Browsing by Author "Raza SHA"

Now showing 1 - 3 of 3
  • Thumbnail Image
    Item
    Genetic Association of PPARGC1A Gene Single Nucleotide Polymorphism with Milk Production Traits in Italian Mediterranean Buffalo.
    (Hindawi Limited, 2021-03-20) Hosseini SM; Tingzhu Y; Pasandideh M; Liang A; Hua G; Farmanullah; Schreurs NM; Raza SHA; Salzano A; Campanile G; Gasparrini B; Yang L; Kontos CK
    PPARGC1A gene plays an important role in the activation of various important hormone receptors and transcriptional factors involved in the regulation of adaptive thermogenesis, gluconeogenesis, fiber-type switching in skeletal muscle, mitochondrial biogenesis, and adipogenesis, regulating the reproduction and proposed as a candidate gene for milk-related traits in cattle. This study identified polymorphisms in the PPARGC1A gene in Italian Mediterranean buffaloes and their associations to milk production and quality traits (lactation length, peak milk yield, fat and protein yield, and percentage). As a result, a total of seven SNPs (g.-78A>G, g.224651G>C, g.286986G>A, g.304050G>A, g.325647G>A, g.325817T>C, and g.325997G>A) were identified by DNA pooled sequencing. Analysis of productivity traits within the genotyped animals revealed that the g.286986G>A located at intron 4 was associated with milk production traits, but the g.325817T>C had no association with milk production. Polymorphisms in g.-78A>G was associated with peak milk yield and milk yield, while g.304050G>A and g.325997 G>A were associated with both milk yield and protein percentage. Our findings suggest that polymorphisms in the buffalo PPARGC1A gene are associated with milk production traits and can be used as a candidate gene for milk traits and marker-assisted selection in the buffalo breeding program.
  • Thumbnail Image
    Item
    Identification of genetic variants the CCKAR gene and based on body measurement and carcass quality characteristics in Qinchuan beef cattle (Bos taurus)
    (Elsevier B.V., 2021-05) Nurgulsim K; Raza SHA; Khan R; Shah MA; Jahejo AR; Batool U; Hongbao W; Zhigerbayevich KN; Schreurs N; Zan L
    Background: This study aimed to explore genetic polymorphisms of the CCKAR gene and their relationship with the growth and development of Qinchuan cattle which could be used as molecular markers for the improvement of the breeding of Qinchuan cattle. Results: Here, we have identified seven single nucleotide polymorphisms (SNPs) at loci g. 1463 C>G; g. 1532 T>A; g. 1570 G>A; g. 1594 C>A; g. 1640 T>C; g. 1677 G>C; and g. 1735 C>T in the coding region of the bovine CCKAR gene. The frequencies identified on allelic and genotypic characteristics have shown that all seven SNPs diverged from the Hardy-Weinberg-Equilibrium. The SNP2, SNP3, SNP6 and SNP7 had the lowest polymorphism information content values, and remaining SNPs were found to be moderate (0.25 < PIC < 0.50). The genotype CG in SNP1 at loci g.1463 C>G had the greatest association with WH, HW, CD and CCF, while the genotype TA at the very same loci was associated with BFT, ULA and IMF content in Qinchuan cattle. The CCKAR gene expression level in adipose tissue, small intestine, liver and skeleton muscle was found to be higher, whereas, the expression level of mRNA in organs of other digestive system including reticulum, abomasum and omasum was moderate. Some expression of CCKAR mRNA was found in the large intestine, kidney and rumen. Conclusion: In summary, our finding suggested that the CCKAR gene could be used as a potential candidate for the improvement of carcass quality and body measurements of Qinchuan cattle.
  • Thumbnail Image
    Item
    Screening and Identification of Muscle-Specific Candidate Genes via Mouse Microarray Data Analysis.
    (Frontiers Media S.A., 2021-12-13) Raza SHA; Liang C; Guohua W; Pant SD; Mohammedsaleh ZM; Shater AF; Alotaibi MA; Khan R; Schreurs N; Cheng G; Mei C; Zan L; Ibelli AMG
    Muscle tissue is involved with every stage of life activities and has roles in biological processes. For example, the blood circulation system needs the heart muscle to transport blood to all parts, and the movement cannot be separated from the participation of skeletal muscle. However, the process of muscle development and the regulatory mechanisms of muscle development are not clear at present. In this study, we used bioinformatics techniques to identify differentially expressed genes specifically expressed in multiple muscle tissues of mice as potential candidate genes for studying the regulatory mechanisms of muscle development. Mouse tissue microarray data from 18 tissue samples was selected from the GEO database for analysis. Muscle tissue as the treatment group, and the other 17 tissues as the control group. Genes expressed in the muscle tissue were different to those in the other 17 tissues and identified 272 differential genes with highly specific expression in muscle tissue, including 260 up-regulated genes and 12 down regulated genes. is the genes were associated with the myofibril, contractile fibers, and sarcomere, cytoskeletal protein binding, and actin binding. KEGG pathway analysis showed that the differentially expressed genes in muscle tissue were mainly concentrated in pathways for AMPK signaling, cGMP PKG signaling calcium signaling, glycolysis, and, arginine and proline metabolism. A PPI protein interaction network was constructed for the selected differential genes, and the MCODE module used for modular analysis. Five modules with Score > 3.0 are selected. Then the Cytoscape software was used to analyze the tissue specificity of differential genes, and the genes with high degree scores collected, and some common genes selected for quantitative PCR verification. The conclusion is that we have screened the differentially expressed gene set specific to mouse muscle to provide potential candidate genes for the study of the important mechanisms of muscle development.