GLIS1, a potential candidate gene affect fat deposition in sheep tail.
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ABSTRACT:
SUBMITTER: Luo R
PROVIDER: S-EPMC8260413 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundIdentification of genomic regions that have been targets of selection for phenotypic traits is one of the most important and challenging areas of research in animal genetics. However, currently there are relatively few genomic regions identified that have been subject to positive selection. In this study, a genome-wide scan using ~50,000 Single Nucleotide Polymorphisms (SNPs) was performed in an attempt to identify genomic regions associated with fat deposition in fat-tail breeds. This trait and its modification are very important in those countries grazing these breeds.ResultsTwo independent experiments using either Iranian or Ovine HapMap genotyping data contrasted thin and fat tail breeds. Population differentiation using FST in Iranian thin and fat tail breeds revealed seven genomic regions. Almost all of these regions overlapped with QTLs that had previously been identified as affecting fat and carcass yield traits in beef and dairy cattle. Study of selection sweep signatures using FST in thin and fat tail breeds sampled from the Ovine HapMap project confirmed three of these regions located on Chromosomes 5, 7 and X. We found increased homozygosity in these regions in favour of fat tail breeds on chromosome 5 and X and in favour of thin tail breeds on chromosome 7.ConclusionsIn this study, we were able to identify three novel regions associated with fat deposition in thin and fat tail sheep breeds. Two of these were associated with an increase of homozygosity in the fat tail breeds which would be consistent with selection for mutations affecting fat tail size several thousand years after domestication.
| S-EPMC3351017 | biostudies-literature
Project description:Variations in body weight and in the distribution of body fat are associated with feed availability, thermoregulation, and energy reserve. Ethiopia is characterized by distinct agro-ecological and human ethnic farmer diversity of ancient origin, which have impacted on the variation of its indigenous livestock. Here, we investigate autosomal genome-wide profiles of 11 Ethiopian indigenous sheep populations using the Illumina Ovine 50 K SNP BeadChip assay. Sheep from the Caribbean, Europe, Middle East, China, and western, northern and southern Africa were included to address globally, the genetic variation and history of Ethiopian populations. Population relationship and structure analysis separated Ethiopian indigenous fat-tail sheep from their North African and Middle Eastern counterparts. It indicates two main genetic backgrounds and supports two distinct genetic histories for African fat-tail sheep. Within Ethiopian sheep, our results show that the short fat-tail sheep do not represent a monophyletic group. Four genetic backgrounds are present in Ethiopian indigenous sheep but at different proportions among the fat-rump and the long fat-tail sheep from western and southern Ethiopia. The Ethiopian fat-rump sheep share a genetic background with Sudanese thin-tail sheep. Genome-wide selection signature analysis identified eight putative candidate regions spanning genes influencing growth traits and fat deposition (NPR2, HINT2, SPAG8, INSR), development of limbs and skeleton, and tail formation (ALX4, HOXB13, BMP4), embryonic development of tendons, bones and cartilages (EYA2, SULF2), regulation of body temperature (TRPM8), body weight and height variation (DIS3L2), control of lipogenesis and intracellular transport of long-chain fatty acids (FABP3), the occurrence and morphology of horns (RXFP2), and response to heat stress (DNAJC18). Our findings suggest that Ethiopian fat-tail sheep represent a uniquely admixed but distinct genepool that presents an important resource for understanding the genetic control of skeletal growth, fat metabolism and associated physiological processes.
