scholarly journals Fine mapping of candidate regions associated with fat deposition in thin and fat tail sheep breeds suggests new insights into molecular aspects of fat tail selection

2021 ◽  
Author(s):  
Mohammad Hossein Moradi ◽  
Ardeshir Nejati-Javaremi ◽  
Mohammad Moradi-Shahrbabak ◽  
Ken G. Dodds ◽  
Rudiger Brauning ◽  
...  
Keyword(s):  
Statistical Tests ◽  
Fat Deposition ◽  
Chromosome 5 ◽  
Sheep Breeds ◽  
Fat Tail ◽  
Signature Of Selection ◽  
Sheep Production ◽  
Molecular Aspects ◽  
Candidate Regions ◽  
Actual Target

Abstract Background Fatness related traits are economically very important in sheep production and are associated with serious diseases in humans. The fat tail is a phenotype that divides domesticated sheep into two major groups. The objective of the present study is to refine the map location of candidate regions associated with fat deposition, obtained via two separate whole genome scans contrasting thin and fat tail breeds, and to determine the nature of the selection occurring in these regions using hitchhiking approach. Results Zel (thin tail) and Lori-Bakhtiari (fat tail) breed samples that had previously been run on the Illumina Ovine 50k BeadChip, were genotyped with a denser set of SNPs in the three candidate regions using a Sequenom Mass ARRAY platform. Statistical tests were then performed using different and complementary methods based on either site frequency (FST and Median homozygosity) or haplotype (iHS and XP-EHH). Results from candidate regions on chromosome 5 and X revealed clear evidence of selection with the derived haplotypes that were consistent with selection to near fixation for the haplotypes affecting fat tail size in the fat tail breed. Analysis of the candidate region on chromosome 7 indicated that selection differentiated the beneficial alleles between breeds and homozygosity has increased in the thin tail breed which also had the ancestral haplotype. These results enabled us to confirm the signature of selection in these regions and refine the critical intervals from 113kb, 201kb and 2,831kb to 28kb, 142kb and 1,006kb on chromosome 5, 7 and X respectively. These regions contain several genes associated with fat metabolism or developmental processes consisting TCF7 and PPP2CA (OAR5), PTGDR and NID2 (OAR7), AR, EBP, CACNA1F, HSD15B, SLC35A2, BMP15, WDR13 and RBM3 (OAR X), each of which could potentially be the actual target of selection. Study of core haplotypes alleles in our regions of interest also supported the hypothesis that the first domesticated sheep were thin tailed and fat tail animals were developed later. Conclusions Our results provide a comprehensive assessment of how and where selection has affected the patterns of variation in candidate regions associated with fat deposition in thin and fat tail sheep breeds. The hitchhiking mapping approach in this study was novel in the sense that most of the exploratory genome scan studies in domestic animals have not clarified the signal from the candidate regions, probably due to the lack of suitable genomic resources.

scholarly journals Genomic scan of selective sweeps in thin and fat tail sheep breeds for identifying of candidate regions associated with fat deposition

BMC Genetics ◽  
2012 ◽  
Vol 13 (1) ◽  
pp. 10 ◽  
Author(s):  
Mohammad Hossein Moradi ◽  
Ardeshir Nejati-Javaremi ◽  
Mohammad Moradi-Shahrbabak ◽  
Ken G Dodds ◽  
John C McEwan
Keyword(s):  
Fat Deposition ◽  
Selective Sweeps ◽  
Sheep Breeds ◽  
Fat Tail ◽  
Candidate Regions

scholarly journals Genomic analysis of worldwide sheep breeds reveals PDGFD as a major target of fat-tail selection in sheep

2020 ◽  
Author(s):  
Kunzhe Dong ◽  
Min Yang ◽  
Jiangang Han ◽  
Qing Ma ◽  
Jilong Han ◽  
...  
Keyword(s):  
Statistical Tests ◽  
Genomic Analysis ◽  
Fixation Index ◽  
Data Set ◽  
Sheep Breeds ◽  
Fat Tail ◽  
Geographic Origins ◽  
Predominant Factor ◽  
Major Target ◽  
Selection Of

