GENOMIC CHARACTERIZATION OF RICE GERMPLASM
Location: Dale Bumpers National Rice Research Center
Title: ADVANCES IN MARKER-ASSISTED SELECTION FOR RICE BLAST RESISTANCE
Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: January 1, 2006
Publication Date: February 15, 2006
Citation: Boyett, V.A., Gibbons, J.W., Moldenhauer, K.A., Jia, Y., McClung, A.M., Fjellstrom, R.G. 2006. Advances in marker-assisted selection for rice blast resistance. Rice Technical Working Group Meeting Proceedings, February 29-March 1, 2006, Houston, Texas. 2006 CDROM.
Marker-Assisted Selection (MAS) is being used in US rice breeding programs to enhance development of rice cultivars with improved genetic resistance to rice blast disease. Because there is a continuous threat of race shifts within the Magnaporthe grisea populations found in Southern US rice fields, which can lead to a breakdown in host plant resistance, it is important to identify, introgress, and pyramid additional sources of resistance into new cultivars. Using molecular marker technology to accomplish these goals can accelerate the breeding process, as it is more efficient for identifying major gene resistance and can be performed without regard to environmental influences or confounding phenotypic traits.
As a result of research performed by the molecular genetics programs of the USDA-ARS/TAES in Beaumont, TX and USDA-ARS in Stuttgart, AR, several major resistance genes to rice blast have been mapped and DNA markers have been developed for public use. Pi-ta confers resistance to races IB1, IB49, IB54, IB45, IH1, IG1, IC17, and IE1, but not IE1K. However, Pi-b and Pi-z confer resistance to IE1K as well as several of the same races as Pi-ta. Pi-kh, Pi-ks, Pi-LEAH, Pi-i, and Pi-d also confer resistance to some of the races covered by Pi-ta, Pi-b, and Pi-z. By pyramiding overlapping resistance genes into an improved cultivar, phenotypic resistance may be maintained even if one source of genetic resistance breaks down.
Markers are available for the above resistance genes except Pi-d, which is reported to be linked to Pi-kh. Most are microsatellite markers, but both the microsatellite markers OSM 89, RM 155, and RM 7102 and the SNLP markers YL 155 and YL 183 are available for analyzing Pi-ta alleles. Presence of Pi-b alleles can be determined by using RMs 138, 166, 266, and 208. Pi-z alleles are detected by the microsatellites AP3540, AP5413, AP5659-3, RM 527, or RM 6836. RMs 144, 224, and 1233 differentiate Pi-k alleles, and Pi-i is analyzed with RM 3855.
In the UA RREC breeding program, testing usually begins using a SNLP marker for Pi-ta in the F3 generation of single crosses or F1 of triple crosses. Leaf tissue is sampled for genomic DNA using a high-throughput DNA extraction. PCR is performed with fluorescent-labeled forward primers, and the resulting PCR products are detected with an Applied Biosystems 3730 DNA Analyzer and analyzed with GeneMapper software. After the first round of MAS, progeny of parents that may also possess Pi-b or Pi-z resistance undergo another series of marker analysis for these additional genes.
Thousands of samples have been processed for MAS in the UA RREC program, eliminating about 40% of the material on average from the breeding populations and thus extensively reducing field and greenhouse labor costs. By increasing the efficiency of early rounds of selection for blast resistance, the breeders gain confidence in the selected materials and can quickly cease investing resources in material that would otherwise never perform to the breeders’ standards.