| S-EPMC6334744 | biostudies-literature
Project description:It is a unique feature that fat can be deposited in sheep tails and rumps. To elucidate the genetic mechanism underlying this trait, we collected 120 individuals from three Chinese indigenous sheep breeds with extreme tail types, namely large fat-tailed sheep (n = 40), Altay sheep (n = 40), and Tibetan sheep (n = 40), and genotyped them using the Ovine Infinium HD SNP BeadChip. Then genomic scan for selection signatures was performed using the hapFLK. In total, we identified 25 genomic regions exhibiting evidence of having been under selection. Bioinformatic analysis of the genomic regions showed that selection signatures related to multiple candidate genes had a demonstrated role in phenotypic variation. Nine genes have documented association with sheep tail types, including WDR92, TBX12, WARS2, BMP2, VEGFA, PDGFD, HOXA10, ALX4, and ETAA1. Moreover, a number of genes were of particular interest, including RXFP2 associated with the presence/absence and morphology of horns; MITF involved in coat color; LIN52 and SYNDIG1L related to the number of teats; MSRB3 gene associated with ear sizes; LTBP2 considered as a positional candidate genes for number of ribs; JAZF1 regulating lipid metabolism; PGRMC2, SPAG17, TSHR, GTF2A1, and LARP1B implicated with reproductive traits. Our findings provide insights into fat tail formation and a reference for carrying out molecular breeding and conservation in sheep.
| S-EPMC7278473 | biostudies-literature
Project description:Hulun Buir sheep of similar genetic background were divided into two lines based on tail types: Small- and big fat-tailed. To explore the molecular mechanism of fat deposition in sheep tails, we firstly evaluated the morphology and transcription level differences of tail fat between these two lines. RNA-Seq technology was used to identify differentially expressed genes (DEGs) in phenotypic extremes of tail sizes. Five comparisons were performed taking into account two factors, sex and tail type. We screened out 373 DEGs between big-tailed and small-tailed Hulun Buir sheep, and 775 and 578 DEGs between two types of tails in male and female sheep, respectively. The results showed an obvious sex difference in the fat metabolism in sheep based on gene ontology (GO), pathway, and network analyses. Intriguingly, there were two different co-expression networks only respectively shown in male and female sheep, which were insulin-related network acting on upstream pathways and PPARG-related network effect in downstream pathways. Furthermore, these two networks were linked by a classic pathway of regulating adipogenesis. This is the first study to investigate the sex differences of fat metabolism in domestic animals, and it demonstrates a new experimental way to study fat metabolism. Our findings will provide theoretical background in understanding the tail-size phenotype in sheep and can be exploited in breeding small-tailed sheep.
| S-EPMC6770480 | biostudies-literature
Project description:Chinese indigenous sheep can be classified into three types based on tail morphology: fat-tailed, fat-rumped, and thin-tailed sheep, of which the typical breeds are large-tailed Han sheep, Altay sheep, and Tibetan sheep, respectively. To unravel the molecular genetic basis underlying the phenotypic differences among Chinese indigenous sheep with these three different tail types, we used ovine high-density 600K single nucleotide polymorphism (SNP) arrays to detect genome-wide associations, and performed general linear model analysis to identify candidate genes, using genotyping technology to validate the candidate genes. Tail type is an important economic trait in sheep. However, the candidate genes associated with tail type are not known. The objective of this study was to identify SNP markers, genes, and chromosomal regions related to tail traits. We performed a genome-wide association study (GWAS) using data from 40 large-tailed Han sheep, 40 Altay sheep (cases) and 40 Tibetan sheep (controls). A total of 31 significant (P<0.05) SNPs associated with tail-type traits were detected. For significant SNPs' loci, we determined their physical location and performed a screening of candidate genes within each region. By combining information from previously reported and annotated biological functional genes, we identified SPAG17, Tbx15, VRTN, NPC2, BMP2 and PDGFD as the most promising candidate genes for tail-type traits. Based on the above identified candidate genes for tail-type traits, BMP2 and PDGFD genes were selected to investigate the relationship between SNPs within the tails in the Altay and Tibetan populations. rs119 T>C in exon1 of the BMP2 gene and one SNP in exon4 (rs69 C>A) of the PDGFD gene were detected. rs119 was of the TT genotype in Altay sheep, while it was of the CC genotype in Tibetan sheep. On rs69 of the PDGFD gene, Altay sheep presented with the CC genotype; however, Tibetan sheep presented with the AA genotype.
