Identification of genome diversity in Lari chicken 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

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

3 Research Assistant Professor from Animal Science Research Department, Fars Agricultural and Natural Resources research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Shiraz, Iran.

Abstract

Objective
Evaluation and conservation of native chickensas valuable genomic resources is essential.This is the first study for discovering variants in Lari chicken by whole genome sequencing data. The study of genetic diversity of Lari chicken at genomic level can provide useful information for its preservation and breeding. In this study, genomic diversity of five Lari individuals was investigated using whole genome sequencing technique.
Materials and methods
Blood samples were taken from five Lari chickens from cites of Shiraz and Zabol, Iran. Whole genome sequencing (paired end sequencing) was done by Illumina Company) Hiseq 2500). Data quality was determined by FastQC program. Whole genome sequencing datawere aligned with chicken genome reference(Gallus_gallus-5.0/galGal5) using MEM algorithm applied in burrows wheeler aligner program (BWA). Processing of bam files was done in several steps. PCR duplicates were removed using Pi‌card program. The Percentage of alignment with‌ the reference genome and coverage or depth were calculated using the flagstat and depth commands in samtools software. Single nucleotide polymorphisms (SNPs) and small insertions and deletions (INDELs) were identified by the genomic analysis toolkit (GATK)program. Annotation of SNPs and Indels was done using SnpEff program. Genetic diversityof five chicken genomes was calculated with VCFtools.
Results
The mean percentage mapping of short sequences with the reference genome was 99.85% and the mean coverage depth was 7.65 X. In this study, 9.8 million SNPs and 10 million Indels were identified with the most counts of them in the intron and intergenic regions. The mean ofobserved and expected heterozygosity percentages for SNPs in five chicken genomes were 0.30 and 0.35, respectively.
Conclusions
Results from annotation showed that percentage of silentSNPs (74.38%) is higher than that nonsynomous SNPs (missense and nonsense, 25.62%) in Lari chicken genome. The lower observed genetic diversity than the expected genetic diversity, can be due to the forces such as inbreeding in the population of Lari chicken. The information provided herein can be useful for breed conservation and breeding programs and population structure survey.

Keywords

References

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Agricultural Biotechnology Journal
Volume 13, Issue 2
July 2021
Pages 189-204

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