scholarly journals Avian Beta Defensin 2 (AvBD2) Gene Polymorphism Identification in IPB-D1 Chicken

2021 ◽  
Vol 26 (2) ◽  
pp. 82
Author(s):  
Masrurah Masrurah ◽  
Isyana Khaerunnisa ◽  
Sri Murtini ◽  
Cece Sumantri
Keyword(s):  
Gene Polymorphism ◽  
Tissue Injury ◽  
Chromosome 3 ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Exon 2 ◽  
Direct Dna Sequencing ◽  
Body Tissues ◽  
Intron 1 ◽  
Intron 2

<p class="abstrak3">Avian Beta Defensin 2 (AvBD2) gene, which is located in chromosome 3, plays an important role in the immune system of the chicken by inhibiting the development of microorganisms such as bacteria that infect body tissues. Defensins are produced through epithelial cells immediately after tissue injury or infection, which then processes the maturation of dendritic cells to initiate an immune response in the lymph nodes. The purpose of this study was to discover the polymorphism of the AvBD2 gene in IPB-D1 chickens. PCR and direct-DNA sequencing methods were used to identify the diversity of intron 1, exon 2, and intron 2 AvDB2 genes in 47 chickens. Genotype and allele frequency, and heterozygosity calculations were carried out to obtain information of the AvBD2 gene polymorphism. A total of 10 single nucleotide polymorphisms were found in the AvBD2 gene located in intron 1 (g.4843T&gt;A, g.4853G&gt;A, and g.4859T&gt;C), exon 2 (g.4881A&gt;G, g.4889G&gt;A, and g.5002C&gt;T), and intron 2 (g.5075C&gt;T, g.5111T&gt;G, g.5116G&gt;T, and g.5177G&gt;T). All SNPs are polymorphic. The g.5002C&gt;T mutation causes changes in the amino acid Ala to Val which has the potential to be a candidate for characterizing disease resistance in IPB-D1 chickens.</p>

Polymorphisms of LHβ and GnRHR genes and their association with the number of embryos recovered in goats

2014 ◽  
Vol 54 (8) ◽  
pp. 987 ◽  
Author(s):  
M. Z. Fu ◽  
G. Li ◽  
Z. Q. Zhou
Keyword(s):  
Polymerase Chain Reaction ◽  
Single Nucleotide Polymorphisms ◽  
Gene Polymorphism ◽  
Corpus Luteum ◽  
Nucleotide Polymorphisms ◽  
Chain Reaction ◽  
Single Strand Conformational Polymorphism ◽  
Single Nucleotide ◽  
Exon 2 ◽  
Polymerase Chain

The objective of the present study was to explore a predictor of superovulation response on the basis of associations between the number of embryos recovered and gene polymorphism. Variation in the goat LHβ and GnRHR genes was investigated using polymerase chain reaction–single-strand conformational polymorphism and DNA sequencing. Two single nucleotide polymorphisms (SNPs) were identified in the 5′-UTR of LHβ gene (A59C, P1 locus) and in the Exon 2 of GnRHR gene (T177A, P6 locus). At the P1 locus in both breeds, the frequencies of one allele were 0.46 and 0.51, respectively. At the P6 locus, the minor allele frequency was 0.23. Associations of both SNPs with the number of embryos recovered and the corpus luteum number were evaluated in Boer and Shaanbei goat breeds. Association analysis showed that both SNPs had significant (P < 0.05) effects on the number of embryos recovered and corpus luteum number. These results indicate that LHβ and GnRHR genes are potential markers for the number of embryos recovered.

scholarly journals Associations between Leptin Gene Polymorphisms and Somatic Cell Count in Milk of Jersey Cows

2010 ◽  
Vol 79 (2) ◽  
pp. 237-242 ◽  
Author(s):  
Hanna Kulig ◽  
Marek Kmieć ◽  
Katarzyna Wojdak-Maksymiec
Keyword(s):  
Somatic Cell ◽  
Cell Count ◽  
Gene Polymorphisms ◽  
Somatic Cell Count ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Exon 2 ◽  
Jersey Cows ◽  
Intron 2 ◽  
Genotype And Allele Frequencies

