Comparative analysis of IGFBP-3 gene sequence in Egyptian sheep, cattle, and buffalo

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, 651bp 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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Comparative analysis of IGFBP-3 gene sequence in Egyptian sheep, cattle, and buffalo

10.21203/rs.2.13545/v2 ◽

2019 ◽

Author(s):

Ahmed Abdel-kader Saleh ◽

Amr M.A. Rashad ◽

Nada. N.A.M. Hassanine ◽

Mahmoud A. Sharaby ◽

Yongju Zhao

Keyword(s):

Comparative Analysis ◽

Gene Sequence ◽

Restriction Enzymes ◽

Restriction Pattern ◽

Nucleotide Sequencing ◽

Sequencing Analysis ◽

Exon 2 ◽

Pcr Rflp ◽

Digestion Profile ◽

Igfbp 3

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, 651bp 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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Comparative analysis of IGFBP-3 gene sequence in Egyptian sheep, cattle, and buffalo

10.21203/rs.2.13545/v4 ◽

2019 ◽

Author(s):

Ahmed Abdel-kader Saleh ◽

Amr M.A. Rashad ◽

Nada. N.A.M. Hassanine ◽

Mahmoud A. Sharaby ◽

Yongju Zhao

Keyword(s):

Comparative Analysis ◽

Gene Sequence ◽

Restriction Enzymes ◽

Restriction Pattern ◽

Nucleotide Sequencing ◽

Sequencing Analysis ◽

Exon 2 ◽

Pcr Rflp ◽

Digestion Profile ◽

Igfbp 3

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, 651bp 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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Comparative analysis of IGFBP-3 gene sequence in Egyptian sheep, cattle and buffalo

10.21203/rs.2.13545/v1 ◽

2019 ◽

Author(s):

Ahmed Abdel-kader Saleh ◽

Amr M.A. Rashad ◽

Nada. N.A.M. Hassanine ◽

Mahmoud A. Sharabi ◽

Yongju Zhao

Keyword(s):

Comparative Analysis ◽

Gene Sequence ◽

Restriction Enzymes ◽

Restriction Pattern ◽

Nucleotide Sequencing ◽

Sequencing Analysis ◽

Livestock Species ◽

Pcr Rflp ◽

Digestion Profile ◽

Igfbp 3

Abstract Objective: A total of 205 animals from four Egyptian livestock species were used in this study to detect polymorphism and perform comparative analysis for IGFBP-3 gene using DNA sequencing and (PCR-RFLP). Results: The digestion of 654 bp with HaeIII restriction enzyme yielded a single restriction pattern of eight fragments in sheep revealing the absence of polymorphism, while in cattle 3 genotypes were identified; (AA), (AB), and (BB). Moreover, one genotype (AA) only was found in buffalo using HeaIII and MspI restriction enzymes, separately. Digestion profile for a goat with HaeIII revealed only one pattern for three DNA fragments, which means the absence of polymorphism within the IGFBP-3 gene in the tested goats. The nucleotide sequencing analysis indicated similarity percentages in IGFBP-3 gene fragments of 77, 30 and 58% between ''sheep and cattle '', ''sheep and buffalo '', and ''cattle and buffalo'', respectively.

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Genetic biodiversity studies on IGFBP-3 gene in Egyptian sheep breeds

Biotechnology in Animal Husbandry ◽

10.2298/bah0902101a ◽

2009 ◽

Vol 25 (1-2) ◽

pp. 101-109 ◽

Cited By ~ 6

Author(s):

B.A. Ali ◽

A.A. El-Hanafy ◽

H.H. Salem

Keyword(s):

Growth And Development ◽

Genomic Dna ◽

Dna Polymorphism ◽

Restriction Pattern ◽

Exon 2 ◽

Sheep Breeds ◽

Pcr Rflp ◽

Intron 2 ◽

Igfbp 3 ◽

Indian Sheep

The insulin-like growth factor binding protein-3 (IGFBP-3) gene is a structural gene associated with the growth and development of the animals. The present investigation was carried out to study DNA polymorphism by PCR-RFLP of IGFBP-3 gene in four Egyptian local sheep breeds and its comparison with Indian sheep breeds. Genomic DNA was isolated from a total of 20 animals from four Egyptian breeds of sheep namely Rahmani, Ossimi, Awassi, and Barki. A fragment of IGFBP-3 gene, comprising of a part of exon 2, complete intron 2, exon 3, and a part of intron 3, was amplified. The amplified fragment was found to be 654 bp in sheep as compared to earlier reports of 651 bp in cattle and 655 bp in buffalo. On digestion of 654 bp with Hae III restriction enzyme yielded single restriction pattern of five fragments of sizes 201, 201, 87, 67, 57 in all the animals belonging to the four Egyptian breeds studied revealing absence of polymorphism in those four Egyptian sheep breeds. On comparison, this fragment was monomorphic in Indian sheep breeds and buffalo ,while it was reported to be polymorphic in cattle.

