Identifying Novel Resistance Genes in Newly Introduced Blast Resistant Rice Germplasm

Blast, Magnaporthe oryzae B. Couch, and sheath blight, Rhizoctonia solani Kühn, are major fungal diseases of cultivated rice (Oryza sativa L.) in theUSA. Resistance toU.S.M. oryzae races was observed in 91 newly introduced rice accessions, suggesting these accessions are possible sources of novel blast resistance genes (Pi-genes) that could be incorporated into U.S. rice cultivars. The genes Pi-ta and Pi-b have been introduced into U.S. cultivars and characterized molecularly. The objective of this research was to identify new Pi-genes in the aforementioned accessions by differentiating known Pi-genes, determining relatedness of the accessions with SSR markers, and identifying associations of SSR markers with blast resistance and sheath blight resistance. Twenty-seven accessions were identified with resistance to U.S. blast races and as having neither thePi-ta norPi-b gene. Based on 125 SSR markers distributed over the rice genome, 11 of the 27 accessions were closely related to each other, but the remaining 16 accessions had varying levels of genotypic diversity, including two accessions selected from crosses of the Asian cultivated species, O. sativa, with the African cultivated species, O. glaberrima. Blast resistance traits were associated with 32 of the 125 SSRmarkers and sheath blight resistance traits with 19 markers. Of the 32 blast-associated markers, 20 were located in chromosomal regions previously identified as containing Pi-genes. The remaining 12 markers will provide the basis for discovering additional Pi-genes. PLANT breeders often use cultivars developed in other countries to broaden the germplasm base for developing improved cultivars. Dilday (1990) observed that all U.S. rice cultivars developed before 1990 could be traced back to 22 plant introductions that were made into the southern USA (Arkansas, Louisiana, Texas) and 23 introductions made into California. To expand the germplasm base of U.S. cultivars most rice breeding programs are incorporating more diverse rice germplasm into the cultivars being developed (Mackill and McKenzie, 2003). Using 169 SSR markers, Lu et al. (2005) genotyped 145 U.S. rice cultivars and showed cultivars released more recently clustered close to older cultivars in their pedigree. In addition, the cultivars clustered based on their subspecies (tropical japonica, temperate japonica, or indica) and grain type (long, medium, or short grain). Blast (Couch and Kohn, 2002), causes major rice yield losses worldwide with resistant cultivars and fungicides being the primary methods of disease control (Bonman, 1992; Lee, 1994). Based on the rice genome sequence, Monosi et al. (2004) determined that the rice genome carries approximately 500 nucleotide-binding site (NBS)-leucine-rich repeat (LRR) genes. Many of these NBS-LRR regions are associated with a broad spectrum of disease resistance genes (R-genes), as initially reported for the rice blast resistance genes, Pi-ta (Bryan et al., 2000) and Pi-b (Wang et al., 1999). Monosi et al. (2004) determined the distribution of the NBS-encoding genes in the ‘Nipponbare’ rice genome and identified the approximate map position of blast resistance (designated Pi-) genes, which had been previously mapped to a chromosome region based on phenotype, using various mapping populations. The U.S. rice breeding programs incorporated Pi-ta from the Vietnamese landrace Tetep into ‘Katy’ (Moldenhauer et al., 1990) and Pi-b from the Chinese cultivar Te Qing into ‘Saber’ (McClung et al., 2004). In an effort to utilize molecular markers as part of U.S. breeding programs, SSRmarkers associated with resistance to Pi-b, Pi-k, Pi-k, Pi-ta, and Pi-z were identified in the background of U.S. cultivars (Conaway-Bormans et al., 2003; Fjellstrom et al., 2004, 2006; Jia et al., 2004b). Rice sheath blight is another major fungal disease of rice worldwide (Rush and Lee, 1992). Recently, Pinson et al. (2005) confirmed six previously identified QTLs for sheath blight resistance and identified eight new QTLs. Three of the confirmed QTLs were independent for plant height and maturity which affect sheath blight resistance. Based on identification of the aforementioned sheath blight resistance QTLs, additional studies are in progress to further map sheath blight resistance genes. To characterize additional rice germplasm useful to U.S. rice breeders Dilday et al. (2001), Yan et al. (2002), Lee et al. (2003), and Yan et al. (2003) conducted field evaluations on approximately 1000 rice germplasm accessions recently introduced into the USA. Accessions were evaluated for desirable agronomic characteristics and for resistance to the two major diseases blast and sheath blight. Ninety-one accessions identified as blast resistant in the field tests were selected for further greenhouse tests to determine resistance to blast races commonly found in the USA (Correll et al., 2000). The objective of this research was to identify new blast resistance genes in the 91 selected resistant accessions by (i) differentiating known Pi-genes, (ii) determining relatedness of the accessions with SSR markers, and (iii) identifying associations of SSRmarkers with blast resistance, sheath blight resistance, and/or the morphological traits, plant height and heading date, that affect the expression of sheath blight resistance. G.C. Eizenga, W. Yan, Y. Jia, USDA-ARS, Dale Bumpers National Rice Research Center, P.O. Box 1090, Stuttgart, AR 72160-1090 and H.A. Agrama, F.N. Lee, Rice Res. & Ext. Ctr., Univ. of Arkansas, 2900 Hwy 130 E, Stuttgart, AR 72160. Received 31 Mar. 2006. *Corresponding author ([email protected]). Published in Crop Sci. 46:1870–1878 (2006). Plant Genetic Resources doi:10.2135/cropsci2006.0143 a Crop Science Society of America 677 S. Segoe Rd., Madison, WI 53711 USA Abbreviations: Polymerase chain reaction (PCR); Quantitative trait locus (QTL); Simple sequence repeat (SSR); Nucleotide-binding site leucine-rich repeat (NBS-LRR). R e p ro d u c e d fr o m C ro p S c ie n c e . P u b lis h e d b y C ro p S c ie n c e S o c ie ty o f A m e ri c a . A ll c o p y ri g h ts re s e rv e d . 1870 Published online July 25, 2006