A total of 181 Jersey cows were used to investigate how leptin gene polymorphisms affect somatic cell count (SCC) in milk. Three single nucleotide polymorphisms were genotyped, namely the R4C polymorphism in exon 2, the Sau3AI polymorphism in intron 2 and the A59V polymorphism in exon 3. The genotype and allele frequencies for each polymorphism and the haplotype frequencies for all polymorphisms were estimated in the herd under study. Statistical analysis revealed that the R4C and Sau3AI polymorphisms significantly affected SCC (P &#x2AAC 0.01) with C and T as a desirable allele, respectively. No associations were found between the A59V polymorphism and SCC in this study. However, all the genotype combinations (haplotypes) significantly affected this trait. The results indicate that selection for the R4C CC and Sau3AI TT animals might contribute to a reduction of SCC in Jersey cattle.

scholarly journals Analysis of HorseMyostatinGene and Identification of Single Nucleotide Polymorphisms in Breeds of Different Morphological Types

2010 ◽  
Vol 2010 ◽  
pp. 1-11 ◽  
Author(s):  
Stefania Dall'Olio ◽  
Luca Fontanesi ◽  
Leonardo Nanni Costa ◽  
Marco Tassinari ◽  
Laura Minieri ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Tata Box ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Analysis Of Molecular Variance ◽  
Molecular Variance ◽  
Intron 1 ◽  
Significant Difference ◽  
Intron 2 ◽  
Negative Modulator

Myostatin (MSTN) is a negative modulator of muscle mass. We characterized the horse (Equus caballus)MSTNgene and identified and analysed single nucleotide polymorphisms (SNPs) in breeds of different morphological types. Sequencing of coding, untranslated, intronic, and regulatory regions ofMSTNgene in 12 horses from 10 breeds revealed seven SNPs: two in the promoter, four in intron 1, and one in intron 2. The SNPs of the promoter (GQ183900:g.26TC and GQ183900:g.156TC, the latter located within a conserved TATA-box like motif) were screened in 396 horses from 16 breeds. The g.26C and the g.156C alleles presented higher frequency in heavy (brachymorphic type) than in light breeds (dolichomorphic type such as Italian Trotter breed). The significant difference of allele frequencies for the SNPs at the promoter and analysis of molecular variance (AMOVA) on haplotypes indicates that these polymorphisms could be associated with variability of morphology traits in horse breeds.

scholarly journals Distribution of QPY and RAH haplotypes of granzyme B gene in distinct Brazilian populations

2012 ◽  
Vol 45 (4) ◽  
pp. 496-499
Author(s):  
Fernanda Bernadelli Garcia ◽  
Simone Kashima ◽  
Evandra Strazza Rodrigues ◽  
Israel Tojal Silva ◽  
Tathiane Maistro Malta ◽  
...  
Keyword(s):  
Granzyme B ◽  
Treatment Strategies ◽  
Cytotoxic Lymphocytes ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Exon 2 ◽  
Significant Difference ◽  
Novel Treatment Strategies ◽  
Brazilian Populations ◽  
Afro Brazilian

INTRODUCTION: The cytolysis mediated by granules is one of the most important effector functions of cytotoxic T lymphocytes and natural killer cells. Recently, three single nucleotide polymorphisms (SNPs) were identified at exons 2, 3, and 5 of the granzyme B gene, resulting in a haplotype in which three amino acids of mature protein Q48P88Y245 are changed to R48A88H245, which leads to loss of cytotoxic activity of the protein. In this study, we evaluated the frequency of these polymorphisms in Brazilian populations. METHODS: We evaluated the frequency of these polymorphisms in Brazilian ethnic groups (white, Afro-Brazilian, and Asian) by sequencing these regions. RESULTS: The allelic and genotypic frequencies of SNP 2364A/G at exon 2 in Afro-Brazilian individuals (42.3% and 17.3%) were significantly higher when compared with those in whites and Asians (p < 0.0001 and p = 0.0007, respectively). The polymorphisms 2933C/G and 4243C/T also were more frequent in Afro-Brazilians but without any significant difference regarding the other groups. The Afro-Brazilian group presented greater diversity of haplotypes, and the RAH haplotype seemed to be more frequent in this group (25%), followed by the whites (20.7%) and by the Asians (11.9%), similar to the frequency presented in the literature. CONCLUSIONS: There is a higher frequency of polymorphisms in Afro-Brazilians, and the RAH haplotype was more frequent in these individuals. We believe that further studies should aim to investigate the correlation of this haplotype with diseases related to immunity mediated by cytotoxic lymphocytes, and if this correlation is confirmed, novel treatment strategies might be elaborated.

