جستجوی مقالات مرتبط با کلیدواژه "حذف و اضافه های کوچک" در نشریات گروه "بیوتکنولوژی و ژنتیک گیاهی"

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.

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.

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.

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

 Evaluation and conservation of native chickens as future genomic resources are essential. In this study, genomic diversity of four Marandi breeds was investigated using whole genome sequencing technique.  

 Blood samples were taken from four chickens in East Azerbaijan province, Iran. Whole genome sequencing (paired end sequencing) was done by Illumina Company) Hiseq 2500). Data quality control was performed by FastQC program. Whole genome sequencing data were aligned with genome reference (Gallus_gallus-5.0/galGal5) using MEM algorithmimplemented in burrows wheeler aligner program (BWA). Single nucleotide polymorphisms (SNPs) and small insertions and deletions (INDELs) were identified by the GATK program. Annotation of SNPs and Indels was done using SnpEff program. Genetic diversity of 4 chicken genomes was calculated with VCFtools.   

The short sequences were compared with the reference genome of over 99% and with the mean depth of 7X coverage. In this study, 8.7 million SNPs and 9.1 Indels were identified with the most counts of them in the intron and intergenic regions. The mean of observed and expected heterozygosity percentages for SNPs in four chicken genomes were 0.33 and 0.35, respectively.  

Results from annotation showed that percentage of the silent SNPs (74.64%) is higher than that the nonsynomous SNPs (missense and nonsense) in Marandi chicken genome. The results obtained from this research can be useful for Marandichicken breeding and conservation programs.