scholarly journals The association of SNP g.880A/G with body weight in F1 cross Dorper x Garut sheep

2021 ◽  
Vol 888 (1) ◽  
pp. 012002
Author(s):  
A P Z N L Sari ◽  
I R Athifa ◽  
Panjono ◽  
R Hidayat ◽  
Y G Noor ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Body Weight ◽  
Birth Weight ◽  
Direct Sequencing ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Mc4r Gene ◽  
Hardy Weinberg Equilibrium ◽  
F1 Cross ◽  
Sequencing Process

Abstract Single nucleotide polymorphism (SNP) in the MC4R gene has been known to be associated with feed intake and growth performance. Our objective was to analyze the association of SNP g.880A>G to birth weight (BW), weaning weight (WW), and 6-month body weight (MW) in F1 cross Dorper x Garut sheep. In forty-one F1 cross Dorper x Garut sheep with phenotypic records, genotyping based on SNP g.880A>G was achieved using the direct-sequencing process. As a result, the homozygous AA genotype was absent in the samples. The frequency of the G allele (90%) was higher than the A allele (10%), followed by GG (80%) and AG (20%) genotypes. The population did not deviate from Hardy Weinberg Equilibrium (p > 0.05) based on SNP g.880A>G. The SNP g.880A>G was significantly associated with MW but not significant in BW and WW. The GG genotype (32.33 ± 4.81 kg) was higher MW than the AG genotype (27.19 ± 1.86 kg). In conclusion, the findings suggested that SNP g.880A>G of the MC4R gene could be used as a potential selection tool for high MW in F1 cross Dorper x Garut sheep.

5 A SINGLE NUCLEOTIDE POLYMORPHISM IN COQ9 AFFECTS MITOCHONDRIAL FUNCTION, BODY WEIGHT CHANGE AFTER CALVING, AND FERTILITY IN HOLSTEIN COWS

2016 ◽  
Vol 28 (2) ◽  
pp. 132
Author(s):  
M. S. Ortega ◽  
S. Wohlgemuth ◽  
D. J. Null ◽  
J. B. Cole ◽  
P. J. Hansen
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Body Weight ◽  
Electron Transport ◽  
Transport System ◽  
Respiratory Function ◽  
Electron Transport System ◽  
Holstein Cows ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Days Open

