Dataset Information

Association between single nucleotide polymorphism in ovine Calpain gene and growth performance in three Egyptian sheep breeds.

ABSTRACT: The aim of the present study was to assess the association of single nucleotide polymorphisms (SNPs) of Calpain (CAPN) gene with birth weight (BW), final weight (FW) and average daily gain (ADG) in three Egyptian sheep breeds: Barki, Rahmani and Ossimi. Blood samples were collected from 108 animals representing the three breeds. DNA was isolated using salting out procedure and then the quality and quantity of DNA extracted were measured. A 190 bp of CAPN was amplified by PCR using specific primers. The allele and genotype frequencies for all the identified SNPs were calculated. The PCR products corresponding to each genotype were sequenced to identify SNPs associated with the traits in question. Two SNPs (C?T) were detected in the nucleotides 44 and 154. For each SNP, the two mentioned alleles were named C and T, respectively. The sequenced CAPN segments were subjected to nucleotide blast at NCBI, which revealed 99% identity with that reported for sheep in Genbank. The TT was the least common genotype, whereas frequencies of CT and CC genotypes were fluctuated in the three sheep breeds under study. Animal carrier TT genotype had higher BW, FW and ADG than those with CT genotype, while the lowest values were associated with CC genotype. For the three traits under study, Rahmani had the highest estimates followed by Ossimi and Barki. Males exhibited heavier BW and FW as well as higher ADG compared with females. The results generated provide preliminary indication of the functional diversity present in Barki, Rahmani and Ossimi sheep and the possibility of using this polymorphism in Egyptian sheep genetic improvement.

SUBMITTER: Mahrous KF

PROVIDER: S-EPMC6299862 | biostudies-literature | 2016 Dec

REPOSITORIES: biostudies-literature

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Association between single nucleotide polymorphism in ovine Calpain gene and growth performance in three Egyptian sheep breeds.

Mahrous K F KF Hassanane M S MS Shafey H I HI Abdel Mordy M M Rushdi H E HE

Journal, genetic engineering & biotechnology 20161101 2

The aim of the present study was to assess the association of single nucleotide polymorphisms (SNPs) of Calpain (<i>CAPN</i>) gene with birth weight (BW), final weight (FW) and average daily gain (ADG) in three Egyptian sheep breeds: Barki, Rahmani and Ossimi. Blood samples were collected from 108 animals representing the three breeds. DNA was isolated using salting out procedure and then the quality and quantity of DNA extracted were measured. A 190 bp of <i>CAPN</i> was amplified by PCR using ...[more]

PMID: 30647620

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Project description:Acute myelogenous leukemia (AML) is a heterogeneous disease characterized by myeloid progenitor cells uncontrolled proliferation gradually replacing normal hematopoiesis. To evaluate Ten Eleven Translocation 2 gene (TET2) single nucleotide polymorphism (SNP) (rs2454206, rs34402524, rs61744960) in AML, and chronic myeloid leukemia (CML) in relation to their disease prognostic criteria. The study included 136 subjects; 52 AML, 54 CML and 30 subjects as control group matched for age and sex. Routine investigations including CBC, bone marrow aspiration, flow cytometry biochemical investigations and cytogenetics and molecular study were performed accordingly. DNA extraction and SNP assay for TET2 gene polymorphism was done using (Thermo-Fisher predesigned SNP, USA) PCR prism 7500. The mean age was 43.4?±?14.0 years in AML patients, 45.98?±?15.7 years in CML patients and 39.3?±?6.587 years in control group (p?>?0.05). The frequency of TET2 SNP rs 34402524 ranged from heterozygous to homozygous in both AML (46%, 54%) and CML (48%, 46.2%) groups but was mainly homozygous among the control (80%) group (p?=?0.012). TET2 SNP rs 2454206 was mainly wild in CML (65.4%) and control (63.3%) groups compared to AML as wild was only in (46%) and heterozygous in (44%) with only 10% being homozygous (p?=?0.046). TET2 SNP rs 61744960 showed a homozygous pattern among all three group (AML CML and control) showing no statistical significance (p?=?0.528). Eventhough, higher non responders to treatment were among homozygous and heterozygous groups yet, response to therapy as respect to specific TET2 SNP showed no significant variation (p?>?0.05). TET2 SNP in CML cases did not alter the prognostic criteria as no statistical significance was noted (p?>?0.05) except for TET2 SNP rs 34402524 where homozygous cases had larger spleen size (p?=?0.019). TET2 SNP is common in Egyptian myeloid neoplasm. This is the first study in this field and further studies are recommended to investigate TET2 and relation to other hematological malignancies and leukemogenesis transformation.

Project description:Aim:The present study was performed to assess the association of single-nucleotide polymorphisms (SNPs) in the fatty acid-binding protein 4 (FABP4) gene with birth weight (BW), final weight (FW), and average daily gain (ADG) in three Egyptian sheep breeds. Materials and Methods:Genomic DNA was extracted from the blood samples of 50 male and female individuals representing Ossimi, Rahmani, and Barki sheep breeds. A 407 bp nucleotide (nt) segment from the first intron of FABP4 was amplified by polymerase chain reaction, sequenced, and analyzed in the different samples. Results:Sequence analysis of the determined segment (407 bp) revealed four SNPs (all transition types) at nt position 372 (CP011894.1:g.57605471) A>G, nt position 211 (CP011894.1:g.57605632) A>G, nt position 143 (CP011894.1:g.57605700) T>C, and nt position 111 (CP011894.1:g.57605732) T>C. The allelic and genotypic frequencies for the identified SNPs in the sheep breeds were calculated. At nt positions 372 and 211, two alleles were identified (A and G). Only two genotypes were present at nt position 372 (AA and AG), while three genotypes were present at nt position 211 (AA, AG, and GG). Two alleles (T and C) and three identified genotypes (TT, TC, and CC) were detected at nt positions 143 and 111. Analysis of the results revealed that AA genotype at nt position 372 is associated with higher estimates for BW, FW, and ADG when compared to all the other genotypes. Very high correlation coefficients were found between the genotypes 143-TT and 111-TT and also between 143-TC and 111-TC. The genotypes 372-AG, 211-GG, 211-AA, 143-TT, 143-CC, 111-TT, 111-TC, and 111-CC were associated with negative effects on BW, FW, and ADG. Conclusion:The detection of four SNPs in a partial sequence of the Egyptian ovine FABP4 gene intron 1 reflected that this gene harbors substantial diversity. In addition, a novel SNP at nt position 372 (CP011894.1:g.57605471) A>G was associated with higher estimates for BW, FW, and ADG.

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Dataset Information

Association between single nucleotide polymorphism in ovine Calpain gene and growth performance in three Egyptian sheep breeds.

Publications

Association between single nucleotide polymorphism in ovine Calpain gene and growth performance in three Egyptian sheep breeds.

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