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

2000 ◽  
Vol 70 (2) ◽  
pp. 221-226 ◽  
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.

scholarly journals Detection and Differentiation of Primate α-herpesviruses by PCR

1997 ◽  
Vol 9 (3) ◽  
pp. 225-231 ◽  
Author(s):  
Daria H. Black ◽  
R. Eberle
Keyword(s):  
Pcr Primers ◽  
Restriction Pattern ◽  
Restriction Enzyme Digestion ◽  
Gene Encoding ◽  
B Virus ◽  
Pcr Rflp ◽  
Pcr Products ◽  
Unique Restriction ◽  
Polymerase Chain ◽  
Simplex Virus

A rapid method for detection and differentiation of 5 primate αpha-herpesviruses (human herpes simplex virus types 1 and 2 [HSV1, HSV2], green monkey simian agent 8, baboon herpesvirus 2 [HVP2], and macaque B virus [BV]) was developed utilizing the polymerase chain reaction (PCR). PCR primers were located in conserved regions of the gene encoding the glycoprotein B, which flanks an intervening region that is highly divergent among the 5 viruses. Amplified PCR products from the 5 viruses were readily differentiated by their unique restriction enzyme digestion patterns. No variation in digestion patterns was noted among strains of HSV1, HSV2, or HVP2. One clinical isolate of BV exhibited variation in a single restriction site, but its overall restriction pattern remained typical of BV. This method (PCR/RFLP) allowed the presence of herpesvirus DNA in clinical swabs from primates to be readily detected and the virus unambiguously identified.

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

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Ahmed. A. 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, 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.

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

2009 ◽  
Vol 25 (1-2) ◽  
pp. 101-109 ◽  
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.

scholarly journals Comparitive Genome Sequence Analysis of Bovine Lymphocyte Antigen BoLA DRB3.2 Alleles in Deoni and Ongole (Bos indicus) Cattle Breeds of India

2021 ◽  
Author(s):  
R. Saravanan ◽  
N. Murali ◽  
A.K. Thiruvenkadan ◽  
D.N. Das
Keyword(s):  
Sequence Analysis ◽  
Direct Sequencing ◽  
Major Gene ◽  
Rflp Analysis ◽  
Mobility Shift ◽  
Exon 2 ◽  
Lymphocyte Antigen ◽  
Pcr Rflp ◽  
Bovine Lymphocyte ◽  
Indian Cattle

Background: India, a major livestock region of the Asian countries is rich in animal genetic resources having special qualities of hardy nature, resistance to many diseases and adopted to adverse climatic conditions. The cattle MHC, Bovine Lymphocyte Antigen DRB3 (BoLA-DRB3) is considered to be a major gene linked with disease resistance traits of Indian cattle. Methods: The present study was carried out to sequence the BoLA-DRB3.2 alleles in Deoni and Ongole breeds of Indian cattle. PCR RFLP analysis of the BoLA-DRB3.2 alleles in Deoni (n=51) and Ongole (n=60) cattle using three different restriction enzymes RsaI, BstYI and HaeIII to find out the possible restriction pattern. Based on the combined allelic patterns, each sample was further analyzed by PCR- SBT technique to detect the SNP variations present in BoLA-DRB3.2 alleles.Result: The PCR RFLP analysis revealed that the highest frequent alleles are *6 (0.216) and *15 (0.225) in Deoni and Ongole breeds of cattle, respectively. The second-highest frequency was observed for BoLA alleles *11 and *6 which were present at a frequency of 0.167 and 0.200 in Deoni and Ongole breeds of cattle, respectively. To get the complete picture of polymorphic pattern of BoLA-DRB3.2 allele direct sequencing was carried out for each plymorphic pattern. The interesting feature noticed in the Ongole breed was that at position 91 and 133 of the sequence, it had both A and G nucleotides in contrast to Bos taurus breed, which had only TT nucleotides. The sequence analysis of BoLA-DRB3 exon 2 between two breeds revealed that there are numerous variations in exon 2, whatever variation, that lead to different mobility shift and band pattern in gels. Deoni and Ongole breeds of cattle had similar variations at positions 94, 134, 211, 235 and 258noticed due to the unique nature of native breeds.

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

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.

