1- Agricultural and Natural Resources University of Khuzestan
2- University of Arak
2- University of Arak
Abstract: (8 Views)
Introduction and Objective: Fat Tail comprises 20% of the carcass weight, which greatly reduces the economic value of the carcass, so sheep breeders should investigate the mechanisms that genetically control fat development, in order to design sheep breeding programs to reduce tail size. Fat storage in the tail is one of the issues raised in our country and many developing countries. In recent years, various researches have been conducted in the field of crossbreeding between tailless and tailless breeds to investigate how these traits are inherited in different places. However, the investigation of these researches has generally been associated with conflicting results, so the genomic region or regions affecting this trait is still unknown. Therefore, identifying genes or genomic regions related to fat storage is one of the most important and challenging research areas in many countries that breed these breeds. Methods such as genome study and gene expression analysis have been used to describe the potential genetic background of fat deposition in sheep. Epistatic studies are interesting for researchers because they play a key role in understanding the functional relationship of genes. Over the past few decades, GWAS have provided a central role in the field of epistasis. In GWAS analysis, SNPs are first tested by a standard statistical method, and by that they determine the relationship between the SNP and the phenotype. It is this type of analysis that is widely used, but it is not as responsive as expected and in fact it identifies a small part of the genetic variance and does not indicate the remaining part or in other words the lost heritability. It is generally accepted that lost heritability is partly due to a variety of genetic effects and their interaction with one or more other factors. According to the conducted researches, many researches have been done on GWAS, but GWAS studies on the tail are limited, and considering the importance of epistasis effects, there is no place to investigate them through chip snaps, and many questions remain in this matter. Therefore, this research is designed to investigate and answer these questions.
Material and Methods: About 3000 data including different types of sheep were prepared from the Sheep Hap Map database after writing a letter and obtaining permission. The samples were genotyped using llumina50K chips. Data editing was done in terms of frequencies, genotypes, Hardy-Weinberg equilibrium and Maf. Breeds were examined in terms of tail formation and tail type and phenotype was determined. By using PLINK software, it was started to find the relationship between the effective snips and the tail formation phenotype. A P-value was determined for each of the snaps and a Manhattan diagram was drawn using R. According to the results, PCA analysis was done. Epistasis effects were estimated using PLINK. The physical locations of the snaps were determined to confirm the chromosomes. Gene detection and function analysis and genomic and bioinformatics comparisons were performed using the latest genomic information from databases. Finally, the mutual effects between genes and SNPs affecting tail (epistasis effects) were investigated.
Results: Effective loci and their epistasis effects were investigated in 19 breeds and 806 animals. Extensive genome scanning was done to find the gene loci and their epistasis by logistic regression method and with the help of Plink program. The Manhattan diagram was drawn with the help of R program and the effective genes were determined based on the GWAS result in Ensemble database. The results showed that 8 snaps in chromosomes 1, 2, 3, 6, 10, 15, and 18 are effective on tailiness. A total of 23 genes were found in 500 thousand bases upstream and downstream of effective snips. Gene network drawn using TCHHL, S100A10, LCE3D, C1orf6, NR1H4, U6, SLC17A8 ANO4, SCYL2, ACRT6, CCSER1 MED4, ITM2B RB1, LPAR6, RCBTB2, GPC6 ALKBH3, MIR129-2, C11orf96, TTC17, ACCS genes. and EXT2 from He did not have good wealth. Therefore, little biological interactions can be reported. But in the statistical epistasis section, many interaction effects were seen. Among the effective snips, the snip on S08620.1 of chromosome 2 has the greatest epistasis effect with other sheep genomic loci.
Conclusion: According to the importance of the loci affecting the tail fat deposition, there is a relationship between their genomic locations. According to the results of this research, it can be said that the tail formation process is influenced by genomic loci and epistasis effects. In this research, using population structure analysis by GWAS, 23 genes and nearly 4000 interactions were identified. NR1H4, EXT2, ANO4, and SLC17A8 are among the effective genes. The gene network of effector genes showed few biological interactions. But in statistical epistasis, many mutual effects were observed. 7 effective snips were identified on a number of chromosomes, the most interactions were observed on snip S08620.1 of chromosome number 2. As a result, the most epistasis interactions on the snips of chromosome number 2 are related to 1841 snips on other chromosomes. After chromosome number 2, chromosome 1 and 18 showed the most epistasis effects.
Keywords: GWAS, SNP, Gene network , Epistasis,Sheep fat-tail
Material and Methods: About 3000 data including different types of sheep were prepared from the Sheep Hap Map database after writing a letter and obtaining permission. The samples were genotyped using llumina50K chips. Data editing was done in terms of frequencies, genotypes, Hardy-Weinberg equilibrium and Maf. Breeds were examined in terms of tail formation and tail type and phenotype was determined. By using PLINK software, it was started to find the relationship between the effective snips and the tail formation phenotype. A P-value was determined for each of the snaps and a Manhattan diagram was drawn using R. According to the results, PCA analysis was done. Epistasis effects were estimated using PLINK. The physical locations of the snaps were determined to confirm the chromosomes. Gene detection and function analysis and genomic and bioinformatics comparisons were performed using the latest genomic information from databases. Finally, the mutual effects between genes and SNPs affecting tail (epistasis effects) were investigated.
Results: Effective loci and their epistasis effects were investigated in 19 breeds and 806 animals. Extensive genome scanning was done to find the gene loci and their epistasis by logistic regression method and with the help of Plink program. The Manhattan diagram was drawn with the help of R program and the effective genes were determined based on the GWAS result in Ensemble database. The results showed that 8 snaps in chromosomes 1, 2, 3, 6, 10, 15, and 18 are effective on tailiness. A total of 23 genes were found in 500 thousand bases upstream and downstream of effective snips. Gene network drawn using TCHHL, S100A10, LCE3D, C1orf6, NR1H4, U6, SLC17A8 ANO4, SCYL2, ACRT6, CCSER1 MED4, ITM2B RB1, LPAR6, RCBTB2, GPC6 ALKBH3, MIR129-2, C11orf96, TTC17, ACCS genes. and EXT2 from He did not have good wealth. Therefore, little biological interactions can be reported. But in the statistical epistasis section, many interaction effects were seen. Among the effective snips, the snip on S08620.1 of chromosome 2 has the greatest epistasis effect with other sheep genomic loci.
Conclusion: According to the importance of the loci affecting the tail fat deposition, there is a relationship between their genomic locations. According to the results of this research, it can be said that the tail formation process is influenced by genomic loci and epistasis effects. In this research, using population structure analysis by GWAS, 23 genes and nearly 4000 interactions were identified. NR1H4, EXT2, ANO4, and SLC17A8 are among the effective genes. The gene network of effector genes showed few biological interactions. But in statistical epistasis, many mutual effects were observed. 7 effective snips were identified on a number of chromosomes, the most interactions were observed on snip S08620.1 of chromosome number 2. As a result, the most epistasis interactions on the snips of chromosome number 2 are related to 1841 snips on other chromosomes. After chromosome number 2, chromosome 1 and 18 showed the most epistasis effects.
Keywords: GWAS, SNP, Gene network , Epistasis,Sheep fat-tail
Type of Study: Research |
Subject:
ژنتیک و اصلاح نژاد دام
Received: 2024/11/22 | Accepted: 2025/08/31
Received: 2024/11/22 | Accepted: 2025/08/31
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