A single nucleotide polymorphism for COQ9 has been associated with genetic merit for fertility in 2 separate populations of Holstein cattle, with the A allele associated with higher fertility. COQ9 is necessary for the synthesis of coenzyme Q10, a component of the electron transport system of the mitochondria. We evaluated the effect of COQ9 genotype on the electron transport system, body weight changes after calving, and phenotypic measurements of fertility and production in Holstein cows. The single nucleotide polymorphism in COQ9 was genotyped using a Sequenom MassARRAY® (Sequenom Inc., San Diego, CA, USA). In the first study, cows ≥200 days in milk were selected for analysis of mitochondrial oxygen consumption [COQ9 genotype: AA (n = 12), AG (n = 12), and GG (n = 12)]. Peripheral blood mononuclear cells were isolated and respiration assessed using the Oroboros O2k high-resolution respirometer to evaluate routine respiration, R; leak respiration, L; and electron transport system capacity, E. There were additive effects of genotype on respiratory function (P < 0.05): R was 3.4 ± 0.3, 4.7 ± 0.3, and 4.9 ± 0.3 pmol of O2/s per 106 cells, L was 1.9 ± 0.3, 2.7 ± 0.3, and 3.0 ± 0.3 pmol of O2/s per 106 cells, and the uncoupling control ratio (E/R) was 3.4 ± 0.2, 2.5 ± 0.2, and 2.1 ± 0.2 for AA, AG, and GG, respectively. In a second study, body weight was recorded for AA (n = 106), AG (n = 223), and GG (n = 86) cows during the first 20 weeks postpartum for 2 consecutive lactations. In both lactations, body weight postpartum was affected by genotype × time postpartum (P < 0.001), with cows of the AA genotype experiencing less weight loss than AG (second lactation only) and GG cows. Days open, services per conception, and 305-day milk yield (MY) for the first 2 lactations were evaluated in a population of 2273 Holstein cows grouped based on predicted transmitting ability for daughter pregnancy rate: ≤–1 (n = 1220) and ≥1.5 (n = 1053). Continuous data were analysed using the MIXED procedure of SAS, and categorical data were analysed using the GLIMMIX procedure. The model included farm, genotype, and the numerator relationship matrix to account for (co)variances among animals. Additive and dominance effects were estimated. Genotype affected each trait (P < 0.05). Values for AA, AG, and GG for the first lactation were as follows: days open, 123.6 ± 3.5, 134.3 ± 2.8, and 139.4 ± 3.5 days; services per conception, 2.4 ± 0.1, 2.5 ± 0.1, and 2.7 ± 0.1; and MY, 11 278 ± 65, 11 416 ± 51, and 11 478 ± 65 kg. For the second lactation COQ9 affected (P < 0.05) days open (133.2 ± 4.7, 142.9 ± 3.1, and 147.9 ± 3.9 days) and services per conception (2.5 ± 0.1, 2.6 ± 0.8, and 2.7 ± 0.1), but there was no effect (P = 0.63) on MY (11 486 ± 66, 11 502 ± 52, and 11 526 ± 57 kg). Results indicate that the same genotype associated with genetic merit for fertility (AA) is associated with more efficient respiratory function and less body-weight loss postpartum. Moreover, the favourable genotype was associated with higher phenotypic measurements of fertility and lower MY. Results indicate the single nucleotide polymorphism in COQ9 could be a potential marker for fertility and that allelic variants may affect fertility by altering respiratory efficiency. Study was supported by USDA AFRI 2013–68004–20365.

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 Detection of Single Nucleotide Polymorphism rs2013162 of IRF6 Gene in Patient with Cleft Lip and Palate

2019 ◽  
Vol 3 (1) ◽  
pp. 28-40
Author(s):  
Husnain Shehzad ◽  
Osheen Shehzad
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Cleft Lip ◽  
Cleft Lip And Palate ◽  
Melting Curve ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Pakistani Population ◽  
Irf6 Gene ◽  
High Resolution Melting Curve ◽  
Hardy Weinberg Equilibrium

Abstract: Background: Cleft lip and palate are congenital disorders which induce affected individuals medically, socially and psychologically. The objective of this study was to investigate the association of Single Nucleotide Polymorphism(SNP); rs2013162 of IRF6 Gene in Patient with Cleft Lip and Palate. Materials and Methods: Fifty patients with non-syndromic CL/P were included in present study alongwith fifty individuals with no psychiatric history as controls. In all of the these individuals, search for Single nucleotide polymorphism was carried out by designing sequence specific primers. The sequence was amplified by using Real time PCR and products were investigated by visualizing high resolution melting curve upon HRM-PCR. Results: The logistic regression and Hardy-Weinberg equilibrium were applied to investigate the association of IRF6 SNP rs2013162 with disease. Results revealed no association of this polymorphism with non-syndromic CL/P. Conclusion: We found no association of IRF6 SNP rs2013162 in patients with non-syndromic CL/P. Further study is required with larger sample size to validate the findings of the present study in Pakistani population and along with this SNP other polymorphisms of the same gene should be analyzed to find out the association with the non-syndromic CL/P.

scholarly journals FANCA Polymorphism Is Associated with the Rate of Proliferation in Uterine Leiomyoma in Korea

2020 ◽  
Vol 10 (4) ◽  
pp. 228
Author(s):  
Eunyoung Ha ◽  
Seungmee Lee ◽  
So Min Lee ◽  
Jeeyeon Jung ◽  
Hyewon Chung ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Missense Mutation ◽  
Uterine Leiomyoma ◽  
Direct Sequencing ◽  
Uterine Leiomyomas ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Slow Group ◽  
Fresh Frozen ◽  
Fast Group