Rapid and reliable identification of rice genomes by RFLP analysis of PCR-amplified Adh genes

Genome ◽  
2001 ◽  
Vol 44 (6) ◽  
pp. 1136-1142 ◽  
Author(s):  
Song Ge ◽  
Tao Sang ◽  
Bao-rong Lu ◽  
De-yuan Hong
Keyword(s):  
Rflp Analysis ◽  
Restriction Enzymes ◽  
Pcr Primers ◽  
Specific Pcr ◽  
Adh Genes ◽  
Pcr Rflp ◽  
Restriction Sites ◽  
Pcr Products ◽  
Adh Gene ◽  
Genus Oryza

The rice genus (Oryza L.) consists of 24 species with 10 recognized genome types. With the realization of many useful genes in species of wild rice, continuous efforts have been made to understand their genomic composition and relationships. However, the identification of rice genomes has often been difficult owing to complex morphological variation and formation of allotetraploids. Here we propose a rapid and reliable method for identifying rice genomes based on the restriction sites of PCR-amplified Adh genes. The experimental procedure was as follows: (i) amplify a portion of Adh1 and Adh2 genes with the locus-specific PCR primers; (ii) digest PCR products with restriction enzymes that distinguish different genomes; and (iii) run the digested products on 1.4% agarose gel, and photograph. Using various combinations of restriction digestion of the two Adh genes, all of the rice genomes can be identified.Key words: Adh gene, genome, identification, Oryza L., PCR–RFLP.

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

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.

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

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.

Estudio del polimorfismo y poligenismo de los loci DRB en caballos criollo argentino

2003 ◽  
Author(s):  
◽  
Silvina Díaz
Keyword(s):  
Exon 2 ◽  
Pcr Rflp

El objetivo del trabajo de Tesis Doctoral consistió en estudiar el polimorfismo y el poligenismo de los genes de clase II DRB del Complejo Principal de Histocompatibilidad en Equinos (ELA). La variabilidad genética de las regiones promotoras y de la región de reconocimiento del antígeno (exón 2) se analizó mediante los métodos de PCR-RFLP y PCR-SSCP. Se detectaron tres nuevos alelos del exón 2 definidos por PCR-RFLP, los que se confirmaron por clonado y secuenciación de los productos de amplificación. Además, el número de variantes detectadas en cada animal permitió inferir la presencia de al menos tres copias de genes DRB en los haplotipos equinos analizados. Estos datos se confirmaron a través de análisis filogenético y de segregación. El clonado y secuenciación de la región reguladora (URR) de los genes DRB permitió caracterizar la organización del promotor proximal. Los resultados obtenidos mostraron la presencia en dirección 5´ - 3´ de las cajas conservadas W, X, Y, CCAAT y TATA. Esta estructura es semejante a la reportada en los genes ortólogos de otras especies de mamíferos y evidenciaría que la región analizada corresponde a un gen DRB funcional. Por otra parte, el análisis del polimorfismo del promotor permitió identificar cinco alelos definidos por SSCP. El conjunto de resultados obtenidos mostró que los genes ELA-DRB presentan las principales características descriptas para los genes de Clase II de mamíferos: existencia de copias múltiples, alto grado de polimorfismo, alta tasa de sustituciones no sinónimas en los sitios de reconocimiento del antígeno, y conservación de secuencia y estructura del promotor proximal.

Association Study of Fecundity Gene BMPR1B with Prolificacy in Surti Goats under Farm and Field Condition

2019 ◽  
Vol 14 (04) ◽  
Author(s):  
N. S. Dangar ◽  
G. M. Pandya ◽  
U. V. Ramani ◽  
Y. D. Padheriya ◽  
T. Sangma ◽  
...  
Keyword(s):  
Litter Size ◽  
Transforming Growth Factor Beta ◽  
Transforming Growth Factor ◽  
Pcr Primers ◽  
Dual Purpose ◽  
Protein Receptor ◽  
Morphogenetic Protein ◽  
Pcr Rflp ◽  
Base Size ◽  
Mutation Information

The Surti is a dual purpose goat breed of Gujarat. The bone morphogenetic protein receptor type 1B (BMPR1B) gene of transforming growth factor beta (TGF-β) superfamily ligands is playing a role in ovulation as well as litter size. Mutation in Exon-6 region of BMPR1B gene with base size 190 bp reported increasing litter size. Based on the known mutation information in goat and sheep, PCR primers were designed to screen polymorphism in total 100 Surti goats, 50 Surti goats from University Farm, Navsari and 50 Surti goats from field units of Southern part of Gujarat. During PCR-RFLP study no polymorphic sites were found for Exon-6 region of BMPR1B on Surti goats. Moreover, the twinning rate was 10% in first parity and higher in subsequent second (62.5%) and third (76.8%) parties.

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