نوع مقاله : مقاله پژوهشی
نویسندگان
گروه علوم دامی، دانشکدگان کشاورزی و منابع طبیعی دانشگاه تهران، کرج، ایران
چکیده
کلیدواژهها
موضوعات
عنوان مقاله [English]
نویسندگان [English]
Nowadays, with the progress obtained in molecular genetic techniques and bioinformatics, alternative methods have been invented to increase the speed and efficiency of DNA sequencing and their roles in genome level. In the whole-genome sequencing method, the whole genome sequence of organism (nuclear-genome with mitochondrial DNA) is sequenced. One of the important topics in genomics is genome differences, including single-nucleotide polymorphisms and INDELs for the relationship between genotype and phenotype. Polymorphisms are powerful tools for molecular analysis of economic traits and are important in breeding programs. For this purpose, whole-genome variations of Mazandarani buffaloes were identified and classified. In this study, the whole-genome of 4 Mazandarani buffaloes was sequenced with the Illumina platform. Data quality was measured by FastQC software. BWA-MEM was used for alignment with reference genome. Finally, the variants were obtained using freebayes and the SnpEff was used to calculate the effects of the variants. The result of aligning led us to identification of 56537534 SNPs, and 6128529 indels with an average coverage of x4 to x13. The most number of variants were observed on 1 and X chromosomes, and the least number were in 23 and mitochondrial chromosomes. The transition, transversion and rate of transition/transversion mutations were 236549743, 108015966 and 2/19 respectively. Also, the mutations was calculated. The frequency of variants in intergenic regions was estimated to be 52746727, intron 23560994, downstream 3713594, upstream 3571409 and exon 574093. Considering that this research is the only one that carried out to identify the genomic variations of Mazandarani buffalo, the identified genomic variations can be used for the development of SNP-arrays for Iranian breeds.
کلیدواژهها [English]
Extended Abstract
Introduction
Livestock breeding is one of the main sectors of animal production, with important role in economy, self-sufficiency and food security. Existing genetic diversity and resource in native populations with good adaptation to their environmental conditions are very valuable for breeding and production plans. Buffalo is one of the important native livestock of the country and has an important contribution in the production of milk, meat.
Objective
Research on DNA variants that directly affect the phenotype is one of the main and key field of genetic research in domestic animals. In the past few years, single nucleotide polymorphisms have played a important role in the field of genetics studies of domestic animals. One of the important topics in genomics studies is genome differences, including single-nucleotide polymorphisms and INDELs to consider relation between genotype and phenotype. Polymorphisms are powerful tools for molecular analysis of economic traits and are important in breeding programs. Thus the aim of this research was to identify single-nucleotide polymorphisms and INDELs across the whole genome of Mazanderani buffaloes.
Research method
In this study, the whole-genome of 4 Mazandarani buffaloes was sequenced with the Illumina platform. Data quality was measured by FastQC software. This software uses 11 different tests to measure data quality. Trimmomatic software was used to edit the data. This software is a flexible tool with effective pre-processing and compatible with paired end data, and it is optimized for Illumina company's next generation sequencing data. The tasks of this software include removing adapters and removing or editing poor quality readings. Then, using the samtools software package, we converted the output file in sam format to bam. To obtain the alignment and coverage percentage, we used the flagstat and depth commands used in SamTools software. The file of genomic variants was obtained using freebayes. After receiving the reference genome file and its annotation file, it was necessary first to index the information related to the reference genome. BWA-MEM software package was used to align and index the data with the cow reference genome (UMD3.1). Compared to other algorithms, it has a higher processing speed. the SnpEff was used to calculate the effects of the variants.
Results
The result of aligning led to identification of 56537534 SNPs, 6128529 indels with an average coverage of x4 to x13. The most number of variants were observed on 1 and X chromosomes, and the least number were in 23 and mitochondrial chromosomes. The transition, transversion and rate of transition/transversion mutations were 236549743, 108015966 and 2/19 respectively. Also, the mutations were calculated as. The frequency of variants in intergenic regions was estimated to be 52746727, intron 23560994, downstream 3713594, upstream 3571409 and exon 574093.
Conclusion
Considering the important role of buffalo in providing part of the income and necessities of the rural population, special attention should be paid to these animals in order to raise the level of welfare of the rural population and also to increase the production efficiency of buffaloes in the country. Therefore, in order to improve and raise the production level of these animals, it is very important to know the genetic variations. The present study is the only research carried out to identify the genomic variations of Mazandarani buffalo, so the genomic variations identified in this study can be used for the development of high-density SNP arrays for genetic and breeding applications in Iranian breeds.
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