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Rehman MSU, Mushtaq M, Hassan FU, Zia-ur Rehman, Mushahid M, Shokrollahi B. Comparative Genomic Characterization of Insulin-Like Growth Factor Binding Proteins in Cattle and Buffalo. BIOMED RESEARCH INTERNATIONAL 2022; 2022:5893825. [PMID: 35924270 PMCID: PMC9343199 DOI: 10.1155/2022/5893825] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/30/2022] [Accepted: 07/06/2022] [Indexed: 11/30/2022]
Abstract
The somatotropic axis consists of genes associated with economic traits like muscle growth and carcass traits in livestock. Insulin-like growth factor binding proteins (IGFBPs) are the major proteins that play a vital role in the somatotropic axis. The present study performed a genome-wide characterization of IGFBP genes in cattle. Genomic sequences of the IGFBP gene family for different mammals (cattle, buffalo, goat, and sheep) were recovered from the NCBI database. Sequence analyses were performed to investigate cattle's genomic variations in the IGFBP gene family. Phylogenetic analysis, gene structure, motif patterns, and conserved domain analysis (CDA) of the IGFBP family revealed the evolutionarily conserved nature of the IGFBP genes in cattle and other studied species. Physicochemical properties of IGFBP proteins in cattle revealed that most of these proteins are unstable, hydrophilic, thermostable, and acidic. Comparative amino acid analysis revealed variations in all protein sequences with single indels in IGFBP3 and IGFBP6. Mutation analysis revealed only one nonsynonymous mutation D212 > E in the IGFBP6 protein of cattle. A total of 245 nuclear hormone receptor (NHRs) sites were detected, including 139 direct repeats (DR), 65 everted repeats (ER), and 41 inverted repeats (IR). Out of 133 transcription factors (TFs), 10 TFs (AHR, AHRARNT, AP4, CMYB, E47, EGR2, GATA, SP1, and SRF) had differential distribution (P value < 0.05) of putative transcriptional binding sites (TFBS) in cattle compared to buffalo. Synteny analysis revealed the conserved nature of genes between cattle and buffalo. Two gene pairs (IGFBP1/IGFBP3 and IGFBP2/IGFBP5) showed tandem duplication events in cattle and buffalo. This study highlights the functional importance of genomic variation in IGFBP genes and necessitates further investigations better to understand the role and mechanisms of IGFBPs in bovines.
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Affiliation(s)
- Muhammad Saif-ur Rehman
- Institute of Animal and Dairy Sciences, University of Agriculture, Faisalabad 38040, Pakistan
| | - Muqeet Mushtaq
- Institute of Animal and Dairy Sciences, University of Agriculture, Faisalabad 38040, Pakistan
| | - Faiz-ul Hassan
- Institute of Animal and Dairy Sciences, University of Agriculture, Faisalabad 38040, Pakistan
| | - Zia-ur Rehman
- University of Agriculture, Faisalabad–Subcampus Toba Tek Singh, Pakistan
| | - Muhammad Mushahid
- Institute of Animal and Dairy Sciences, University of Agriculture, Faisalabad 38040, Pakistan
| | - Borhan Shokrollahi
- Department of Animal Science, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran
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Comparative analysis of IGFBP-3 gene sequence in Egyptian sheep, cattle, and buffalo. BMC Res Notes 2019; 12:623. [PMID: 31547834 PMCID: PMC6757409 DOI: 10.1186/s13104-019-4657-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 09/17/2019] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE A total of 205 animals from four Egyptian livestock species; cattle (n = 18), buffaloes (n = 12), sheep (n = 150) and goats (n = 25) were used in this study to detect polymorphism and perform comparative analysis for IGFBP-3 gene using DNA sequencing and (PCR-RFLP). RESULTS The amplified fragments were found to be of length 654 bp in sheep, 651 bp in cattle and 655 bp in buffalo. For Falahy goats, PCR was performed to amplify a 316 bp fragment from exon 2 of the IGFBP-3 gene. The digestion of 654 bp with HaeIII restriction enzyme yielded a single restriction pattern for goats, while for cattle, 3 genotypes were identified; (AA), (AB), and (BB). Moreover, for buffalo one genotype (AA) only was found with HaeIII and TaqI restriction enzymes, separately. Also, the digestion profile for goats with HaeIII revealed one pattern only. Nucleotide sequencing of the amplified fragments of IGFBP-3 gene in sheep, cattle, buffalo, and goat was submitted to the NCBI GenBank (Accession no. MG738671.1, MG738673.1, MG738674.1, and MG738672.1, respectively). The nucleotide sequencing analysis indicated similarity percentages in IGFBP-3 gene fragments of 88.54, 89.63 and 95.06% between "sheep and cattle", "sheep and buffalo", and "cattle and buffalo", respectively.
