American Journal of Scientific Research ISSN 1450-223X Issue 19(2011), pp. 6-12 © EuroJournals Publishing, Inc. 2011 http://www.eurojournals.com/ajsr.htm Phylogenetic Study of HKT-Gene in Gramineae via Insilico cDNA-AFLP Analysis Parviz Heidari Agronomy and Plant Breeding Department, Ilam University, Ilam, Iran E-mail: hidarip@yahoo.com Mehran Falaknaz Agronomy and Plant Breeding Department, Ilam University, Ilam, Iran E-mail: m.falaknaz@Agr.ilam.ac.ir Ali Ashraf Mehrabi Agronomy and Plant Breeding Department, Ilam University, Ilam, Iran E-mail: mehrabi_a@hotmail.com Danial Kahrizi Corresponding Author Biotechnology for Drought Resistance Research Department Razi University, Kermanshah, Iran E-mail:dkahrizi@yahoo.com Tel: +98-9183322235 Kheirollah Yari Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran E-mail: kyari@kums.ac.ir Abstract Increasing the salinity tolerance of crop plants will provide an important contribution to the maintenance of crop yields. The HKT family of ion transporters originally was named for the high-affinity potassium transporter properties of the first member of this family that was isolated, but it is more complex than originally realized, as the affinity and selectivity of many proteins encoded by members of this gene family are different to that indicated by the name. Different molecular marker types have been used to assess genetic diversity in plant such as amplified fragment length polymorphism (AFLP). Bioinformatics has become an essential tool not only for basic research but also for applied research in biotechnology and biomedical sciences. In this study we use an in silico analysis of the complete cDNA sequences HKT gene at eight genus the gramineae family to phylogeny within AFLP profiles that product by restriction enzymes. By online software webcutter selective the best of restriction enzymes to cutting the sequences and length of product in software excel saved, and then based of data 0 and 1 matrix with DARwin software draw the dissimilarity matrix (Dice and Jacard) and with MEGA3.1 software draw the phylogentic tree. Result showed that plants classification in four group, group 1 consist of 4 plants (Secale cereale,Triticum monococum, Triticum turgidum and Aegilops tauschii),