Novel loop-mediated isothermal amplification (LAMP) assay with a universal QProbe can detect SNPs determining races in plant pathogenic fungi

• Published in: Scientific reports Vol. 7; no. 1; pp. 4253 - 9
• Main Authors: Ayukawa, Yu, Hanyuda, Saeri, Fujita, Naoko, Komatsu, Ken, Arie, Tsutomu
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 26-06-2017; Nature Publishing Group; Nature Portfolio
• Subjects: 45/70; 45/77; 631/1647/1513/2192; 631/326/193/2542; 631/326/2522; Eye Proteins - genetics; Fungi; Fungi - genetics; Fungi - pathogenicity; Fusarium oxysporum; Homeobox Protein SIX3; Homeodomain Proteins - genetics; Humanities and Social Sciences; Kinases; multidisciplinary; Mutation; Nerve Tissue Proteins - genetics; Nucleic Acid Amplification Techniques; Pathogenicity; Plant Diseases - genetics; Plant Diseases - microbiology; Point Mutation; Polymorphism, Single Nucleotide - genetics; Resistant mutant; Science; Science (multidisciplinary); Single-nucleotide polymorphism; Six3 gene; Solanum lycopersicum - genetics; Solanum lycopersicum - microbiology; Wilt; Xylem
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-017-04084-y

Tomato wilt pathogen
Fusarium oxysporum
f. sp.
lycopersici
(
Fol
) is grouped into three races based on their pathogenicity to different host cultivars. Rapid detection and discrimination of
Fol
races in field soils is important to prevent tomato wilt disease. Although five types of point mutations in
secreted in xylem 3
(
SIX3
) gene, which are characteristic of race 3, have been reported as a molecular marker for the race, detection of these point mutations is laborious. The aim of this study is to develop a rapid and accurate method for the detection of point mutations in
SIX3
of
Fol
. Loop-mediated isothermal amplification (LAMP) of
SIX3
gene with the universal QProbe as well as two joint DNAs followed by annealing curve analysis allowed us to specifically detect
Fol
and discriminate race 3 among other races in about one hour. Our developed method is applicable for detection of races of other plant pathogenic fungi as well as their pesticide-resistant mutants that arise through point mutations in a particular gene.