Sequence variation and phylogenetic relationship among rice (Oryza sativa L.) genotypes in Iraq

Abstract

In the present study PCR technique was performed using specific primer (RM 171) was used to evaluate the genetic diversity and determining identity among fifteen rice genotypes. Results, obtained from the PCR amplification and analysis of nucleotide sequences of RM171 amplified products using BLAST (Basic Local Alignment Search Tool), Alignment of RM171 marker sequence was carried out for each genotype. Showed that the Khazar and Branamge-4 had the highest similarity with 99% identity and Amber Baghdad was aligned with Yasmin showed the similarity with 98% identits, Furthermore, Amber furta was aligned with Alabasia showed the similarity with 98% identity. In addition, Sumar was aligned with Nipponbare showed the similarity with 98% identity while Neda was aligned with Mashkhab-1 similarity with 96% identist. From the comparison of nucleotide sequence obtained from the identified rice genotype with the nucleotide sequences deposited at the National Center for Biotechnology (NCBI), it was revealed that the identified rice genotype of Sumar, Amber Furat, Khazar, Neda, Amber Baghdad were not previously recorded at NCBI. Therefore; the five identified sequences have been deposited and recorded in GenBank database (NCBI) under the accession number: MK419157, MK419158, MK419159, MK419160, MK419161, respectively. In order to detect the Phylogenetic relationships among all genotypes were achieved, Results also showed that Cluster analysis of two main groups they were distribution depending on geographical and common ancestor. The result of this study could be useful in the future for rice breeding programs.