Abstract Background: Fat tail is a unique trait in sheep acquired during domestication. Several genomic analyses have been conducted in sheep breeds from limited geographic origins to identify the genetic factors underlying this trait. Nevertheless, these studies obtained different candidates. The results of these regional studies were easily biased by the breed structures. Results: To minimize the bias and distinguish the true candidates, we used an extended data set of 968 sheep representing 18 fat-tailed breeds and 14 thin-tailed breeds from around the world, and integrated two statistical tests to detect selection signatures, including Genetic Fixation Index (FST) and difference of derived allele frequency (ΔDAF). The results showed that platelet derived growth factor D (PDGFD) exhibited the highest genetic differentiation between fat- and thin-tailed sheep breeds. Analysis of sequence variation identified that a 6.8-kb region within the first intron of PDGFD is likely the target of positive selection and contains regulatory mutation(s) in fat-tailed sheep. Histological and gene expression analyses demonstrated that PDGFD expression is associated with maturation and hemostasis of adipocytes. Further retrospective analysis of public transcriptomic datasets revealed that PDGFD expression is down-regulated during adipogenesis in both human and mouse, and is higher in fat tissues of obese individuals than that in lean individuals. Conclusions: These results reveal that PDGFD is the predominant factor for the fat tail phenotype in sheep by contributing to adiopogenesis and maintaining the hemostasis of mature adipocytes. This study provides insights into the selection of fat-tailed sheep and has important application to animal breeding, as well as obesity-related human diseases.

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

2018 ◽  
Author(s):  
Salvatore Mastrangelo ◽  
Hussain Bahbahani ◽  
Bianca Moioli ◽  
Abulgasim Ahbara ◽  
Mohammed Al Abri ◽  
...  
Keyword(s):  
Fat Deposition ◽  
Domestic Sheep ◽  
Selection Signatures ◽  
Selection Signature ◽  
Sheep Breeds ◽  
Fat Tail ◽  
Genome Wide ◽  
Geographic Origins ◽  
Genomic Regions ◽  
Great Complexity

Genomic regions subjected to selection frequently show signatures such as within-population reduced nucleotide diversity and outlier values of differentiation among differentially selected populations. In this study, we analyzed 50K SNP genotype data of 373 animals belonging to 23 sheep breeds of different geographic origins using the Rsb and FST statistical approaches, to identify loci associated with the fat-tail phenotype. We also checked if these putative selection signatures overlapped with regions of high-homozygosity (ROH). The analyses identified novel signals and confirmed the presence of selection signature in genomic regions that harbor candidate genes known to affect fat deposition. Several genomic regions that frequently appeared in ROH were also identified within each breed, but only two ROH islands overlapped with the putative selection signatures. The results reported herein provide the most complete genome-wide study of selection signatures for fat-tail in African and Eurasian sheep breeds; they also contribute insights into the genetic basis for the fat tail phenotype in sheep, and confirm the great complexity of the mechanisms that underlie quantitative traits, such as the fat-tail.

scholarly journals Genomic analysis of worldwide sheep breeds reveals PDGFD as a major target of fat-tail selection in sheep

2020 ◽  
Author(s):  
Kunzhe Dong ◽  
Min Yang ◽  
Jiangang Han ◽  
Qing Ma ◽  
Jilong Han ◽  
...  
Keyword(s):  
Statistical Tests ◽  
Genomic Analysis ◽  
Fixation Index ◽  
Data Set ◽  
Sheep Breeds ◽  
Fat Tail ◽  
Geographic Origins ◽  
Predominant Factor ◽  
Major Target ◽  
Selection Of

Abstract Background: Fat tail is a unique trait in sheep acquired during domestication. Several genomic analyses have been conducted in sheep breeds from limited geographic origins to identify the genetic factors underlying this trait. Nevertheless, these studies obtained different candidates. The results of these regional studies were easily biased by the breed structures.Results: To minimize the bias and distinguish the true candidates, we used an extended data set of 968 sheep representing 18 fat-tailed breeds and 14 thin-tailed breeds from around the world, and integrated two statistical tests to detect selection signatures, including Genetic Fixation Index (FST) and difference of derived allele frequency (ΔDAF). The results showed that platelet derived growth factor D (PDGFD) exhibited the highest genetic differentiation between fat- and thin-tailed sheep breeds. Analysis of sequence variation identified that a 6.8-kb region within the first intron of PDGFD is likely the target of positive selection and contains regulatory mutation(s) in fat-tailed sheep. Histological and gene expression analyses demonstrated that PDGFD expression is associated with maturation and hemostasis of adipocytes. Further retrospective analysis of public transcriptomic datasets revealed that PDGFD expression is down-regulated during adipogenesis in both human and mouse, and is higher in fat tissues of obese individuals than that in lean individuals. Conclusions: These results reveal that PDGFD is the predominant factor for the fat tail phenotype in sheep by contributing to adiopogenesis and maintaining the hemostasis of mature adipocytes. This study provides insights into the selection of fat-tailed sheep and has important application to animal breeding, as well as obesity-related human diseases.

scholarly journals Comparative tail fat transcriptome analysis of key genes and pathways activated in response to fat deposition in two sheep breeds with extreme fat-tail phenotype differences