Uterine leiomyomas are the most common benign gynecologic tumors. This study was aimed to identify single nucleotide polymorphism of Fanconi anemia complementation group A (FANCA), associated with the rate of proliferation in uterine leiomyomas. In vitro study of patient-derived primary-cultured leiomyoma cells and direct sequencing of fresh frozen leiomyoma from each subject was conducted. Leiomyomas obtained from 44 patients who had underwent surgery were both primary-cultured and freshly frozen. Primary-cultured leiomyoma cells were divided into, according to the rate of proliferation, fast and slow groups. Single nucleotide polymorphism (SNP) of FANCA were determined from fresh frozen tissues of each patient using direct sequencing. Direct sequencing revealed a yet unidentified role of FANCA, a caretaker in the DNA damage-response pathway, as a possible biomarker molecule for the prediction of uterine leiomyoma proliferation. We identified that rs2239359 polymorphism, which causes a missense mutation in FANCA, is associated with the rate of proliferation in uterine leiomyomas. The frequency of C allele in the fast group was 35.29% while that in slow group was 11.11% (odds ratio (OR) 4.036 (1.176–13.855), p = 0.0266). We also found that the TC + CC genotype was more frequently observed in the fast group compared with that in the slow group (OR 6.44 (1.90–31.96), p = 0.0227). Taken together, the results in the current study suggested that a FANCA missense mutation may play an important regulatory role in the proliferation of uterine leiomyoma and thus may serve as a prognostic marker.

scholarly journals Polymorphism of Prolactin Gene and Its Association with Egg Production Trait in Four Commercial Chicken Lines

2018 ◽  
Vol 68 (3) ◽  
pp. 391 ◽  
Author(s):  
MOHAMED M.M. OSMAN ◽  
SHAABAN A. HEMEDA ◽  
ABEER A.I. HASSANIN ◽  
WALAA A. HUSSEINY
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Egg Production ◽  
Direct Sequencing ◽  
Nucleotide Polymorphism ◽  
Wing Vein ◽  
Single Nucleotide ◽  
Exon 2 ◽  
Avian Reproduction ◽  
Commercial Chicken ◽  
Prolactin Gene

Broodiness is a behavioral trait observed in most common breeds of domestic fowl and due to its fundamental role in avian reproduction, it has been of great interest to poultry scientists, breeders and producers of hatching eggs. Prolactin gene (PRL) is generally accepted as crucial to the onset and maintenance of broodiness in birds and thus plays a crucial role in egg production. Therefore, the present study aimed to screen the Single Nucleotides Polymorphisms (SNPs) of prolactin gene in four commercial chicken lines namely Hubbard F15, Lohmann, Cobb500, and Avian48 using PCR and direct sequencing. A total number of forty chickens (ten females from each of the four commercial chicken lines) were used. Blood samples were collected aseptically from brachial (wing) vein of the chickens for genomic DNA extraction. PCR reaction was done using five pairs of primers, one sense (F) and one antisense (R) primer for each of the five exons of prolactin gene. Finally, DNA sequencing and Single Nucleotide Polymorphisms (SNPs) analysis was done using Laser gene Megalign program. The results showed three SNPs in Hubbard F15 chicken line; one synonymous SNP at the position 3838 bp (ACC/ACT-transition) in exon 2 while in exon 5, two SNPs were detected; one non-synonymous single nucleotide polymorphism at the position 7921bp (CCT/TCT-transition) which results in amino acid changes at codon positions 169 (P/S), and one synonymous single nucleotide polymorphism at the position 8187 bp T/ C. The study concluded that this SNP in PRL gene could be used as the potential molecular markers for egg production traits in chicken.

