Specific PCR-based detection of Alternaria helianthi: the cause of blight and leaf spot in sunflower

• Published in: Archives of microbiology Vol. 194; no. 11; pp. 923 - 932
• Main Authors: Udayashankar, A. C., Chandra Nayaka, S., Archana, B., Anjana, G., Niranjana, S. R., Mortensen, C. N., Lund, Ole S., Prakash, H. S.
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer-Verlag 01-11-2012; Springer; Springer Nature B.V
• Subjects: Agricultural commodities; Agricultural production; Alternaria; Alternaria - genetics; Alternaria - isolation & purification; Biochemistry; Biological and medical sciences; Biomedical and Life Sciences; Biotechnology; Blight; Cell Biology; Cross-reaction; Data processing; Deoxyribonucleic acid; DNA; DNA Primers; DNA, Fungal - genetics; DNA, Ribosomal Spacer - genetics; Ecology; Fundamental and applied biological sciences. Psychology; Fungal plant pathogens; Fungi; Helianthus; Helianthus - microbiology; India; Leafspot; Leaves; Life Sciences; Microbial Ecology; Microbiology; Miscellaneous; Morphology; Mycology; Nucleotide sequence; Original Paper; Pathogens; Phytopathology. Animal pests. Plant and forest protection; Plant Leaves - microbiology; Polymerase Chain Reaction; Primers; RNA, Ribosomal, 5.8S - genetics; rRNA; Seeds; Seeds - microbiology; Sensitivity and Specificity; Taxonomy; India; Mumbai India; Molecular diagnosis; ITS sequences; Specific primers; Alternaria blight; Seed-borne fungi; Seed health; PCR; Plant pathogen; Alternaria helianthi; Fungi; Polymerase chain reaction; Fungi Imperfecti; Diagnosis; Detection
• ISSN: 0302-8933; 1432-072X
• DOI: 10.1007/s00203-012-0826-x

Alternaria helianthi
is an important seed-borne pathogenic fungus responsible for blight disease in sunflower. The current detection methods, which are based on culture and morphological identification, are time-consuming, laborious and are not always reliable. A PCR-based diagnostic method was developed with species-specific primers designed based on the sequence data of a region consisting of the 5.8S RNA gene and internal transcribed spacers—ITS 1 and ITS 2 of nuclear ribosomal RNA gene (rDNA) repeats of
A. helianthi
. The specificity of the primer pairs AhN1F and AhN1R designed was verified by PCR analysis of DNA from 18
Alternaria helianthi
strains isolated from India, 14 non-target
Alternaria
spp. and 11 fungal isolates of other genera. A single amplification product of 357-bp was detected from DNA of
A. helianthi
isolates. No cross-reaction was observed with any of the other isolates tested. The detection limit of the PCR method was of 10 pg from template DNA. The primers could also detect the pathogen in infected sunflower seed. This species-specific PCR method provides a quick, simple, powerful and reliable alternative to conventional methods in the detection and identification of
A. helianthi
. This is the first report of an
A. helianthi
-specific primer set.