Euphytica 131: 275–284, 2003. © 2003 Kluwer Academic Publishers. Printed in the Netherlands. 275 Genetic diversity and relatedness of selected Iranian rice cultivars and disease resistance donors assayed by simple sequence repeats and candidate defense gene markers Ali Moumeni 1,3 , Bahman Yazdi Samadi 2 , Jianli Wu 3 & Hei Leung 3 ∗ 1 Rice Research Institute of Iran, P.O. Box 1658, Rasht, Iran; 2 College of Agriculture, University of Tehran, Karaj, Iran; 3 Entomology and Plant Pathology Division, International Rice Research Institute, DAPO 7777, Metro Manila, Philippines; ( ∗ author for correspondence: e-mail: H.Leung@cgiar.org) Received 16 April 2002; accepted 27 September 2002 Key words: cluster analysis, DNA fingerprints, microsatellites, plant defense candidate genes, rice blast Summary 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. Introduction Rice, after wheat, is the second most important cer- eal in Iran. Rice cultivation in Iran is over 600,000 hectares with yield of 4–5 ton/ha. Two provinces, Mazandaran and Gilan, account for more than 80% of Iran’s rice production. Most rice cultivars grown in Iran are indica type and under irrigation. However, productivity was limited by inadequate water, soil con- ditions, biotic and abiotic stresses. Grain shape and aroma are two important quality factors for consumers in Iran. Between 1970 and 2000, more than 20 high- yielding rice cultivars were released to farmers but most of them have not gained popularity because of inadequate grain quality to match market needs. Local traditional varieties have good grain quality but they are susceptible to diseases. Rice blast, caused by Magnaporthe grisea (Hebert) Barr. was reported for the first time in 1949 in Iran, but only recognized as an important disease causing economic losses in 1969. Currently, blast is endemic throughout Iran, and in some early maturity variet- ies, yield loss up to 90% has been reported (Behdad, 1990). All types of blast infection can be found in farmers’ field, including seedling, collar, neck, pan- icle, and grain. Developing effective blast resistance