1
|
Yan H, Yang W, Yan Y, Liu J, Zhu H, Qu L, Gao Y. Detection of small sequence variations within the goat GHR gene and its effects on growth traits. Anim Biotechnol 2023; 34:4256-4261. [PMID: 36369830 DOI: 10.1080/10495398.2022.2143791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Growth hormone receptor (GHR) gene is considered to be an important candidate gene in growth traits. Therefore, the purpose of this study was to detect whether there were potential indel variations in the GHR gene that were related to the growth traits of the Shaanbei white cashmere goats (SBWC). In this study, genomic DNA from 931 healthy SBWC individuals were used to verify the relationship between the indel of the GHR gene and growth traits. Two indel variants, P49-bp indel in intron 1 and P1410-bp indel in 3'-UTR, were confirmed. Association analyses demonstrated that these two indel polymorphism loci were associated with the chest circumference and chest width of SBWC. Additionally, for the P49-bp and P1410-bp indel loci, the ID and II genotypes were dominant genotypes, respectively. Moreover, the genotypic distributions of these two indel loci in SBWC were significantly different from those in three other Chinese indigenous goat breeds (HNBG, GZDG and IMWC) (p < 0.05). Taken together, two indel loci (P49-bp indel and P1410-bp indel) both significantly affected the growth traits of goats. This illustrated that these two indel loci might be the potential DNA marker for use in improving the selection and breeding of goats.
Collapse
Affiliation(s)
- Hailong Yan
- Department of Neurology, Institute of Brain Science, Medical School, Shanxi Datong University, Datong, China
| | - Wenjing Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yuqing Yan
- Department of Neurology, Institute of Brain Science, Medical School, Shanxi Datong University, Datong, China
| | - Jinwang Liu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, China
| | - Haijing Zhu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, China
| | - Lei Qu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, China
| | - Ye Gao
- Department of Neurology, Institute of Brain Science, Medical School, Shanxi Datong University, Datong, China
| |
Collapse
|
2
|
Zhang L, Zhang S, Zhan F, Song M, Shang P, Zhu F, Li J, Yang F, Li X, Qiao R, Han X, Li X, Liu G, Wang K. Population Genetic Analysis of Six Chinese Indigenous Pig Meta-Populations Based on Geographically Isolated Regions. Animals (Basel) 2023; 13:ani13081396. [PMID: 37106959 PMCID: PMC10135051 DOI: 10.3390/ani13081396] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/28/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
The diversification of indigenous pig breeds in China has resulted from multiple climate, topographic, and human cultural influences. The numerous indigenous pig breeds can be geographically divided into six meta-populations; however, their genetic relationships, contributions to genetic diversity, and genetic signatures remain unclear. Whole-genome SNP data for 613 indigenous pigs from the six Chinese meta-populations were obtained and analyzed. Population genetic analyses confirmed significant genetic differentiation and a moderate mixture among the Chinese indigenous pig meta-populations. The North China (NC) meta-population had the largest contribution to genetic and allelic diversity. Evidence from selective sweep signatures revealed that genes related to fat deposition and heat stress response (EPAS1, NFE2L2, VPS13A, SPRY1, PLA2G4A, and UBE3D) were potentially involved in adaptations to cold and heat. These findings from population genetic analyses provide a better understanding of indigenous pig characteristics in different environments and a theoretical basis for future work on the conservation and breeding of Chinese indigenous pigs.
Collapse
Affiliation(s)
- Lige Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Songyuan Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Fengting Zhan
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Mingkun Song
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Peng Shang
- Animal Science College, Tibet Agriculture and Animal Husbandry University, Linzhi 860000, China
| | - Fangxian Zhu
- National Animal Husbandry Service, Beijing 100193, China
| | - Jiang Li
- National Supercomputing Center in Zhengzhou, Zhengzhou 450001, China
| | - Feng Yang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Xiuling Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Ruimin Qiao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Xuelei Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Xinjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Gang Liu
- National Animal Husbandry Service, Beijing 100193, China
| | - Kejun Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| |
Collapse
|
3
|
