Exploring genetic diversity and potential novel disease resistance genes in a collection of rice (Oryza spp.) wild relatives

Wild relatives of rice (Oryza spp.) are an important source of novel resistance (R-) genes for rice improvement. Rice sheath blight, caused by Rhizotonia solani, and leaf blast, caused by Magnaportha oryzae, are major fungal diseases of rice worldwide. To identify novel R-genes, a group of Oryza spp. accessions represented by O. alta, O. australiensis, O. barthii, O. glaberrima, O. glumaepatula, O. latifolia, O. meridionolis, O. nivara, O. officinalis, and O. rufipogon, were evaluated for their reaction to leaf blast and sheath blight disease, and genotyped with 176 microsatellite (SSR) markers. Selected rice (O. sativa) accessions were included as reference. Cluster analysis performed with PowerMarker software using Rogers genetic distance and UPGMA, revealed most Oryza spp. accessions clustered with the same species or a closely related Oryza spp. Only a few Oryza spp. accessions grouped with the O. sativa accessions included as a reference. Analysis of this genotypic data in the software Structure revealed that the Oryza spp. accessions were assigned into eight different subpopulations and fit well into eight different backgrounds. Marker-trait associations between the SSR markers and disease reactions to blast and sheath blight were ascertained using the software TASSEL. Associations with blast disease were identified in ten different chromosomal regions and five of the ten were not located near known blast R-genes. Three associations were discovered with sheath blight disease and one was not near previously reported sheath blight QTL. These newly identified regions may represent novel R-genes that will be the basis future fine mapping studies.