GENOMIC CHARACTERIZATION OF RICE GERMPLASM
Location: Dale Bumpers National Rice Research Center
Title: MAPPING R-GENES IN RICE WILD RELATIVES (ORYZA SPP.)
Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: December 5, 2005
Publication Date: January 15, 2006
Citation: Eizenga, G.C., Agrama, H.A., Lee, F.N. 2006. Mapping r-genes in rice wild relatives (oryza spp.). Rice Technical Working Group Meeting Proceedings, February 29-March1, 2006, Houston, TX. CDROM.
Rice sheath blight caused by Rhizoctonia solani Kühn and leaf blast caused by Magnaporthe grisea (T.T. Herbert) Yaegashi & Udagawa are major fungal diseases of cultivated rice (Oryza sativa L.). Rice wild relatives (Oryza spp.) are the source of several resistance (R-) genes including those for blast and sheath blight resistance. Simple sequence repeat (SSR) markers were used to genotype rice accessions and determine the relatedness between the accessions. Recently, methodology to identify associations between DNA markers and specific traits was developed and it should be possible to use this methodology to identify R-genes in Oryza spp. accessions. The objectives of this research were to 1) determine the genetic distance between three groups of Oryza accessions (Oryza spp., blast resistant O. sativa accessions and U.S. rice cultivars) with SSR markers; 2) identify marker-trait associations between the SSR markers and disease reactions; and 3) compare the marker-trait associations identified between the three groups to further define novel R-genes.
Oryza spp. accessions were obtained from IRRI or are available from the U.S. rice germplasm collection (GRIN) (http://www.ars-grin.gov/npgs/). The blast resistant O. sativa accessions are being introduced into the GRIN system. Seed of the U.S. cultivars are available through GRIN or from the appropriate breeding program.
Pathogenicity tests of M. grisea and R. solani were adapted from standard procedures. Genomic DNA was extracted from leaf tissue for amplification of PCR-based SSR primers. A total of 176 SSR markers were visualized by fluorescent-labeled products, processed by an ABI Prism 3700 DNA Analyzer, and data analyzed with GeneScan 3.6/Genotyper 2.6 software. The distance between each two genotypes was calculated using Rogers’ distance (RD). Unweighted Pair-Group Method using Arithmetic Average (UPGMA) clustering was calculated based on the RD estimate pairs of genotypes matrix. Genetic distance and cluster analysis was conducted using the software program PowerMarker. Associations between the SSR markers and disease resistance traits also were delineated using PowerMarker.
The genetic distance between the three groups, Oryza spp. accessions, newly introduced, blast resistant O. sativa accessions and U.S. rice cultivars, delineated the U.S. cultivars in one cluster with sub-clusters representing the parentage. The Oryza spp. group was represented by O. alta, O. australiensis, O. barthii, O. glumaepatula, O. latifolia, O. meridionalis, O. nivara, O. officinalis and O. rufipogon. The close relationship between many accessions of O. barthii, O. nivara and O. rufipogon was readily apparent. One cluster of O. glaberrima and its ancestral species, O. barthii, was identified. The O. sativa ancestral species, O. nivara and O. rufipogon are grouped together in several clusters. The Oryza spp. and O. sativa groups are distinct except for one O. rufipogon included in the ‘Tox’ lines obtained from Ivory Coast. It should be noted that this O. rufipogon accession originated in Cameroon. A cluster of O. sativa accessions originating from China also was identified.
In order to identify possible new R-genes, associations between the aforementioned SSR markers and disease ratings were determined within each of the three groups. Preliminary results identified 28 marker-disease trait associations in the Oryza spp. group, 44 associations in the blast resistant O. sativa group, and 21 associations in the group of U.S. cultivars. Most likely more associations were identified in the O. sativa group because these accessions were identified as blast resistant in the field. There is little overlap between the associations of the three groups suggesting a number of R-genes are present in these accessions. Approximately 34 chromosomal regions which do not have known blast (Pi-) resistance genes were identified by these marker-trait associations. These regions will be investigated further to identify novel R-genes in both the Oryza spp. and O. sativa accessions. Only five associations with sheath blight were identified and these are in regions of previously identified sheath blight QTLs.
Using blast resistant O. nivara accessions, mapping populations are being developed from crosses with susceptible U.S. rice lines for fine mapping and identification of novel R-genes. In addition, disease resistant backcross progenies obtained from these mapping populations will be made available to rice breeding programs.