Molecular phylogeny of plant pathogenic fungi based on start codon targeted (SCoT) polymorphism.

BACKGROUND: A number of molecular marker systems have been developed to assess genetic diversity, carry out phylogenetic analysis, and diagnose and discriminate plant pathogenic fungi. The start codon targeted (SCoT) markers system is a novel approach used here to investigate intra and interspecific polymorphisms of phytopathogenic fungi. MATERIALS AND METHODS: This study assessed genetic variability between and within 96 isolates of ten fungal species associated with a variety of plant species using 36 SCoT primers. RESULTS: The six primers generated 331 distinct and reproducible banding patterns, of which 322 were polymorphic (97.28%), resulting in 53.67 polymorphic bands per primer. All primers produced informative amplification profiles that distinguished all fungal species. With a resolving power of 10.65, SCoT primer 12 showed the highest polymorphism among species, followed by primer 33 and primer 29. Polymorphic loci (PPL), Nei's diversity index (h), and Shannon index (I) percentages were 6.25, 0.018, and 0.028, respectively. UPGMA analysis separated all isolates based on morphological classification and revealed significant genetic variation among fungal isolates at the intraspecific level. PCoA analysis strongly supported fungal species discrimination and genetic variation. The other parameters of evaluation proved that SCoT markers are at least as effective as other DNA markers. CONCLUSIONS: SCoT markers were effective in identifying plant pathogenic fungi and were a powerful tool for estimating genetic variation and population structure of different fungi species.

Analysis of genetic diversity among common bean germplasm by start codon targeted (SCoT) markers.

BACKGROUND: Breeding strategies to improve modern varieties having high yield, high nutritional value and resistance to biotic and abiotic stress, etc. is very important to make up for the food deficiencies. Molecular studies as a tool in breeding programs for the characterization of germplasm have been performed with several DNA marker systems. MATERIALS AND METHODS: In the present study, the genetic diversity of 53 common bean landraces and 22 registered varieties from Turkey, and 12 genotypes from USDA was investigated using start codon targeted (SCoT) markers for the first time worldwide. The 8 primers having stronger and more polymorphic bands were used for PCR amplification. RESULTS: The mean polymorphic band of all primers was found as 13.13. The average of polymorphic information content and resolving power values was 0.34 and 7.55, respectively. Analysis of molecular variance (AMOVA) explored the existence of higher genetic diversity within populations accounting for 92% compared to among populations variations. According to cluster analysis (UPGMA) and genetic structure based on SCoT data, accessions were separated into Andean (PopA) and Mesoamerican PopB) gene pools. Moreover, accessions were mostly placed in the same groups/subgroups according to their geographical origin. CONCLUSIONS: A high level of genetic diversity was observed between the investigated accessions in this work. The findings will help to plant breeders to characterize common bean accessions.

Characterization and Pathogenicity of Rhizoctonia Species Causing Root Rot and Damping-off on Sugar Beet in Turkey.

During 2015-2017 growing seasons, seventy-one isolates of Rhizoctonia spp. were obtained from the samples collected from the sugar beet fields of Konya province, which is one of the most important sugar beet growing areas of Turkey. Anastomosis groups (AGs) of Rhizoctonia spp. isolates were determined by hyphal conjugation with the tester strains and sequence analysis of the rDNA ITS region. The obtained data confirmed the species identity of 61 isolates out of 71 as R. solani (AG-2-2-IIIB, AG-4-(HGI, HGII, HGIII), AG-5, AG-11) and the remaining 10 isolates as binucleate Rhizoctonia (AG-K, AG-A). Pathogenicity tests revealed that AG-2-2-IIIB, AG-4-(HGI, HGII, HGIII) and AG-K isolates were highly virulent on sugar beet. The disease severity of 71 isolates varied between 13 and 100%. Based on the virulence, the isolates formed four categories; (i) 11 isolates: non-pathogenic, (ii) 15 isolates: low virulent, (iii) 6 isolates: moderately virulent and (iv) 39 isolates: highly virulent. To our knowledge, the AGs of AG-4-(HGI, HGII, HGIII), AG-11, AG-A are first reports on sugar beet in Turkey and the AG-5, AG-11 and AG-K are first AG groups for Konya region.