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Zhou F, Yang Q, Lei C, Chen H, Lan X. Relationship between genetic variants of POU1F1 , PROP1 , IGFBP3 genes and milk performance in Guanzhong dairy goats. Small Rumin Res 2016. [DOI: 10.1016/j.smallrumres.2016.05.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Othman OE, Alam SS, Abd El-Aziem SH. Single nucleotide polymorphism in Egyptian cattle insulin-like growth factor binding protein-3 gene. JOURNAL OF GENETIC ENGINEERING AND BIOTECHNOLOGY 2014. [DOI: 10.1016/j.jgeb.2014.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Liu H, Liu C, Yang G, Li H, Dai J, Cong Y, Li X. DNA Polymorphism of Insulin-like Growth Factor-binding Protein-3 Gene and Its Association with Cashmere Traits in Cashmere Goats. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 25:1515-20. [PMID: 25049511 PMCID: PMC4093038 DOI: 10.5713/ajas.2012.12351] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 08/21/2012] [Accepted: 08/03/2012] [Indexed: 11/27/2022]
Abstract
Insulin-like growth factor binding protein-3 (IGFBP-3) gene is important for regulation of growth and development in mammals. The present investigation was carried out to study DNA polymorphism by PCR-RFLP of IGFBP-3 gene and its effect on fibre traits of Chinese Inner Mongolian cashmere goats. The fibre traits data investigated were cashmere fibre diameter, combed cashmere weight, cashmere fibre length and guard hair length. Four hundred and forty-four animals were used to detect polymorphisms in the hircine IGFBP-3 gene. A 316-bp fragment of the IGFBP-3 gene in exon 2 was amplified and digested with HaeIII restriction enzyme. Three patterns of restriction fragments were observed in the populations. The frequency of AA, AB and BB genotypes was 0.58, 0.33 and 0.09 respectively. The allelic frequency of the A and B allele was 0.75 and 0.25 respectively. Nucleotide sequencing revealed a C>G transition in the exon 2 region of the IGFBP-3 gene resulting in R158G change which caused the polymorphism. Least squares analysis revealed a significant effect of genotypes on cashmere weight (p<0.0001), cashmere fibre length (p<0.001) and hair length (p<0.05) of the animals. The effect of genotypes on cashmere fibre diameter was not statistically significant (p>0.05). The animals of AB and BB genotypes showed higher cashmere weight, cashmere fibre length and hair length than the animals possessing AA genotype. These results suggested that polymorphisms in the hircine IGFBP-3 gene might be a potential molecular marker for cashmere weight in cashmere goats.
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Affiliation(s)
- Haiying Liu
- Procurement Department, China Petroleum LONGWAY Engineering Project Management CO., LTD., Langfang, 065000, China
| | - Chao Liu
- Procurement Department, China Petroleum LONGWAY Engineering Project Management CO., LTD., Langfang, 065000, China
| | - Guiqin Yang
- Procurement Department, China Petroleum LONGWAY Engineering Project Management CO., LTD., Langfang, 065000, China
| | - Hui Li
- Procurement Department, China Petroleum LONGWAY Engineering Project Management CO., LTD., Langfang, 065000, China
| | - Jin Dai
- Procurement Department, China Petroleum LONGWAY Engineering Project Management CO., LTD., Langfang, 065000, China
| | - Yuyan Cong
- Procurement Department, China Petroleum LONGWAY Engineering Project Management CO., LTD., Langfang, 065000, China
| | - Xuejian Li
- Procurement Department, China Petroleum LONGWAY Engineering Project Management CO., LTD., Langfang, 065000, China
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Sharma A, Dutt G, Jayakumar S, Saroha V, Dixit S. Sequence characterization and genetic variability analysis of GHR, IGF1, and IGFBP-3 genes in nine Indian goat breeds. JOURNAL OF APPLIED ANIMAL RESEARCH 2014. [DOI: 10.1080/09712119.2013.875899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Sharma A, Dutt G, Sivalingam J, Singh M, Pathodiya O, Khadda B, Dixit S. Novel SNPs in IGF1, GHR and IGFBP-3 genes reveal significant association with growth traits in Indian goat breeds. Small Rumin Res 2013. [DOI: 10.1016/j.smallrumres.2013.08.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Xi D, Wu M, Fan Y, Liu Q, Leng J, Gou X, Mao H, Deng W. Polymorphisms of the insulin-like growth factor-binding protein 3 gene (IGFBP3) in gayal (Bos frontalis). Gene 2012; 497:98-102. [PMID: 22310386 DOI: 10.1016/j.gene.2012.01.051] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2011] [Revised: 12/15/2011] [Accepted: 01/21/2012] [Indexed: 10/14/2022]
Abstract
The gene coding for insulin-like growth factor-binding protein 3 (IGFBP3) is important for regulation of growth, development and metabolism in mammals. The present investigation was conducted to study nucleotide polymorphism of the IGFBP3 in gayal (Bos frontalis) and to compare the variations with those which occur in other ruminants. A fragment of 645 base pairs of the IGFBP3 covering a part of exon 2, the complete intron 2 and exon 3 and a part of intron 3 was amplified, sequenced (n=46) and digested (n=79) with HaeIII restriction enzyme from 125 collected gayal samples. Nine single nucleotide polymorphisms (SNPs) [C14T, A122C, C137T, G144C, C155T, G213A, C279A, G334A and G460A] were identified and located in intron 2, revealing high genetic variability. The alignment of nucleotide sequences was found to be very similar to those for other bovid species. Sequencing and HaeIII digestion showed that frequency of alleles C and A [consisting of fragments of sizes 56, 64, 228, 264, 282, 298 and 497 bp (CC genotype)] was 0.96 and 0.04 for the SNP C279A. Moreover, the genotype frequency of the SNP C279A in gayal was compared with that in other ruminants and it appears that this polymorphism may be associated with low fat content and rapid growth in this rare species.
