Genetic variation in Pythium myriotylum based on SNP typing and development of a PCR-RFLP detection of isolates recovered from Pythium soft rot ginger

Le, D. P., Smith, M. K. and Aitken, E. A. B. (2017) Genetic variation in Pythium myriotylum based on SNP typing and development of a PCR-RFLP detection of isolates recovered from Pythium soft rot ginger. Letters in Applied Microbiology, 65 4: 319-326. doi:10.1111/lam.12779


Author Le, D. P.
Smith, M. K.
Aitken, E. A. B.
Title Genetic variation in Pythium myriotylum based on SNP typing and development of a PCR-RFLP detection of isolates recovered from Pythium soft rot ginger
Journal name Letters in Applied Microbiology   Check publisher's open access policy
ISSN 0266-8254
1472-765X
Publication date 2017-08-25
Year available 2017
Sub-type Article (original research)
DOI 10.1111/lam.12779
Open Access Status Not yet assessed
Volume 65
Issue 4
Start page 319
End page 326
Total pages 8
Place of publication Chichester, West Sussex United Kingdom
Publisher Wiley-Blackwell Publishing
Language eng
Abstract Pythium myriotylum is responsible for severe losses in both capsicum and ginger crops in Australia under different regimes. Intraspecific genomic variation within the pathogen might explain the differences in aggressiveness and pathogenicity on diverse hosts. In this study, whole genome data of four P. myriotylum isolates recovered from three hosts and one Pythium zingiberis isolate were derived and analysed for sequence diversity based on single nucleotide polymorphisms (SNPs). A higher number of true and unique SNPs occurred in P. myriotylum isolates obtained from ginger with symptoms of Pythium soft rot (PSR) in Australia compared to other P. myriotylum isolates. Overall, SNPs were discovered more in the mitochondrial genome than those in the nuclear genome. Among the SNPs, a single substitution from the cytosine (C) to the thymine (T) in the partially sequenced CoxII gene of 14 representatives of PSR P. myriotylum isolates was within a restriction site of HinP1I enzyme which was used in the PCR-RFLP for detection and identification of the isolates without sequencing. The PCR-RFLP was also sensitive to detect PSR P. myriotylum strains from artificially infected ginger without the need for isolation for pure cultures.
Keyword Isothermal Amplification
Ribosomal Dna
Cocoyam
Australia
Disease
Pathogenicity
Polymorphisms
Irregulare
Region
Wilt
Q-Index Code C1
Q-Index Status Provisional Code
Grant ID PRJ-008410
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: HERDC Pre-Audit
School of Agriculture and Food Sciences
 
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Created: Sun, 31 Dec 2017, 01:50:35 EST