Genome-Wide Variation, Candidate Regions and Genes Associated With Fat Deposition and Tail Morphology in Ethiopian Indigenous Sheep

Ahbara, Abulgasim; Bahbahani, Hussain; Almathen, Faisal; Al-Abri, Mohammed; Agoub, Mukhtar Omar; Abeba, Ayelle; Kebede, Abebaw; Musa, Hassan Hussein; Mastrangelo, Salvatore; Pilla, Fabio; Ciani, Elena; Hanotte, Olivier; Mwacharo, Joram M.

doi:10.3389/fgene.2018.00699

Cited by 73 publications

(104 citation statements)

References 64 publications

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“…The availability of single nucleotide polymorphism (SNP) panels consisting of thousands of markers has greatly improved the power of genome‐wide studies allowing the identification of highly differentiated genomic regions between breeds. In sheep, several studies have been conducted to identify the genomic regions involved in breed‐associated phenotypic differences (e.g., Ahbara et al, ; Fariello, Servin, Tosser‐Klopp, Rupp, & Moreno, ; Kijas et al, ). Many of these studies are performed based on the comparison among genetically distant breeds.…”

Section: Introductionmentioning

confidence: 99%

Combined approaches to identify genomic regions involved in phenotypic differentiation between low divergent breeds: Application in Sardinian sheep populations

Mastrangelo

Jemaa

Sottile

et al. 2019

J Animal Breeding Genetics

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Selective breeding has led to modifications in the genome of many livestock breeds.In this study, we identified the genomic regions that may explain some of the phenotypic differences between two closely related breeds from Sardinia. A total of 44 animals, 20 Sardinian Ancestral Black (SAB) and 24 Sardinian White (SW), were genotyped using the Illumina Ovine 50K array. A total of 68, 38 and 15 significant markers were identified using the case-control genome-wide association study (GWAS), the Bayesian population differentiation analysis (F ST ) and the Rsb metric, respectively. Comparisons among the approaches revealed a total of 22 overlapping markers between GWAS and F ST and one marker between GWAS and Rsb. Three markers detected by Rsb were also located near (<2 Mb) to highly significant regions identified by GWAS and F ST analyses. Moreover, one candidate marker identified by GWAS and F ST approaches was located in a run of homozygosity island that was shared by both breeds. We identified several genes involved in many phenotypic differences (such as stature and growth, reproduction, ear size, coat colour, behaviour) between the two analysed breeds. This study shows that combining several genome-wide approaches could improve discovery of regions involved in the variability of breeding traits and responsible for the phenotypic diversity even between closely related breeds. Overall, the combination of such genome-wide methods can be extended to other livestock breeds that share between them a similar genetic background, to understand the process that shapes the patterns of genetic variability between closely related populations. K E Y W O R D Sgenome-wide methods, genomic regions, Ovine BeadChip50K, Sardinian sheep breeds

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Section: Introductionmentioning

confidence: 99%

Combined approaches to identify genomic regions involved in phenotypic differentiation between low divergent breeds: Application in Sardinian sheep populations

Mastrangelo

Jemaa

Sottile

et al. 2019

J Animal Breeding Genetics

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“…Arid environments are characterized by a number of bio-physical stressors including high temperatures, solar radiation, feed and water stress. Indigenous domestic animals are known to be well adapted to these stressors and several studies on signatures of selection have been undertaken to unravel the genetic basis of adaptations to environments in a number of livestock species [7,13,15,26,66]. A paralog of TBC1D14, namely TBC1D12, was present in one of our candidate regions and was identi ed previously by Lv et al (26) to be candidate gene for environmental adaptation in sheep.…”

Section: Discussionmentioning

confidence: 91%

Genomic signatures of divergent selection for production and adaptation in domestic goats (Capra hircus)