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Affiliation(s)
- Dongmei Xi
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
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Ganguly I, Sharma A, Mitra A, Kumar N, Ganguly A. Analysis of genetic variations of complete TM4 of buffalo (Bubalus bubalis) Slc11A1 gene. JOURNAL OF APPLIED ANIMAL RESEARCH 2011. [DOI: 10.1080/09712119.2011.607943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Indrajit Ganguly
- a Genome Analysis Laboratory, Animal Genetics Division, Indian Veterinary Research Institute , Indian Council of Agricultural Research , Izatnagar, Bareilly, India
- c National Bureau of Animal Genetic Resources , Karnal, Haryana, 132001, India
| | - Arjava Sharma
- a Genome Analysis Laboratory, Animal Genetics Division, Indian Veterinary Research Institute , Indian Council of Agricultural Research , Izatnagar, Bareilly, India
| | - Abhijit Mitra
- a Genome Analysis Laboratory, Animal Genetics Division, Indian Veterinary Research Institute , Indian Council of Agricultural Research , Izatnagar, Bareilly, India
| | - Nishant Kumar
- a Genome Analysis Laboratory, Animal Genetics Division, Indian Veterinary Research Institute , Indian Council of Agricultural Research , Izatnagar, Bareilly, India
- d FVSc, SKUASTJ , RS.Pura, Jammu, 181102, India
| | - Anita Ganguly
- b Division of Biochemistry and Food Science , Indian Veterinary Research Institute, Indian Council of Agricultural Research , Izatnagar, Bareilly, India
- e Department of Veterinary Physiology and Biochemistry , COVS, LLRUVAS , Hisar, Haryana, 125004, India
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Kumar P, Kumar KG, Bhattacharya TK, Bhushan B, Sharma A, Ahlawat SP. Molecular and Cytogenetic Evaluation of Four Indian Breeds of Sheep. JOURNAL OF APPLIED ANIMAL RESEARCH 2009. [DOI: 10.1080/09712119.2009.9707072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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[A novel polymorphism of IGFBP-3 gene and its relationship with several wool traits in Chinese Merino sheep]. YI CHUAN = HEREDITAS 2009; 30:1182-6. [PMID: 18779177 DOI: 10.3724/sp.j.1005.2008.01182] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In this study, PCR-SSCP analysis was used to identify genetic variation in IGFBP-3 gene in Chinese Merino and Kazakh sheep. A PCR product of 178 bp corresponding to partial intron1 illustrated three unique binding patterns by SSCP analysis. Frequencies of the genotype AA, AB, BB and allele A, B in Chinese Merino sheep were 0.70, 0.24, 0.06, and 0.82, 0.18 respectively , and they were 0.87, 0.13, 0.00, and 0.93, 0.07 respectively in Kazaka sheep. Sequence analysis revealed a G/T transversion at position 122 of the fragment. This polymorphic locus of IGFBP-3 gene was at Hardy-Weinberg dis-equilibrium (P<0.01) in the two breeds. Different genotypes slightly affected several wool traits of Chinese Merino sheep. The individuals of genotype AA, AB, and BB had no significant difference in post-shearing weight and clean wool rate. Sta-ple length (SL) was decreased with the genotype of AA, AB, and BB, and the difference between AA and AB was significant (P<0.01). Greasy fleece weight (GFW) and follicle density in individuals of genotype AA was significantly lower than that in individuals of genotype AB (P<0.01) and BB (P<0.05); Average fiber diameter (AFD) in individuals of genotype AA was significantly higher than that in individuals of genotype AB (P<0.01) and BB (P<0.05).
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Lan X, Pan C, Chen H, Lei C, Liu S, Zhang Y, Min L, Yu J, Li J, Zhao M, Hu S. The HaeIII and XspI PCR-RFLPs detecting polymorphisms at the goat IGFBP-3 locus. Small Rumin Res 2007. [DOI: 10.1016/j.smallrumres.2007.01.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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