Ebrahimi Ghale Jogh, Masoud (2019) The Single Nucleutide Polymorphisms (SNPs), Allele Spesific Expression (ASE), codon usage bias and gene expression profiling on the genes coding of Caseinate proteins in milk for Holstein (Bos taurus) and Cholistani (Bos indicus) cattle. Masters thesis, university of zabol.
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The Single Nucleutide Polymorphisms (SNPs), Allele Spesific Expression (ASE), codon.pdf Download (254kB) | Preview |
Abstract
Milk and dairy products derived from cow's milk are an important nutritional component for humans. Beta-casein is a major component of cow's milk which is coded by various alleles such as A1 and A2 alleles. It has been shown that beta-casein protein in tauros cow’s milk is an integrated product of the A1 and A2 alleles. However, in Indicus cows, only A2 allele encodes this protein. Consuming type A1 and A2 milk can cause symptoms of various diseases, such as the prevalence of type 1 diabetes, neurological disorders such as autism, schizophrenia and other diseases, including celiac disease, while consumption of type A2 milk doesn’t cause symptoms of mentioned disease. Therefore, the aim of this study was to investigate the polymorphism pattern, gene expression difference and caseinate gene network of milk in two populations including 01 American Holstein (Bos taurus) cows and 04 Pakistani cholistani cows (Bos indicus). In this regard, RNA-Seq data of Holstein and cholistani populations were used. Editing and quality control of RNA-Seq data was performed by FASTQC (1.22.0 version) and Trimmomatic (00.1 version) software. To construct the transcriptome, alignment and locating RNA-Seq reads on the reference genome, TopHat2 software (2.1.1 version) was used. SNP detection and screening analysis on the transcriptome was performed using the samtools software package. To compare the expression of casein genes in Bos taurus (Holstein) and Bos indicus (cholistani) cows and investigating the information about chromosome number, mRNA length, number of amino acids, and gene access number, sequences of mRNA was extracted from the NCBI database and compared with data from RNA-Seq data. According to the data from the output file 10, Cuffdiff , CSN1S1, CSN1S2, CSN2, CSN0, CSNK1A1, CSNK1B, CSNK2B, CSNK2A1 , CSNK2A2, CSNK1G1 , CSNK1G2, CSNK1G0, CSNK1E, and CSNK1D genes related to Casein genes were found on the transcriptome of the US Holstein and Pakistani cholistani population samples, in which all 10 genes identified by differential expression (P.value>1.11111) did not have different expressions. The String-db site was used to investigate the association and coexistence of casein genes. The generated network showed high correlation between CSNK2A1 and CSNK2B genes with 1...0 combined score and lowest correlation was between CSNK2B and CSNK1G2 with a combined score of 1.02.. The results of this study showed that casein genes in Holstein and cholistani cows did not have different differential expression, so the differences may be due to gene network, interaction and genes association based on combined scores, extracted articles, performed experiments, and the effect of genes co-expression on each other The highest correlation was between CSNK2A1 and CSNK2B genes and the least between CSNK2B and CSNK1G2 genes.
| Item Type: | Thesis (Masters) |
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| Uncontrolled Keywords: | Casein Proteins Encoding Genes, Cattle, Gene Expression, Gene network |
| Subjects: | Q Science > QL Zoology |
| Depositing User: | Mrs najmeh khajeh |
| Date Deposited: | 18 Feb 2020 08:06 |
| Last Modified: | 18 Feb 2020 08:06 |
| URI: | http://eprints.uoz.ac.ir/id/eprint/2696 |
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