Mwacharo¹,

Kim²,

Elbeltagy³

et al. 2019

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Background : Goats are distributed worldwide and include many breeds with marked phenotypic variation. Both natural and human driven processes have shaped their genomes. Here, 52K genome-wide SNP genotypes were used to investigate signatures of divergent selection between indigenous goats from an arid hot environment in Egypt and breeds developed under temperate environments in Europe. Three selection signature approaches were used, the di derivative of F ST , iHS and Rsb. Results: Out of a total of 36 candidate regions that were detected to be under selection by the three approaches, the analysis detected nine regions with the strongest selection signatures spanning 134 genes of which 68 were the most significantly functionally enriched. In addition to well-known genes affecting dairy traits ( LAP3 , ABCG2 , MEPE , IBSP , MED28 ) and body weight and stature ( LCORL , NCAPG , CCSER1 , DCAF16 ) in several mammalian species, we found evidence for selection in regions spanning genes implicated in the regulation of fatty acid synthesis and metabolic pathways ( PI4K2B and PPARGC1A ), inflammatory gene expression and autoimmune response pathways ( CXCL8 , HERC5 , RGS18 , TROVE2 ) and spermatogenesis ( SPATA18 , LAP3 ). Other genes not reported before in goats included SLIT2 , PACRGL , GRP125 , DHX15 , SOD3 and KCNIP4 which have been associated with thermal nociception in mice. We also detected a paralog of TBC1D12 , namely TBC1D14 , in one of the candidate regions. TBC1D12 has been linked to environmental adaptation in sheep. Gene ontology analysis revealed the 68 candidate genes were highly enriched in two biological processes viz regulation of G protein-coupled receptor signaling pathway (GO:0045744) and cellular response to stress (GO:0033554). Conclusions: Our results provide evidence that goat genomes have evolved, in part, via diverse positive selection directed at breed formation, at past and recent genetic improvement and adaptation to environments. Based on their uniqueness, these breed-group specific signatures of selection can be considered to be footprints of divergence which may be useful in characterizing genome architecture and diversity in domestic animals and for targeted genetic improvement.

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“…These studies have proposed candidate genes, such as MSL1, PFKFB4, TRDN,FBF1,SETD7 and GRM1 [7,8]. On the other side, genomic scan for detecting regions associated with fat deposition were also performed in several sheep breeds [9][10][11][12][13][14][15][16][17]. However, the molecular mechanisms underlying gene expression related to such economically important traits remained mostly unexplored.…”

Section: Introductionmentioning

confidence: 99%

Allele-specific expression reveals the phenotypic differences between thin- and fat-tailed sheep

Shao¹,

He²,

Pan³

et al. 2020

Preprint

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Background: The thin-tailed sheep breeds from Europe and the fat-tailed sheep breeds from China exhibit distinct phenotypic differences in fat deposition and meat production traits. However, the molecular mechanisms underlying gene expression related to these phenotypic differences are not well understood. Allele-specific expression (ASE) refers to the significant imbalance of expression levels of two parental alleles. Characterization of such events in F1 hybrid offspring generated from these two groups of sheep breeds can minimize the external factors influencing gene expression and reveal the variants with a cis -regulatory effect on gene expression. The aim of the present study was to investigate the genetic factors that influence different fat-deposition and meat production traits between thin- and fat-tailed sheep.Results: Fifteen F1 hybrids were generated from crosses between Texel and Kazakh sheep as the representative phenotypes of thin- and fat-tailed breeds, respectively. Totally, 33 whole genomes from F1 individuals and their parents were sequenced with an average depth of ~17.21× coverage per sample. ASE analysis results from 70 RNA-seq samples of adipose and skeleton muscle tissues showed 128 ASE candidate genes were related to the function of fat deposition and meat production traits. A genome-wide scan of selective sweeps was also conducted between these two groups of sheep breeds in an effort to identify genomic regions related to fat deposition and meat production, respectively. We detected signatures of selection in ASE genes associated with fat deposition (e.g., PDGFD ) and meat production traits (e.g., LRCC2 ). Further analysis suggested that PDGFD and LRCC2 genes were speculated to be causative genes for fat deposition and meat production traits in sheep, respectively. Furthermore, AMPK signaling pathway was significantly enriched in ASE genes related to fatty acid biosynthesis in both adipose and skeleton muscle tissues, while PPAR signaling pathway was significantly enriched in ASE genes related to lipid metabolism in adipose tissue. Conclusions: Our finding illustrates that the expression of identified ASE genes could potentially lead to the differences in traits of fat deposition and meat production between thin- and fat-tailed sheep. Keywords: allele-specific expression, phenotypic difference, thin- and fat-tailed sheep, whole-genome sequencing, transcriptome

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Genome-Wide Variation, Candidate Regions and Genes Associated With Fat Deposition and Tail Morphology in Ethiopian Indigenous Sheep

Cited by 73 publications

References 64 publications

Combined approaches to identify genomic regions involved in phenotypic differentiation between low divergent breeds: Application in Sardinian sheep populations

Combined approaches to identify genomic regions involved in phenotypic differentiation between low divergent breeds: Application in Sardinian sheep populations

Genomic signatures of divergent selection for production and adaptation in domestic goats (Capra hircus)

Allele-specific expression reveals the phenotypic differences between thin- and fat-tailed sheep

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