Association of BTNL2 gene single nucleotide polymorphism with knee osteoarthritis

2021 ◽  
Vol 25 (2) ◽  
pp. 89-95
Author(s):  
S. S. Sahoo ◽  
O. K. Choudhari ◽  
J. Bhadra ◽  
B. C. Kabi
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Knee Osteoarthritis ◽  
Indian Population ◽  
Amplification Refractory Mutation System ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genotypic Distribution ◽  
Mutation System ◽  
Hardy Weinberg Equilibrium

Relevance. Osteoarthritis (OA) is one of the chronic debilitating condition mostly seen in the aged population. The etiology behind the OA is multifactorial and the exact cause of the disease often remains uncertain. Apart from the conventional risk factors, there are the speculations of role of genetics playing a pivotal role in the causation of OA. The available literature showed BTNL2 gene polymorphism association with risk of Osteoarthritis whether the same relation is present in north Indian population needs to be elucidated. Objective. To find the association between single nucleotide polymorphism (SNP) (rs10947262) in BTNL2 gene and the susceptibility in knee Osteoarthritis (OA) subjects from northern Indian population. Materials and Methods. Blood samples of 100 patients of knee osteoarthritis and 100 healthy subjects were collected after institutional ethical clearance and participants consent. The BTNL2 gene fragment was amplified using Amplification Refractory Mutation System (ARMS-PCR) with predesigned primers after DNA extraction. The corresponding product bands were identified on the gel electrophoresis for 200 samples and the results were statistically analyzed. Results and Discussion. The genotypic distribution of the SNP followed Hardy-Weinberg Equilibrium. The genotype frequency analysis of the polymorphism was statistically significant (2=7.788; P=0.005) with Odds Ratio of CT+TT/CC: OR=2.303; P=0.008 revealing association of BTNL2 polymorphism with risk of Knee Osteoarthritis. Conclusion. The SNP (rs10947262) in the BTNL2 gene region is associated with risk of knee osteoarthritis.

Single Nucleotide Polymorphism of CDC37, AHSA1 and STIP1 Gene in Three Cattle Breeds using SNaPshot Technology

2021 ◽  
Author(s):  
Xiao Wang ◽  
Guang-Xin E ◽  
Ri-Su Na ◽  
Cheng-Li Liu ◽  
Ze-Hui Guo ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Heat Stress ◽  
Selective Breeding ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Cattle Breeds ◽  
Hardy Weinberg Equilibrium ◽  
Simmental Cattle ◽  
Candidate Gene Locus ◽  
Multiplex System

Background: Heat stress in domestic animals has become a major limit factor for livestock production in tropical and subtropical regions. These traits that adapt to torrid environment are important in livestock breeding.Methods: In this study, we identified and genotyped six Single nucleotide polymorphism for the CDC37, AHSA1 and STIP1 gene in the Droughtmaster, Angus and Simmental cattle breeds using the SNaPshot Multiplex system. Result: Result of pair-wise differences (FST) revealed three SNP locus (CDC37-6 (A16154247/G), CDC37-7 (C16157867/G), AHSA1-10 (G89722567/A) were significantly different in the Droughtmaster population than Angus and Simmental cattle breeds. Moreover, it was found that CDC37-7 (C16157867/G) locus deviated from Hardy-Weinberg equilibrium, suggesting that the CDC37-7 (C16157867/G) genes have been influenced by the selective breeding of the Droughtmaster breed. Therefore, CDC37-7 (C16157867/G) locus could be used as a marker-assisted candidate gene locus of heat tolerance. This study provides valuable information, concerning marker-assisted selection in the breeding of heat stress resistant cattle. 

Association of single nucleotide polymorphism of RB1 gene with body weight traits in chicken

2012 ◽  
Vol 34 (10) ◽  
pp. 1320-1327 ◽  
Author(s):  
Xi CHEN ◽  
Hui ZHANG ◽  
Yu-Xiang WANG ◽  
Shou-Zhi WANG ◽  
Bo-Han CHENG ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Body Weight ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
I Gene
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