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Studies on TLR2 gene variants and their association with milk yield and milk quality traits in Bos indicus (Deoni) cattle

Indian Journal of Animal Research ◽

10.18805/ijar.b-3204 ◽

2017 ◽

Author(s):

U. T. Mundhe ◽

D. N. Das ◽

R. S. Gandhi ◽

P. Divya

Keyword(s):

Milk Yield ◽

Bos Indicus ◽

Restriction Enzymes ◽

Milk Quality ◽

Quality Traits ◽

Exon 2 ◽

Allelic Frequencies ◽

Tlr2 Gene ◽

Pcr Rflp

Present study molecular characterization of exon 2 of TLR2 gene and its association with milk yield and milk quality traits in 104 Deoni cattle using PCR- RFLP technique was done. Polymorphism was observed through HaeIII, HhaI and EcoRV restriction enzymes in Created Restriction Site (CRS) exon 2-1, CRS exon 2-5 and exon 2-1 by PCR- RFLP, respectively. In CRS exon 2-1 allelic frequencies were observed as 0.793 for A and 0.206 for B alleles and that of genotypic frequencies were 0.58 and 0.41 for genotypes AA and AB. In CRS exon 2-5, two genotypes viz., AC and CC with corresponding allelic frequencies were observed as 0.221 for A and 0.778 for C allele and that of genotypic frequencies observed were 0.44 and 0.55 for AC and CC genotypes respectively. TLR2 exon 2-1 exhibited two alleles G and T with frequencies of 0.134 and 0.865 and their Corresponding genotypic frequencies were 0.009, 0.25 and 0.74for GG, GT and TT genotypes respectively. Higher count of somatic cells (SCC) in TT homozygous and TG heterozygous genotypes, and lower in GG homozygous genotypes were observed in exon 2-1. Strongly significant (P£0.01) effect for least squares means of Test Day milk yield (TDMY) and Somatic Cell Count of CRS exon 2-1 were observed.

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Identification of BMP15 Exon 2 for fecundity traits by PCR-RFLP and nucleotide sequencies in Kejobong goat

Journal of the Indonesian Tropical Animal Agriculture ◽

10.14710/jitaa.42.4.220-226 ◽

2017 ◽

Vol 42 (4) ◽

pp. 220 ◽

Cited By ~ 2

Author(s):

A. Febriana ◽

S. Sutopo ◽

E. Kurnianto

Keyword(s):

Insertion Site ◽

Pcr Amplification ◽

Nucleotide Sequencing ◽

Specific Marker ◽

Exon 2 ◽

High Productivity ◽

Morphogenetic Protein ◽

Pcr Rflp ◽

Sequencing Technique ◽

Gene Exon

Kejobong goat is known as prolific and high productivity goat breed in Indonesia. PCR-RFLP and sequencing technique was established in the present study to accomplish the polymorphisms of Bone Morphogenetic Protein 15 (BMP15) gene exon 2 on Kejobong goat does. The blood samples was collected from 48 Kejobong does which were selected based on their litter size. The size of PCR amplification of BMP15 gene exon 2 was 837 bp. The product of PCR-RFLP technique digested by HinfI enzyme showed that the samples were monomorphic. Authentication result using nucleotide sequencing found 4 substitution (A391G, C464G, T828C and C830G), 1 alignment gap (site 817) and 1 insertion nucleotide (site 822). This mutations caused 6 haplotypes formatted. The mutants of BMP15 exon 2 on Kejobong goats indicated that this breed had their own mutation controling the prolific trait. The phylogenetic tree build on the sequences of BMP15 gene exon 2 of Kejobong goats was grouped into 3 clusters. The alignment gap indicated to be the specific marker for the prolific trait (duplet) in Kejobong goat. The particular insertion site could be the recognition site of Kejobong goat based on BMP15 exon 2.

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Polymorphism in exon 2 of the BuLA-DRB3 gene in Indian buffalo (Bubalus bubalis var. indicus) detected by PCR-RFLP

Animal Science ◽

10.1017/s1357729800054680 ◽

2000 ◽

Vol 70 (2) ◽

pp. 221-226 ◽

Cited By ~ 7

Author(s):

T.V. Aravindakshan ◽

A.M. Nainar ◽

S.N. Sivaselvam

Keyword(s):