| S-EPMC8186729 | biostudies-literature
Project description:Genetic basis of fat deposition in sheep tail have not been completely elucidated yet. Understanding the genetic mechanisms controlling fat-tail size can improve breeding strategies to modulate fat deposition. RNA sequencing has made it possible to discover genetic variants that may underlie various phenotypic differences. Hence, to identify genetic variants that are important for describing different fat-tail phenotypes in sheep, RNA sequencing was used for single nucleotide polymorphism (SNP) calling in two Iranian sheep breeds (Lori-Bakhtiari, fat-tailed; n = 4, vs Zel, thin-tailed; n = 4). Using a stringent pipeline, a total of 112,344 known SNPs were genotyped, of which 30,550 and 42,906 SNPs were shared by at least two Lori-Bakhtiari and Zel, respectively. Comparing these SNPs showed 2,774 (including 209 missense and 25 deleterious SNPs) and 10,470 (including 1,054 missense and 116 deleterious SNPs) breed-specific SNPs in Lori-Bakhtiari and Zel sheep, respectively. Potential breed-specific SNPs were detected by considering those located in QTL regions associated with fatness or reported as important candidates in previous similar studies. Of the breed-specific SNPs, 724 and 2,905 were located in the QTL regions. Functional enrichment analysis of the affected genes revealed several enriched gene ontologies and KEGG pathways related to fat metabolism. Based on the results, several affected genes were proposed to be strongly linked with fat deposition such as DGAT2, ACSL1, ACACA, ADIPOQ, ACLY, FASN, CPT2, SCD, ADCY6, PER3, CSF1R, SLC22A4, GFPT1, CDS2, BMP6, ACSS2, ELOVL6, HOXA10 and FABP4. Moreover, several SNPs were found in the candidate genes related to fatty acid oxidation introducing them as promising candidates responsible for lower fat content in tail of Zel. Our findings provided new insights into the genetic mechanisms of fat deposition in sheep, which can serve to designing appropriate breeding programs.
| S-EPMC7419499 | biostudies-literature
Project description:An essential tissue involved in the development and regulation of lipid metabolism in animals is adipose tissue. The “fat-tail” can supply energy for sheep during migration and winter when a low amount of dry matter intake is available. Tail fat content affects meat quality and varies significantly among the different breeds of sheep. Ghezel (fat-tailed) and Zel (thin-tailed) are two important local Iranian sheep breeds that show different patterns of fat storage. The current study presents the transcriptome characterization of tail fat using RNA-sequencing in order to get a better comprehension of the molecular mechanism of lipid storage in the two sheep breeds. The results of sequencing were analyzed with bioinformatics methods, including differentially expressed genes (DEGs) identification, functional enrichment analysis, structural classification of proteins, protein–protein interaction (PPI), network analysis and module analysis. The results revealed a total of332 DEGs between the Zel and Ghezel breed, with78 up-regulated and 254 down-regulated DEGs in the Zel breed. Identification of differential genes showed that some DEGs, such as IL-6, LIPG, SAA1, SOCS3 and HIF-1α, with the largest fold change had close association with lipid deposition. Also, important lipid storage genes such as FASN and SCPEP1 had high levels of expression. Furthermore, functional enrichment analysis revealed some pathways associated with fat deposition, such as “Fatty acid metabolism”, “Fatty acid biosynthesis” and“HIF-1 signaling pathway”. In addition, structural classification of proteins showed major DEGs in transcription factor classes such as JUNB, NR4A3, FOSL1, MAFF, NR4A1, CREB3L1 and ATF3 were up-regulated in the Zel breed. IL-6, JUNB, and related DEGs were up-regulated in the PPI network.HMGCS1, SUCLA2 and STT3B and related DEGs were down-regulated in the PPI network and had high topology scores as hub genes. This implies the DEGs of these modules are important candidate genes for tail fat metabolism and, therefore, can be further studied.
