Development and validation of a SNP-based KASP assay for rapid identification of Aphelenchoides besseyi Christie, 1942

Devran Z., Goknur A.

CROP PROTECTION, cilt.136, 2020 (SCI-Expanded) identifier identifier

  • Yayın Türü: Makale / Tam Makale
  • Cilt numarası: 136
  • Basım Tarihi: 2020
  • Doi Numarası: 10.1016/j.cropro.2020.105235
  • Dergi Adı: CROP PROTECTION
  • Derginin Tarandığı İndeksler: Science Citation Index Expanded (SCI-EXPANDED), Scopus, BIOSIS, Biotechnology Research Abstracts, CAB Abstracts, Environment Index, Geobase, Veterinary Science Database
  • Anahtar Kelimeler: Aphelenchoides besseyi, Detection, FRET, KASP, SNP, NEMATODA
  • Akdeniz Üniversitesi Adresli: Evet

Özet

Rice white tip nematode, Aphelenchoides besseyi, is a globally important seed-borne pathogen causing serious yield losses to rice. Since A. besseyi is transmitted via seed, its rapid identification is necessary for its management, as well as for breeding, seed certification and quarantine of rice. Several molecular markers have been developed for detection of A. besseyi. Kompetitive Allele-Specific PCR (KASP) is a novel molecular technique based on single nucleotide polymorphisms (SNP). The technique has been extensively used in studies of marker-assisted breeding, genotyping and SNP assays. Here, a novel KASP assay based on the small subunit ribosomal DNA (SSU rDNA) was developed for the identification of the rice white tip nematode. The KASP assay was successful in identifying A. besseyi isolates collected from rice fields in different locations of Thrace of Turkey and at various developmental stages. Results of the assays indicated that A. besseyi was successfully distinguished from A. ritzemabosi, A. fragariae and Robustodorus subtenuis (formerly A. subtenuis). To the best of the authors' knowledge, this is the first approach to identify A. besseyi using a KASP assay and to investigate the use of primer extensions in KASP assay design. The developed assay can be used for accurate and rapid identification of A. besseyi.