PJB-2019-1026
Plastome SNPs Analysis of eight barley genotypes displaying hot spot regions, phylogenetic relationships and heteroplasmy
Sherif Edris
Abstract
Organellar genomes are circular, small and provide unique advantages compared to nuclear genome that triggered organellar genome researches. The current study aimed to is evaluating the efficiency of the plastid single nucleotide polymorphisms (SNPs) approach in separating barley cultivars. Sequences generated via next-generation sequencing for the identifications of selected barley cultivars and study the theory of heteroplasmy. Seven cultivated barley (Hordium vulgare subsp. vulgare) (VG) and one wild type (H. vulgare subsp. spontaneum) (SP) genotypes were analyzed. Using the Illumina HiSeq 2000 platform, a plastid genome of eight genotypes of barley were sequenced, around 73 million paired end reads per cultivar were generated per genotypes. Using some bioinformatics software, sequences of each genotype were separately aligned to barley plastid reference genome, and SNPs were detected. The results indicated the use of SNPs as a molecular marker that was highly efficient in distinguishing between barley genotypes. Four out of eight genotype, Specific plastid SNPs were found. Giza131 was the only genotype that did not contain plastid SNPs, while Giza130 gave the largest number of plastid (5) SNPs. Phylogenetic trees generated from SNPs of plastome showed a better discrimination among genotypes. Interestingly, SNP was not fully distinguished between genotypes, and the study also confirmed the validity of the heterogeneity theory in mitochondrial and plastidium genomes.
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