scholarly journals Leptin gene polymorphism of Ongole Grade cattle based on single nucleotide polymorphism

2018 ◽  
Vol 43 (4) ◽  
pp. 309
Author(s):  
N. Hilmia ◽  
D. Rahmat ◽  
D. Dudi
Keyword(s):  
Amino Acids ◽  
Single Nucleotide Polymorphism ◽  
Gene Polymorphism ◽  
Direct Sequencing ◽  
Snp Analysis ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Exon 2 ◽  
Specific Allele ◽  
Polymerase Chain

Point mutation on exon 2 of leptin gene, which changes amino acid encoding from Arginine to Cysteine, may alters the physiological function of the leptin hormone. This study aimed to identify leptin gene polymorphism of Ongole Grade (OG) cattle based on Single Nucleotide Polymorphism (SNP). The DNA sample was taken from 48 head of OG cattle at Balai Pengembangan Perbibitan Ternak Sapi Potong(BPPT SP) Cijeungjing West Java, which was isolated from white blood cell using the high salt method. Amplification of DNA was done by Polymerase Chain Reaction (PCR), followed by direct sequencing to obtain nucleotide sequence. The SNP analysis was carried out from alignment of sequencing result using Bioedit and MEGA 5.2 program. The results indicated in exon 2 leptin gene of OG cattle there was one synonymous SNPs that did not changeamino acids Serine encoding on g.1025T >C/S17S, while two non synonymous SNPaltered amino acids encoding, those were g.1047C> T /R25C and g.1048G>A/R25H. Those mutations changed amino acids encoding from Arginine to Cysteine and Arginine to Histidine respectively.In OG cattle, the frequency of A allele (44.8%) was higher than C allele (33.3%) and T allele (21.9%). Six genotypes were also identified, i.e. AA (41.7%), CC (20.8%), CT (20.8%), CA(4.2%), TT (10.4%) and TA (2.1 %). Heterozigosity of OG cattle based on leptin gene was 0.65 that was a high category. The A allele was a specific allele on Indonesian local cattle.

scholarly journals Heterozygous Ile453Val codon mutation in exon 7, homozygous single nucleotide polymorphisms in intron 2 and 5 of cathepsin C are associated with Haim-Munk syndrome

2014 ◽  
Vol 08 (01) ◽  
pp. 079-084 ◽  
Author(s):  
Nalini Aswath ◽  
Bhuminathan Swamikannu ◽  
Sankar Narayanan Ramakrishnan ◽  
Rajendran Shanmugam ◽  
Jayakar Thomas ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Direct Sequencing ◽  
Sequencing Analysis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Heterozygous Condition ◽  
South Indian ◽  
The Subject ◽  
First Time ◽  
Intron 2

ABSTRACT Objective: In the present study, we have investigated the genetic status of CTSC gene in a HMS subject, who along with her parents belonged to non-Jewish South Indian Dravidian community. Materials and Methods: Genomic deoxyribonucleic acid isolated from the peripheral blood of the subject was amplified with CTSC exon specific primers and were analyzed by direct sequencing. Results: Sequencing analysis identified Ile453Val mutation within exon 7 of CTSC gene in heterozygous condition, and two single nucleotide polymorphisms (SNPs) within intron 2 and 5 in homozygous condition. Conclusion: The present study has identified for the first time the association of Ile453Val mutation within exon 7 and the two SNPs in a subject with HMS.