SINE Insertion in the Intron of Pig GHR May Decrease Its Expression by Acting as a Repressor. Animals (Basel) 2021; 11:ani11071871. [PMID: 34201672 PMCID: PMC8300111 DOI: 10.3390/ani11071871] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/15/2021] [Accepted: 06/19/2021] [Indexed: 11/17/2022] Open
Abstract
Simple Summary GH/IGF axis genes play a central role in the regulation of skeletal accretion during development and growth, and thus represent candidate genes for growth traits. Retrotransposon insertion polymorphisms are major contributors to structural variations. They tend to generate large effect mutations resulting in variations in target gene activity and phenotype due to the fact that they carry functional elements, such as enhancers, insulators, or promoters. In the present study, RIPs in four GH/IGF axis genes (GH, GHR, IGF1, and IGF1R) were investigated by comparative genomics and PCR. Four RIPs in the GHR gene and one RIP in the IGF1 gene were identified. Further analysis revealed that one RIP in the first intron of GHR might play a role in the regulation of GHR expression by acting as a repressor. These findings contribute to the understanding of the role of RIPs in the genetic variation of GH/IGF axis genes and phenotypic variation in pigs. Abstract The genetic diversity of the GH/IGF axis genes and their association with the variation of gene expression and phenotypic traits, principally represented by SNPs, have been extensively reported. Nevertheless, the impact of retrotransposon insertion polymorphisms (RIPs) on the GH/IGF axis gene activity has not been reported. In the present study, bioinformatic prediction and PCR verification were performed to screen RIPs in four GH/IGF axis genes (GH, GHR, IGF1 and IGF1R). In total, five RIPs, including one SINE RIP in intron 3 of IGF1, one L1 RIP in intron 7 of GHR, and three SINE RIPs in intron 1, intron 5 and intron 9 of GHR, were confirmed by PCR, displaying polymorphisms in diverse breeds. Dual luciferase reporter assay revealed that the SINE insertion in intron 1 of GHR significantly repressed the GHR promoter activity in PK15, Hela, C2C12 and 3T3-L1 cells. Furthermore, qPCR results confirmed that this SINE insertion was associated with a decreased expression of GHR in the leg muscle and longissimus dorsi, indicating that it may act as a repressor involved in the regulation of GHR expression. In summary, our data revealed that RIPs contribute to the genetic variation of GH/IGF axis genes, whereby one SINE RIP in the intron 1 of GHR may decrease the expression of GHR by acting as a repressor.
Collapse
|
4
|
Tijjani A, Utsunomiya YT, Ezekwe AG, Nashiru O, Hanotte O. Genome Sequence Analysis Reveals Selection Signatures in Endangered Trypanotolerant West African Muturu Cattle. Front Genet 2019; 10:442. [PMID: 31231417 PMCID: PMC6558954 DOI: 10.3389/fgene.2019.00442] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 04/29/2019] [Indexed: 01/01/2023] Open
Abstract
Like most West African Bos taurus, the shorthorn Muturu is under threat of replacement or crossbreeding with zebu. Their populations are now reduced to a few hundred breeding individuals and they are considered endangered. So far, the genetic variation and genetic basis of the trypanotolerant Muturu environmental adaptation have not been assessed. Here, we present genome-wide candidate positive selection signatures in Muturu following within-population iHS and between population Rsb signatures of selection analysis. We compared the results in Muturu with the ones obtained in N’Dama, a West African longhorn trypanotolerant taurine, and in two European taurine (Holstein and Jersey). The results reveal candidate signatures of selection regions in Muturu including genes linked to the innate (e.g., TRIM10, TRIM15, TRIM40, and TRIM26) and the adaptive (e.g., JSP.1, BOLA-DQA2, BOLA-DQA5, BOLA-DRB3, and BLA-DQB) immune responses. The most significant regions are identified on BTA 23 at the bovine major histocompatibility complex (MHC) (iHS analysis) and on BTA 12 at genes including a heat tolerance gene (INTS6) (Rsb analysis). Other candidate selected regions include genes related to growth traits/stature (e.g., GHR and GHRHR), coat color (e.g., MITF and KIT), feed efficiency (e.g., ZRANB3 and MAP3K5) and reproduction (e.g., RFX2, SRY, LAP3, and GPX5). Genes under common signatures of selection regions with N’Dama, including for adaptive immunity and heat tolerance, suggest shared mechanisms of adaptation to environmental challenges for these two West African taurine cattle. Interestingly, out of the 242,910 SNPs identified within the candidate selected regions in Muturu, 917 are missense SNPs (0.4%), with an unequal distribution across 273 genes. Fifteen genes including RBBP8, NID1, TEX15, LAMA3, TRIM40, and OR12D3 comprise 220 missense variants, each between 11 and 32. Our results, while providing insights into the candidate genes under selection in Muturu, are paving the way to the identification of genes and their polymorphisms linked to the unique tropical adaptive traits of the West Africa taurine, including trypanotolerance.
