A molecular marker identifying subspecific populations of the soybean brown stem rot pathogen, Phialophora gregata

A molecular marker was developed to separate and identify subspecific popul ations of Phialophora gregata, the causal agent of soybean brown stem rot. A variable DNA region in the intergenic spacer of the nuclear rDNA was iden tified. Two specific primers flanking the variable region were developed fo r easy identification of the genotypes using polymerase chain reaction (PCR ). These two specific primers amplified three DNA products. The three PCR p roducts were used to separate isolates of P. gregata into distinct genotype s: A (1,020 bp), B (830 bp), and C (660 bp). Genotype C was found in isolat es obtained from Adzuki beans from Japan, whereas all 292 isolates obtained from soybean and the 8 isolates from mung bean belonged to either genotype A or B. The original nondefoliating (type II) strain ATCC 11073 (type cult ure of P. gregata) belonged to genotype B. The difference between genotypes A and B was due only to an 188-bp insertion or deletion; genotype C, howev er, differs from genotypes A and B at 58 point mutations, in addition to th e length difference. Isolates of both genotypes A and B were widespread in seven Midwestern states. Genotype A was found mostly in certain susceptible soybean cultivars like Sturdy and Pioneer 9305, whereas genotype B was fou nd predominately in brown stem rot-resistant soybean cvs. Bell, IA 3003, an d Seiben SS282N. The specific primers were also used to directly detect cul tivar-preferential infection by the two genotypes in infected soybean stems growing in the same field. Data from direct detection in soybean stems sho wed that cultivar-preferential infection by the two genotypes of P. gregata was significant.