Identification of genome diversity in Iranian goat ecotypes using whole genome sequencing method

Document Type : Research Paper

Authors

1 Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran and Animal Science Research Department, Fars Agricultural and Natural Resources, Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Shiraz, Iran

2 Department of Engineering Animal Sciences, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran

3 Professor, Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran

4 Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China

Abstract

Objective
Due to adaptation to environmental conditions, different ecotypes of native goat can be seen in different geographical regions of the country, which are very diverse in terms of appearance and production characteristics. So far, no comprehensive study has been done at the whole genome level to identify the genetic diversity of native goats. Therefore, the aim of this study is to identify the genomic characteristics of these native reserves in order to organize appropriate programs for their exploitation and protection.
Materials and methods
In this study, the whole genome sequence of 36 Iranian native goats were downloaded from the NCBI database and analyzed. Whole genome sequencing of the studied data was done by Illumina company and Hiseq2500 and Hiseq2000 sequencing machines. Quality control of raw sequence data was done by FastQC program. The BWA-MEM algorithm applied in the BWA software package was used to align the data sequence with the goat reference genome (ARS1, GCF_001704415.1). The alignment outputs with the reference genome were processed in two steps, including realignment around small deletions and insertions and base quality score recalibration using GATK program.The mean depth for the alignment output with the reference genome was calculated using the depth command applied in the samtools software. Single nucleotide polymorphisms (SNPs) were identified by the UnifiedGenotyper tool used in the GATK program. The values of nucleotide diversity and genomic inbreeding coefficient based on homozygous SNPs for each individual were calculated using the het command used in the VCFtools program.
Results
The mean depth of the used data in this study was 11.25 X. The average number of single nucleotide polymorphisms in the 36 Iranian native goat genomes was 7495554. The genomic inbreeding coefficient values in different ecotypes of Iranian native goat varied from -0.01 to 0.4. The lowest genomic inbreeding coefficient value was observed in the Hamedan native goat genome (-0.01) and the highest genomic inbreeding coefficient value was observed in the Balochi goat ecotype genome of Sistan and Baluchistan. Also, the average of percentage observed and expected of heterozygosity values was calculated for single nucleotide polymorphisms in the o Iranian native goat ecotype genomes varied from 10.27 to 17.75 and from 17.33 to 17.57.
Conclusions
This research shows an important insight about the structural diversity of the Iranian native goat genomes, which have not been evaluated genetically so far. The results obtained from this research can be used in the design of conservation and breeding programs for Iranian native goats.

Keywords

References

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Agricultural Biotechnology Journal
Volume 15, Issue 2
June 2023
Pages 1-18

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