EFFICACY OF MOLECULAR DIAGNOSIS TO DETERMINE GENETIC DIVERSITY AMONG INDIGENOUS ISOLATES OF Erwinia carotovora UNDER EGYPTIAN CONDITION

Eman O Hassan ,Medhat Refaat

doi:10.21608/zjar.2018.47891

Abstract

Thirty-Four isolates of Erwinia carotovora subspecies carotovora (Ecc) causing soft rot of potato, were collected from tubers of potato plants grown in North and East Egypt. The frequency of the isolated species of soft rot-associated bacteria, being 10, 10, 8 and 6 isolates from Governorates of Sinai, Sharqia, Gharbia and Beheira, respectively. The isolates were identified as Ecc by biochemical method and molecular identity then was confirmed by polymerase chain reaction (PCR) using specific primers FEc1 and REc1 which amplified the Eca-specific band of 690-733 bp. Pathogenicity test divided these 9 isolates into 3 aggressiveness groups, High infection (2 isolates), moderate infection (5 isolates) and low infection (2 isolates), receptively. These isolates were also characterized using the technique of Inter Simple Sequence Repeats polymerase chain reaction (ISSR-PCR) found that 61 amplified fragments, 56 were polymorphic (91.8%) and the percentage of polymorphism ranged from 100% (844B) to 84.62% (HB12); the fragment sizes were 224bp to 1.36 kb. The unweighted pair-group method with arithmetical average (UPGMA) cluster analysis based on pairwise genetic similarity coefficient revealed that the similarity between the selected 9 soft rot bacterial isolates ranged from 0.125 between Ec6 and Ec9 to 0.875 between Ec1, Ec3 and Ec4. The average of similarity among genotypes was 0.500 and divided the soft rot isolates into three well-defined clusters showing a great level of genetic diversity. However, these clusters were not specific to aggressiveness groups, origin or special potato variety. Isolates with different aggressiveness levels, originated from different potato varieties participate between the same clusters. This means that the isolates likely derived from the same source population and got scattered from one area to another through their hosts.

Highlights

In 2016, Egypt's potato (Solanum tuberosum) production - targeted within the River Delta within the North - has distended at a rate of over 5% a year
In this paper we report the pathogenic and genetic diversity found, using Inter simple sequence repeats (ISSR) techniques, among the different isolates of Erwinia carotovora collected from different geographical areas of the North and East Egypt
Biochemical assays for the isolated bacteria revealed that the 34 isolates are distributed among three species belonging to three genera grouped as Erwinia sp., Bacillus sp., Pseudomonas sp

Summary

Introduction

In 2016, Egypt's potato (Solanum tuberosum) production - targeted within the River Delta within the North - has distended at a rate of over 5% a year. Inter Simple Sequence Repeats polymerase chain reaction (ISSR-PCR), using low strictness conditions and primers having short nucleotide sequences has been used efficiently to distinguish genetic diversity through some plant pathogenic bacteria (Mello et al, 2006). Erwinia carotovora is an important pathogen of potato in Egypt, especially the North and East part of the country.

Results

Conclusion