Pcr Primers ◽

Bubalus Bubalis ◽

Restriction Pattern ◽

Fragment Analysis ◽

Exon 2 ◽

Pcr Rflp ◽

Restriction Sites ◽

Bovine Lymphocyte ◽

High Degree ◽

Bovine Species

AbstractPolymerase chain reaction (PCR) primers specific to exon 2 of the bovine lymphocyte antigen (BoLA)-DRB3 gene were used successfully to amplify the equivalent region in 34 Murrah and 36 Surti buffaloes selected at random. The 304 bp amplified product of the DRB3 gene was separately digested with BstγI, HaeIII and Rsal enzymes. Digestion with BstγI enzyme did not reveal any polymorphism and all animals showed a single restriction pattern, which corresponded exactly to the BstγI pattern ‘b’ previously described for cattle. Digestion with HaeIII enzyme resulted in five patterns, four of which corresponded to the Haelll patterns previously reported in cattle. The new HaeIII pattern was observed in both the breeds of buffaloes studied. The fragment analysis with RsaI revealed 13 different patterns. All of these RsaI patterns corresponded to the RsaI patterns previously described for cattle. The high degree of similarity in the restriction fragment length polymorphism (RFLP) patterns of cattle and buffalo observed in the present study provide evidence for the strong conservation amongst other bovine species, of restriction sites previously reported in cattle.

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Nucleotide Sequencing and SNP Detection of Toll-Like Receptor-4 Gene in Murrah Buffalo (Bubalus bubalis)

ISRN Molecular Biology ◽

10.5402/2012/659513 ◽

2012 ◽

Vol 2012 ◽

pp. 1-7 ◽

Cited By ~ 3

Author(s):

M. Mitra ◽

S. Taraphder ◽

G. S. Sonawane ◽

A. Verma

Keyword(s):

Rflp Analysis ◽

Ovis Aries ◽

Capra Hircus ◽

Nucleotide Sequencing ◽

Toll Like Receptor ◽

Snp Detection ◽

Toll Like Receptor 4 ◽

Exon 2 ◽

Murrah Buffalo ◽

Pcr Rflp

Toll-like receptor-4 (TLR-4) has an important pattern recognition receptor that recognizes endotoxins associated with gram negative bacterial infections. The present investigation was carried out to study nucleotide sequencing and SNP detection by PCR-RFLP analysis of the TLR-4 gene in Murrah buffalo. Genomic DNA was isolated from 102 lactating Murrah buffalo from NDRI herd. The amplified PCR fragments of TLR-4 comprised of exon 1, exon 2, exon 3.1, and exon 3.2 were examined to RFLP. PCR products were obtained with sizes of 165, 300, 478, and 409 bp. TLR-4 gene of investigated Murrah buffaloes was highly polymorphic with AA, AB, and BB genotypes as revealed by PCR-RFLP analysis using Dra I, Hae III, and Hinf I REs. Nucleotide sequencing of the amplified fragment of TLR-4 gene of Murrah buffalo was done. Twelve SNPs were identified. Six SNPs were nonsynonymous resulting in change in amino acids. Murrah is an indigenous Buffalo breed and the presence of the nonsynonymous SNP is indicative of its unique genomic architecture. Sequence alignment and homology across species using BLAST analysis revealed 97%, 97%, 99%, 98%, and 80% sequence homology with Bos taurus, Bos indicus, Ovis aries, Capra hircus, and Homo sapiens, respectively.

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Sequencing Analysis and Phylogenetic Tree of HPV Isolated from Breast Cancer Patients at Thi-Qar Province/Iraq

10.32792/utq/utjsci/vol7/2/10 ◽

2020 ◽

pp. 37-40

Keyword(s):

Nucleotide Sequence ◽

Phylogenetic Tree ◽

Evolutionary Relationship ◽

Nucleotide Sequencing ◽

Sequencing Analysis ◽

Breast Cancer Patients ◽

The North ◽

Formalin Fixed Paraffin ◽

Formalin Fixed Paraffin Embedded ◽

History Of

Genetic variety examination has demonstrated fundamental to the understanding of the epidemiological and developmental history of Papillomavirus (HPV), for the development of accurate diagnostic tests and for efficient vaccine design. The HPV nucleotide diversity has been investigated widely among high-risk HPV types. To make the nucleotide sequence of HPV and do the virus database in Thi-Qar province, and compare sequences of our isolates with previously described isolates from around the world and then draw its phylogenetic tree, this study done. A total of 6 breast formalin-fixed paraffin-embedded (FFPE) of the female patients were included in the study, divided as 4 FFPE malignant tumor and 2 FFPE of benign tumor. The PCR technique was implemented to detect the presence of HPV in breast tissue, and the real-time PCR used to determinant HPV genotypes, then determined a complete nucleotide sequence of HPV of L1 capsid gene, and draw its phylogenetic tree. The nucleotide sequencing finding detects a number of substitution mutation (SNPs) in (L1) gene, which have not been designated before, were identified once in this study population, and revealed that the HPV16 strains have the evolutionary relationship with the South African race, while, the HPV33 and HPV6 showing the evolutionary association with the North American and East Asian race, respectively.

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