Document Type : Research Paper
Authors
1
Department of Animal Science, Faculty of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
2
. Department of Animal Science, Faculty of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
Abstract
Background: Today, progress in bioinformatics, alternative methods have been invented to increase the speed and efficiency of DNA sequencing. In the whole-genome sequencing method, the whole genome sequence of organism (nuclear-genome with mitochondrial DNA) is sequenced.
Objective: 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 Mazandaran buffaloes were identified.
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. 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.
Findings: The result of aligning led to identification of 56,537,534 SNPs, 6,128,529 indels with an average coverage of x4 to x13. The most variants were observed in sex-chromosomes (X) and 1, and the least in mitochondrial chromosomes and 25. The transition, transversion and rate of transition/transversion mutations were 236,549,743 108,015,966 2.19 respectively. Also, the mutations was calculated as. The frequency of variants in intergenic regions was estimated to be 52,746,727, intron 23,560,994, downstream 3,713,594, upstream 3,571,409 and exon 574,093.
Conclusion: This study is the only research carried out to identify the genomic variations of Mazandarani buffalo, the identified genomic variations can be used for the development of SNP-arrays in Iranian breeds for genetic applications.
Keywords
Main Subjects
)