Genetic diversity and relatedness of selected Iranian rice cultivars and disease resistance donors assayed by simple sequence repeats and candidate defense gene markers

As a prerequisite to improving disease resistance and grain quality in Iranian rice cultivars, we determined the genetic relatedness of popular local cultivars and blast-resistance donor germplasm using fingerprints derived from simple sequence repeat (SSR) and plant defense gene markers. Fifty SSR markers and 28 defense candidate genes were used to assess the genetic diversity among popular rice cultivars from Iran and donors of blast resistance from breeding programs in Asia. Gene diversity estimate of the 16 core breeding lines was 0.440 ± 0.028 based on SSR markers. Genetic relationships among the cultivars were determined by cluster analysis using SSR and candidate gene datasets. DNA fingerprints derived from SSR and defense gene markers gave similar groupings of cultivars consistent with their genetic background: a) Iranian local varieties, b) improved varieties in Iran plus donor indica germplasm from Asia, and c) japonica germplasm. Within-group similarities for the traditional and improved cultivars were greater than 80% and 75%, respectively. The traditional and improved cultivars showed differential reaction to blast pathogen isolates; all traditional varieties were susceptible to blast pathogen isolates in Iran but resistant to isolates in the Philippines, whereas the improved varieties showed opposite reaction to pathogen isolates in Iran and the Philippines. Both molecular and phenotypic data suggest a narrow genetic basis in local and improved cultivars in Iran and the need for including more diversity for the breeding program. The high degree of polymorphism observed between local cultivars and donors of blast resistance provide the needed information to follow the transmission of resistance alleles from the donors in advancing breeding lines.