scholarly journals Analytical Validation of the Tag-It High-Throughput Microsphere-Based Universal Array Genotyping Platform: Application to the Multiplex Detection of a Panel of Thrombophilia-Associated Single-Nucleotide Polymorphisms

2004 ◽  
Vol 50 (11) ◽  
pp. 2028-2036 ◽  
Author(s):  
Susan Bortolin ◽  
Margot Black ◽  
Hemanshu Modi ◽  
Ihor Boszko ◽  
Daniel Kobler ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
High Throughput ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
Single Nucleotide ◽  
Direct Dna Sequencing ◽  
Array Platform ◽  
Genotyping Platform ◽  
Universal Array ◽  
Primer Sets

Abstract Background: We have developed a novel, microsphere-based universal array platform referred to as the Tag-It™ platform. This platform is suitable for high-throughput clinical genotyping applications and was used for multiplex analysis of a panel of thrombophilia-associated single-nucleotide polymorphisms (SNPs). Methods: Genomic DNA from 132 patients was amplified by multiplex PCR using 6 primer sets, followed by multiplex allele-specific primer extension using 12 universally tagged genotyping primers. The products were then sorted on the Tag-It array and detected by use of the Luminex xMAP™ system. Genotypes were also determined by sequencing. Results: Empirical validation of the universal array showed that the highest nonspecific signal was 3.7% of the specific signal. Patient genotypes showed 100% concordance with direct DNA sequencing data for 736 SNP determinations. Conclusions: The Tag-It microsphere-based universal array platform is a highly accurate, multiplexed, high-throughput SNP-detection platform.

Association of FSHR gene polymorphisms with endometriosis in women visiting tertiary-care hospitals of Lahore, Pakistan

2021 ◽  
pp. 1-14
Author(s):  
Irfana Liaqat ◽  
Najiya al Arifa ◽  
Saba Asif ◽  
Khalid Parvaiz Lone ◽  
Admin
Keyword(s):  
Tertiary Care ◽  
Nucleotide Polymorphisms ◽  
Yale University ◽  
Blood Leukocytes ◽  
Single Nucleotide ◽  
Direct Dna Sequencing ◽  
Control Subjects ◽  
Fshr Gene ◽  
High Incidence ◽  
Tertiary Care Hospitals

Abstract Objectives: The study was aimed to explore the association of endometriosis risk factors with single nucleotide polymorphisms rs6166 and rs6165 (Asn680Ser and Ala307Thr) of follicle stimulating hormone receptor (FSHR) gene in Pakistani women. Methods: This study was conducted from 2013 to 2016. The sampling and extraction of DNA was done in Department of Zoology GC University Lahore while the sequencing was performed at Yale University USA. This case control study consists of 364 subjects including 156 women diagnosed with endometriosis and 208 randomly recruited controls. Subjects diagnosed at stage II-IV endometriosis with infertility were pooled for study. The women with adenomyosis, ovarian cancer and leiomyoma were excluded. The whole blood leukocytes were used for DNA extraction. Two important polymorphisms of exon 10 of FSHR gene were analyzed by direct DNA sequencing both in endometriosis and controls. Results: SNP rs6166 in the affected endometriosis subjects exhibited high incidence of allele “A” (Asn/Asn) 68.3% as compared to controls 33.7% (OR= 4.240; P =0.001). Similarly, the allele “A” of SNP rs6165 (Thr/Thr) was more frequent in endometriosis 67.3% than in control subjects 37.5% (OR =3.430, P =0.001). The occurrence of haplotype AA (Asn/Thr) was 45.5% in endometriosis and 11 % in control subjects (P= 0.001).  Remarkably, the incidence of haplotype GG (Ser/Ala) was contrary to previous observations, since only 9.9% occurred in endometriosis as opposed to 45.2% in controls (P= 0.001). Continuous...  

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