3, ID3 and PSPC1), immune response (PIK3CD and AKIRIN2) and body stature and size (MBP2, LYN and NPM1). Additionally, the candidate genes were associated with functional terms (e.g. cellular response to stress, DNA repair, inflammatory response) important for physiological adaptation to environmental stresses. The results of our study may shed light on the influence of artificial and natural selection in shaping the genomic diversity of modern cattle breeds and also may serve as a basis for further genetic investigation of traits of tropical adaptation in cattle.

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Section: Resultsmentioning

confidence: 99%

Genome‐wide scan reveals divergent selection among taurine and zebu cattle populations from different regions

Edea

Dadi

Dessie³

et al. 2018

Animal Genetics

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“…However, interestingly enough, it also occurred when reports aiming at the identification of genomic signals of adaptation to extreme environments were considered. It is worth pointing out that most studies in this field aimed at the identification of genomic areas related to adaptation to high altitude 10,17 or to high temperature in basically arid environments 15,63 . Such works involved several sheep populations bred in different geographical areas highly contrasting in environments, production systems and goals 14,15,63 .…”

Section: Discussionmentioning

confidence: 99%

“…It is worth pointing out that most studies in this field aimed at the identification of genomic areas related to adaptation to high altitude 10,17 or to high temperature in basically arid environments 15,63 . Such works involved several sheep populations bred in different geographical areas highly contrasting in environments, production systems and goals 14,15,63 . Therefore, the ability to identify selection signatures related to thermotolerance or hypoxia may be affected by the influence of others more likely linked to production or reproduction performance.…”

Section: Discussionmentioning

confidence: 99%

Genomic scan of selective sweeps in Djallonké (West African Dwarf) sheep shed light on adaptation to harsh environments

Álvarez

Traoré

Pérez‐Pardal

et al. 2020

Sci Rep

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the Djallonké (West African Dwarf) sheep is a small-sized haired sheep resulting from a costly evolutionary process of natural adaptation to the harsh environment of West Africa including trypanosome challenge. However, genomic studies carried out in this sheep are scant. in this research, genomic data of 184 Djallonké sheep (and 12 Burkina-Sahel sheep as an outgroup) generated using medium-density SNP Chips were analyzed. Three different statistics (iHS, XP-EHH and nSL) were applied to identify candidate selection sweep regions spanning genes putatively associated with adaptation of sheep to the West African environment. A total of 207 candidate selection sweep regions were defined. Gene-annotation enrichment and functional annotation analyses allowed to identify three statistically significant functional clusters involving 12 candidate genes. Genes included in functional clusters associated to selection signatures were mainly related to metabolic response to stress, including regulation of oxidative and metabolic stress and thermotolerance. the bovine chromosomal areas carrying QtLs for cattle trypanotolerance were compared with the regions on which the orthologous functional candidate cattle genes were located. The importance of cattle BTA4 for trypanotolerant response might have been conserved between species. the current research provides new insights on the genomic basis for adaptation and highlights the importance of obtaining information from non-cosmopolite livestock populations managed in harsh environments.Drift and selection may cause selective sweep signatures on the genome, characterized by reduced diversity and extensive linkage disequilibrium. Favorable alleles increase in frequency more rapidly than expected for a neutral genetic scenario and further alter the allele frequencies of genomic variants near the beneficial mutation.

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“…According to Xu et al [4] fat tails represent the energy reserve necessary to survive critical conditions such as drought seasons and food shortage. This statement being emphasized by Mwacharo et al [5] who confirmed that the fat-tails are the predominant sheep across the deserts of northern Africa, and in the highlands, semi-arid and arid environments of eastern and southern Africa while the thin-tails occur in Sudan and in the sub-humid and humid regions of West Africa.…”

Section: Introductionmentioning

confidence: 93%

Novel and known signals of selection for fat deposition in domestic sheep breeds from Africa and Eurasia

Mastrangelo¹,

Bahbahani²,

Moioli³

et al. 2018

Preprint

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34Genomic regions subjected to selection frequently show signatures such as within-35 population reduced nucleotide diversity and outlier values of differentiation among differentially 36 selected populations. In this study, we analyzed 50K SNP genotype data of 373 animals belonging 37 to 23 sheep breeds of different geographic origins using the Rsb and F ST statistical approaches, to 38 identify loci associated with the fat-tail phenotype. We also checked if these putative selection 39 signatures overlapped with regions of high-homozygosity (ROH). The analyses identified novel 40 signals and confirmed the presence of selection signature in genomic regions that harbor candidate 41 genes known to affect fat deposition. Several genomic regions that frequently appeared in ROH 42 were also identified within each breed, but only two ROH islands overlapped with the putative 43 selection signatures. The results reported herein provide the most complete genome-wide study of 44 selection signatures for fat-tail in African and Eurasian sheep breeds; they also contribute insights 45 into the genetic basis for the fat tail phenotype in sheep, and confirm the great complexity of the 46 mechanisms that underlie quantitative traits, such as the fat-tail. 47 48 3 51been widely applied to livestock species to achieve more desirable/profitable phenotypes [1]. For 52 instance, sheep (Ovis aries) have been selected since domestication, approximately 9,000 years ago 53 [2]. This process of selection resulted in divergent sheep breeds, reared in different geographic 54 regions due to their different adaptability. Among these, fat-tail are an important class of sheep 55 breeds and represent about 25% of the world's sheep population [3] mainly distributed in the 56 Middle East, North and East Africa and Central Asia. According to Xu et al. [4] fat tails represent 57 the energy reserve necessary to survive critical conditions such as drought seasons and food 58 shortage. This statement being emphasized by Mwacharo et al. [5] who confirmed that the fat-tails 59 are the predominant sheep across the deserts of northern Africa, and in the highlands, semi-arid and 60 arid environments of eastern and southern Africa while the thin-tails occur in Sudan and in the sub-61 humid and humid regions of West Africa. 62The unique genetic patterns inscribed in the genome of individuals by natural and/or 63 artificial selection are defined as signatures of selection, which are usually regions of the genome 64 that harbor functionally important sequence variants [6]. Although human consumption of animal 65 fat has dramatically reduced in preference of leaner meat, the investigation of the potential 66 candidate genes involved in the fat-tail might contribute to exploring the genetics of fat deposition, 67 energy storage and adaptation to climate changes [7][8][9]. With the aim to identify candidate genes 68 with a potential role in these traits, several authors performed studies targeting the fat-tail 69 phenotype contrasted with the thi...

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Genomic footprints of dryland stress adaptation in Egyptian fat-tail sheep and their divergence from East African and western Asia cohorts

Cited by 57 publications

References 78 publications

Genome‐wide scan reveals divergent selection among taurine and zebu cattle populations from different regions

Genome‐wide scan reveals divergent selection among taurine and zebu cattle populations from different regions

Genomic scan of selective sweeps in Djallonké (West African Dwarf) sheep shed light on adaptation to harsh environments

Novel and known signals of selection for fat deposition in domestic sheep breeds from Africa and Eurasia

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