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SINGLE NUCLEOTIDE POLYMORPHISM ANALYSIS OF MT-SHSP GENE OF  GOSSYPIUM ARBOREUM  AND  ITS  RELATIONSHIP WITH OTHER DIPLOID COTTON GENOMES, G. HIRSUTUM AND ARABIDOPSIS THALIANA

TAYYABA SHAHEEN, MUHAMMAD ASIF, YUSUF ZAFAR AND ^*MEHBOOB-UR-RAHMAN

Abstract: Single nucleotide polymorphisms (SNPs) are the most popular DNA markers because of their abundance and consistency in the genomes. House keeping genes are conserved in nature across the genomes of different organisms. Study of variations in these conserved genes can reveal the hidden facts of evolution which can not be excavated with conventional DNA marker systems. In the present study, mitochondrial small heat shock protein gene (MT-sHSP) has been explored to find nucleotide variations within Gossypium arboreum, with the other diploid Gossypium genomes, G. hirsutum and also with Arabidopsis thaliana. A conserved region spanning 300bp was amplified and sequenced from two G. arboreum (A₂) genotypes, species of other diploid genomes belonging to A₁, C₁, E₁, D₄, D₆, D₉ genomes and tetraploid species G. hirsutum (AD). Sequence of the gene of A. thaliana was retrieved from Genbank. These sequences were aligned. Within G. arboreum genome one Indel was found while, ‘C’ genome showed the least nucleotide variations with the ‘A’ genome species (G. arboreum) as compared to other genomes. D genome species and G. hirsutum were closely related with each other. A. thaliana was most distantly related with other genomes. The present studies reveal that SNP markers could be identified in conserved regions where conventional markers are of little or no use. This study will lead to the better understanding of G. arboreum evolution and understanding how these variations can be utilized for the improvement of cotton genome.

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