Splicing-related single nucleotide polymorphism of RAB, member of RAS oncogene family like 2B (RABL2B) jeopardises semen quality in Chinese Holstein bulls

2017 ◽  
Vol 29 (12) ◽  
pp. 2411 ◽  
Author(s):  
Xiuge Wang ◽  
Xiaohui Cui ◽  
Yan Zhang ◽  
Haisheng Hao ◽  
Zhihua Ju ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Splice Variant ◽  
Semen Quality ◽  
Intraflagellar Transport ◽  
Ras Oncogene ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Exon 2 ◽  
Chinese Holstein ◽  
Holstein Bulls

RAB, member of RAS oncogene family like 2B (RABL2B) is a member of a poorly characterised clade of the RAS GTPase superfamily, which plays an essential role in male fertility, sperm intraflagellar transport and tail assembly. In the present study, we identified a novel RABL2B splice variant in bovine testis and spermatozoa. This splice variant, designated RABL2B-TV, is characterised by exon 2 skipping. Moreover, a single nucleotide polymorphism (SNP), namely c.125G>A, was found within the exonic splicing enhancer (ESE) motif, indicating that the SNP caused the production of the RABL2B-TV aberrant splice variant. This was demonstrated by constructing a pSPL3 exon capturing vector with different genotypes and transfecting these vectors into murine Leydig tumour cell line (MLTC-1) cells. Expression of the RABL2B-TV transcript was lower in semen from high- versus low-performance bulls. Association analysis showed that sperm deformity rate was significantly lower in Chinese Holstein bulls with the GG or GA genotype than in bulls with the AA genotype (P < 0.05). In addition, initial sperm motility was significantly higher in individuals with the GG or GA genotype than in individuals with the AA genotype (P < 0.05). The findings of the present study suggest that the difference in semen quality in bulls with different RABL2B genotypes is generated via an alternative splicing mechanism caused by a functional SNP within the ESE motif.

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 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.

scholarly journals A TREM-1 Polymorphism A/T within the Exon 2 Is Associated with Pneumonia in Burn-Injured Patients

2013 ◽  
Vol 2013 ◽  
pp. 1-6 ◽  
Author(s):  
Fernando A. Rivera-Chávez ◽  
Ryan M. Huebinger ◽  
Agnes Burris ◽  
Ming-Mei Liu ◽  
Joseph P. Minei ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Regression Analysis ◽  
Total Body Surface Area ◽  
Burn Patients ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Exon 2 ◽  
Local Inflammatory Response ◽  
Increased Risk ◽  
Injured Patients

Background. The triggering receptor expressed in myeloid cells (TREM-1) is a key mediator in the activation of the local inflammatory response during lung infections. We aimed to evaluate the effect of a functionally relevant TREM-1 single nucleotide polymorphism within the exon 2 (A→T) on the development of pneumonia in burn patients. Objective. To determine whether a single nucleotide polymorphism (SNP) within the exon 2 (A→T) in the TREM-1 gene is associated with ventilator-associated pneumonia (VAP) in burn-injured patients. Methods. 540 patients with ≥10% total body surface area (TBSA) burn injuries or inhalation injury were prospectively enrolled. The influence of a polymorphism (A→T) in exon 2 of the TREM-1 gene was evaluated for association with increased risk of pneumonia by logistic regression analysis. Measurements and Main Results. 209 patients met criteria for VAP. Multivariate regression analysis showed that, after adjustment for potential confounders, we found that carriage of the TREM-1 T allele is associated with more than a 3-fold increased risk of VAP (OR 6.3, 95% CI 4–9). Conclusions. A TREM-1 single nucleotide polymorphism within the exon 2 (A→T) is associated with the development of pneumonia in burn patients.

scholarly journals Identification of novel single nucleotide polymorphism (SNP) in DPB1 gene in ethnic population from West Bengal

Genetika ◽  
2011 ◽  
Vol 43 (1) ◽  
pp. 205-208
Author(s):  
Oindrila Raha ◽  
B.N. Sarkar ◽  
P. Veerraju ◽  
Lucy Pramanik ◽  
V.R. Rao
Keyword(s):  
T Cells ◽  
Single Nucleotide Polymorphism ◽  
Autoimmune Diseases ◽  
Cd4 T Cells ◽  
West Bengal ◽  
Silent Mutation ◽  
Parasitic Infections ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Exon 2

HLA-DP antigens present peptides to CD4+ T cells and play an important role in autoimmune diseases and parasitic infections. We have sequenced HLA-DPB1 exon-2 from the ethnic populations in West Bengal, India and report a novel single nucleotide polymorphism (SNP) - rs111221466. The rs111221466 SNP induced silent mutation from CGA (Arg) to TGA (Stop Codon) and showed a frequency of 83.24%. In conventional sense, the frequency of novel SNP is very high. We have sequenced HLA-DPB1 exon-2 from a Bengali Population in West Bengal, India. HLA-DP antigens present peptides to CD4+ T cells and play an important role in autoimmune diseases and parasitic infections. Here, we report a novel single nucleotide polymorphism of HLA-DPB1 gene in the population. rs111221466 showed a frequency of 83.24, which is important to note, in view of common polymorphisms involved in disease susceptibility.

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