2021-11-22 | GSE142841 | GEO
Project description:Maintenance of appropriate levels of fecundity is critical for efficient sheep production. Opportunities to increase sheep litter size include identifying single gene mutations with major effects on ovulation rate and litter size. Whole-genome sequencing (WGS) data of 89 Chinese domestic sheep from nine different geographical locations and ten Australian sheep were analyzed to detect new polymorphisms affecting litter size. Comparative genomic analysis of sheep with contrasting litter size detected a novel set of candidate genes. Two SNPs, g.71874104G>A and g.71833755T>C, were genotyped in 760 Small Tail Han sheep and analyzed for association with litter size. The two SNPs were significantly associated with litter size, being in strong linkage disequilibrium in the region 71.80?71.87 Mb. This haplotype block contains one gene that may affect litter size, Histone Cell Cycle Regulator (HIRA). HIRA mRNA levels in sheep with different lambing ability were significantly higher in ovaries of Small Tail Han sheep (high fecundity) than in Sunite sheep (low fecundity). Moreover, the expression levels of HIRA in eight tissues of uniparous Small Tail Han sheep were significantly higher than in multiparous Small Tail Han sheep (p < 0.05). HIRA SNPs significantly affect litter size in sheep and are useful as genetic markers for litter size.
| S-EPMC5981282 | biostudies-literature
Project description:Chinese indigenous sheep can be classified into two types according to their tail morphology: fat-rumped and thin-tailed sheep, of which the typical breeds are Altay sheep and Tibetan sheep, respectively. To identify the differentially expressed proteins (DEPs) underlying the phenotypic differences between tail types, we used iTRAQ combined with multi-dimensional liquid chromatography tandem mass spectrometry (LC-MS/MS) technology to detect candidate proteins. We then subjected these to a database search, and identified the DEPs. Finally, bioinformatics technology was used to carry out GO functional and KEGG pathway analyses. A total of 3248 proteins were identified, of which 44 were up-regulated and 40 were down-regulated DEPs. Analyzing their GO function terms and KEGG pathways revealed that the functions of these DEPs are mainly binding, catalytic activity, structural molecule activity, molecular function regulator, and transporter activity. Among the genes encoding the DEPs, APOA2, GALK1, ADIPOQ, and NDUFS4 are associated with fat formation and metabolism.
2022-02-17 | PXD029488 | Pride
Project description:Crosses between Korean and Landrace pigs have revealed a large quantitative trait loci (QTL) region for fat deposition in a region (89 cM) of porcine chromosome 4 (SSC4). To more finely map this QTL region and identify candidate genes for this trait, comparative mapping of pig and human chromosomes was performed in the present study. A region in the human genome that corresponds to the porcine QTL region was identified in HSA1q21. Furthermore, the LMNA gene, which is tightly associated with fat augmentation in humans, was localized to this region. Radiation hybrid (RH) mapping using a Sus scrofa RH panel localized LMNA to a region of 90.3 cM in the porcine genome, distinct from microsatellite marker S0214 (87.3 cM). Two-point analysis showed that LMNA was linked to S0214, SW1996, and S0073 on SSC4 with logarithm (base 10) of odds scores of 20.98, 17.78, and 16.73, respectively. To clone the porcine LMNA gene and to delineate the genomic structure and sequences, including the 3'untranslated region (UTR), rapid amplification of cDNA ends was performed. The coding sequence of porcine LMNA consisted of 1,719 bp, flanked by a 5'UTR and a 3'UTR. Two synonymous single nucleotide polymorphisms (SNPs) were identified in exons 3 and 7. Association tests showed that the SNP located in exon 3 (A193A) was significantly associated with weight at 30 wks (p<0.01) and crude fat content (p<0.05). This association suggests that SNPs located in LMNA could be used for marker-assisted selection in pigs.
| S-EPMC4094157 | biostudies-literature