2020 ◽  
Author(s):  
Wei Zhang ◽  
Mengsi Xu ◽  
Juanjuan Wang ◽  
Shiyin Wang ◽  
Xinhua Wang ◽  
...  
Keyword(s):  
Fat Deposition ◽  
Fat Tissue ◽  
Sheep Breeds ◽  
Coding Regions ◽  
Fat Tail ◽  
Sequence Variations ◽  
Ppar Signaling ◽  
Significant Expression ◽  
Efficient Selection ◽  
Selection Of

Abstract Background Fat tail in sheep presents a valuable energy reserve that has historically facilitated adaptation to harsh environments. However, in modern intensive and semi-intensive sheep industry systems, breeds with leaner tails are preferred. For efficient selection of lean sheep breeds, clarification of the regulatory mechanisms underlying tail fat deposition of sheep is crucial. Altay and Xinjiang Fine Wool (XFW) sheep, two important breeds with distinct tail fat deposition properties, are mainly distributed in the Xinjiang district of China, and serve as ideal models for investigating the mechanisms of tail fat deposition. In the present study, RNA-Seq was applied to determine the transcriptome profiles of tail fat tissues in these two breeds, followed by analysis of differentially expressed genes (DEGs) and their sequence variations. Results In total, 21,527 genes were detected, among which 3,965 displayed significant expression variations in tail fat tissues of the two sheep breeds, including 707 upregulated and 3,258 downregulated genes. Gene Ontology (GO) analysis disclosed that 198 DEGs were related to fat metabolism. In Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, the majority were significantly enriched in adipocytokine signaling, PPAR signaling, and metabolic pathways, with some genes being involved in multiple pathways. Among the 198 DEGs, 22 genes were markedly up or down regulated in tail fat tissue of Altay sheep, supporting their association with the fat tail trait of this breed. A total of 41,724 and 42,193 SNPs were detected in tail fat tissue transcriptomes of Altay and XFW sheep, respectively. The distribution of 7 SNPs in the coding regions of the 22 candidate genes was further investigated in three sheep populations with distinct tail types. In particular, the g.18167532 T/C mutation of ABCA1 and g.57036072 G/T mutation of SLC27A2 showed significantly different distributions and were closely associated with tail type. Conclusions The present study provides transcriptomic evidence explaining the differences in fat- and thin-tailed sheep breeds and reveals numerous DEGs and SNPs associated with tail type. Our data provide a valuable theoretical basis for selection of lean sheep breeds.

scholarly journals ­­­­­­Genomic analysis of worldwide sheep breeds reveals PDGFD as a major target of fat-tail selection in sheep

2020 ◽  
Author(s):  
Kunzhe Dong ◽  
Min Yang ◽  
Jiangang Han ◽  
Qing Ma ◽  
Jilong Han ◽  
...  
Keyword(s):  
Statistical Tests ◽  
Genomic Analysis ◽  
Fixation Index ◽  
Data Set ◽  
Sheep Breeds ◽  
Fat Tail ◽  
Geographic Origins ◽  
Predominant Factor ◽  
Major Target ◽  
Selection Of

Abstract Background: Fat tail is a unique trait in sheep acquired during domestication. Several genomic analyses have been conducted in sheep breeds from limited geographic origins to identify the genetic factors underlying this trait. Nevertheless, these studies obtained different candidates. The results of these regional studies were easily biased by the breed structures. Results: To minimize the bias and distinguish the true candidates, we used an extended data set of 968 sheep representing 18 fat-tailed breeds and 14 thin-tailed breeds from around the world, and integrated two statistical tests to detect selection signatures, including Genetic Fixation Index (FST) and difference of derived allele frequency (ΔDAF). The results showed that platelet derived growth factor D (PDGFD) exhibited the highest genetic differentiation between fat- and thin-tailed sheep breeds. Analysis of sequence variation identified that a 6.8-kb region within the first intron of PDGFD is likely the target of positive selection and contains regulatory mutation(s) in fat-tailed sheep. Histological and gene expression analyses demonstrated that PDGFD expression is associated with maturation and hemostasis of adipocytes. Further retrospective analysis of public transcriptomic datasets revealed that PDGFD expression is down-regulated during adipogenesis in both human and mouse, and is higher in fat tissues of obese individuals than that in lean individuals. Conclusions: These results reveal that PDGFD is the predominant factor for the fat tail phenotype in sheep by contributing to adiopogenesis and maintaining the hemostasis of mature adipocytes. This study provides insights into the selection of fat-tailed sheep and has important application to animal breeding, as well as obesity-related human diseases.