Collapse
Affiliation(s)
- Abdulfatai Tijjani
- Cells, Organisms and Molecular Genetics, School of Life Sciences, University Park Campus, University of Nottingham, Nottingham, United Kingdom.,Center for Genomics Research and Innovation, National Biotechnology Development Agency, Abuja, Nigeria.,International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Yuri Tani Utsunomiya
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University, São Paulo, Brazil
| | - Arinze G Ezekwe
- Department of Animal Science, Faculty of Agriculture, University of Nigeria, Nsukka, Nigeria
| | - Oyekanmi Nashiru
- Center for Genomics Research and Innovation, National Biotechnology Development Agency, Abuja, Nigeria
| | - Olivier Hanotte
- Cells, Organisms and Molecular Genetics, School of Life Sciences, University Park Campus, University of Nottingham, Nottingham, United Kingdom.,International Livestock Research Institute, Addis Ababa, Ethiopia
| |
Collapse
|
5
|
A miR-511-binding site SNP in the 3'UTR of IGF-1 gene is associated with proliferation and apoptosis of PK-15 cells. In Vitro Cell Dev Biol Anim 2019; 55:323-330. [PMID: 30945114 DOI: 10.1007/s11626-019-00329-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/28/2019] [Indexed: 01/07/2023]
Abstract
Insulin-like growth factor-1 (IGF-1) is a functional candidate gene for pig growth and development due to its crucial role in the growth axis of growth hormone-IGF-1. Considering that the 3' untranslated region (3'UTR) of gene may affect its expression, we analyzed the effect of a single-nucleotide polymorphism (SNP) (rs34142920, c.674C > T) on gene expression, cell proliferation, and apoptosis and the possible related molecular mechanisms in PK-15 cells. The SNP was found in the 3'UTR of IGF-1 in Bama Xiang pig in previous investigations. Results showed that the SNP was located at the target site binding to microRNA (miR-511). The 3'UTR of IGF-1 gene with C allele significantly downregulated the expression of IGF-1 gene compared with that of the gene with T allele by luciferase assay. miR-511 was transfected into porcine kidney cell line (PK-15 cells) to reveal its effects on cells and whether or not it targets IGF-1. The expression levels of IGF-1 at mRNA and protein levels were remarkably downregulated. miR-511 significantly inhibited cell proliferation and promoted cell apoptosis by downregulating the phosphorylation level of AKT and ERK1/2. This finding confirmed that miR-511 inhibits proliferation and promotes apoptosis by downregulating the IGF-1 in PK-15 cells.
Collapse
|
6
|
Kim KS, Seibert JT, Edea Z, Graves KL, Kim ES, Keating AF, Baumgard LH, Ross JW, Rothschild MF. Characterization of the acute heat stress response in gilts: III. Genome-wide association studies of thermotolerance traits in pigs. J Anim Sci 2018; 96:2074-2085. [PMID: 29669012 DOI: 10.1093/jas/sky131] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 04/12/2018] [Indexed: 01/09/2023] Open
Abstract
Heat stress is one of the limiting factors negatively affecting pig production, health, and fertility. Characterizing genomic regions responsible for variation in HS tolerance would be useful in identifying important genetic factor(s) regulating physiological responses to HS. In the present study, we performed genome-wide association analyses for respiration rate (RR), rectal temperature (TR), and skin temperature (TS) during HS in 214 crossbred gilts genotyped for 68,549 single nucleotide polymorphisms (SNP) using the Porcine SNP 70K BeadChip. Considering the top 0.1% smoothed phenotypic variances explained by SNP windows, we detected 26, 26, 21, and 14 genes that reside within SNPs explaining the largest proportion of variance (top 25 SNP windows) and associated with change in RR (ΔRR) from thermoneutral (TN) conditions to HS environment, as well as the change in prepubertal TR (ΔTR), change in postpubertal ΔTR, and change in TS (ΔTS), respectively. The region between 28.85 Mb and 29.10 Mb on chromosome 16 explained about 0.05% of the observed variation for ΔRR. The growth hormone receptor (GHR) gene resides in this region and is associated with the HS response. The other important candidate genes associated with ΔRR (PAIP1, NNT, and TEAD4), ΔTR (LIMS2, TTR, and TEAD4), and ΔTS (ERBB4, FKBP1B, NFATC2, and ATP9A) have reported roles in the cellular stress response. The SNP explaining the largest proportion of variance and located within and in the vicinity of genes were related to apoptosis or cellular stress and are potential candidates that underlie the physiological response to HS in pigs.
Collapse
Affiliation(s)
- Kwan-Suk Kim
- Department of Animal Science, Iowa State University, Ames, IA.,Department of Animal Science, Chungbuk National University, Cheongju, Chungbuk, Korea
| | - Jacob T Seibert
- Department of Animal Science, Iowa State University, Ames, IA
| | - Zewde Edea
- Department of Animal Science, Chungbuk National University, Cheongju, Chungbuk, Korea
| | - Kody L Graves
- Department of Animal Science, Iowa State University, Ames, IA
| | - Eui-Soo Kim
- Department of Animal Science, Iowa State University, Ames, IA.,Recombinetics, St. Paul, MN
| | | | | | - Jason W Ross
- Department of Animal Science, Iowa State University, Ames, IA
| | | |
Collapse
|
7
|
Wu Q, Yu H, Fang X, Cheng Y, Dong L, Wei W, Wang G, Fu H, Liu S, Hao L. The association of haplotypes inIGFBP-3gene promoter region and tissue expressions in three pig breeds. Anim Cells Syst (Seoul) 2016. [DOI: 10.1080/19768354.2016.1253614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
|