scholarly journals Genomic analysis of worldwide sheep breeds reveals PDGFD as a major target of fat-tail selection in sheep

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Kunzhe Dong ◽  
Min Yang ◽  
Jiangang Han ◽  
Qing Ma ◽  
Jilong Han ◽  
...  
Keyword(s):  
Statistical Tests ◽  
Genomic Analysis ◽  
Fixation Index ◽  
Data Set ◽  
Sheep Breeds ◽  
Fat Tail ◽  
Geographic Origins ◽  
Predominant Factor ◽  
Major Target ◽  
Selection Of

Abstract Background Fat tail is a unique trait in sheep acquired during domestication. Several genomic analyses have been conducted in sheep breeds from limited geographic origins to identify the genetic factors underlying this trait. Nevertheless, these studies obtained different candidates. The results of these regional studies were easily biased by the breed structures. Results To minimize the bias and distinguish the true candidates, we used an extended data set of 968 sheep representing 18 fat-tailed breeds and 14 thin-tailed breeds from around the world, and integrated two statistical tests to detect selection signatures, including Genetic Fixation Index (FST) and difference of derived allele frequency (ΔDAF). The results showed that platelet derived growth factor D (PDGFD) exhibited the highest genetic differentiation between fat- and thin-tailed sheep breeds. Analysis of sequence variation identified that a 6.8-kb region within the first intron of PDGFD is likely the target of positive selection and contains regulatory mutation(s) in fat-tailed sheep. Histological and gene expression analyses demonstrated that PDGFD expression is associated with maturation and hemostasis of adipocytes. Further retrospective analysis of public transcriptomic datasets revealed that PDGFD expression is down-regulated during adipogenesis in both human and mouse, and is higher in fat tissues of obese individuals than that in lean individuals. Conclusions These results reveal that PDGFD is the predominant factor for the fat tail phenotype in sheep by contributing to adiopogenesis and maintaining the hemostasis of mature adipocytes. This study provides insights into the selection of fat-tailed sheep and has important application to animal breeding, as well as obesity-related human diseases.

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

2019 ◽  
Vol 9 ◽  
Author(s):  
Abulgasim Ahbara ◽  
Hussain Bahbahani ◽  
Faisal Almathen ◽  
Mohammed Al Abri ◽  
Mukhtar Omar Agoub ◽  
...  
Keyword(s):  
Fat Deposition ◽  
Indigenous Sheep ◽  
Genome Wide ◽  
Candidate Regions

scholarly journals Association of TMEM8B and SPAG8 with Mature Weight in Sheep

Animals ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 2391
Author(s):  
Mehmet Ulas Cinar ◽  
Michelle R. Mousel ◽  
Maria K. Herndon ◽  
J. Bret Taylor ◽  
Stephen N. White
Keyword(s):  
Body Size ◽  
Selection Pressure ◽  
Transmembrane Protein ◽  
Genomic Region ◽  
Phenotypic Data ◽  
Functional Roles ◽  
Signature Of Selection ◽  
Organism Growth ◽  
Mature Weight ◽  
Sheep Production

Signature of selection studies have identified many genomic regions with known functional importance and some without verified functional roles. Multiple studies have identified Transmembrane protein 8B (TMEM8B)rs426272889 as having been recently under extreme selection pressure in domesticated sheep, but no study has provided sheep phenotypic data clarifying a reason for extreme selection. We tested rs426272889 for production trait association in 770 U.S. Rambouillet, Targhee, Polypay, and Suffolk sheep. TMEM8Brs426272889 was associated with mature weight at 3 and 4 years (p < 0.05). This suggested selection for sheep growth and body size might explain the historical extreme selection pressure in this genomic region. We also tested Sperm-associated antigen 8 (SPAG8) rs160159557 encoding a G493C substitution. While this variant was associated with mature weights at ages 3 and 4, it was not as strongly associated as TMEM8Brs426272889. Transmembrane protein 8B has little functional information except as an inhibitor of cancer cell proliferation. To our knowledge, this is the first study linking TMEM8B to whole organism growth and body size under standard conditions. Additional work will be necessary to identify the underlying functional variant(s). Once identified, such variants could be used to improve sheep production through selective breeding.

scholarly journals Transcriptome analysis of adipose tissues from two fat-tailed sheep breeds reveals key genes involved in fat deposition

BMC Genomics ◽  
2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Baojun Li ◽  
Liying Qiao ◽  
Lixia An ◽  
Weiwei Wang ◽  
Jianhua Liu ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Fat Deposition ◽  
Adipose Tissues ◽  
Sheep Breeds ◽  
Key Genes
Sign in / Sign up

Export Citation Format

Share Document