APPLICATION OF RICE GENOMICS TO DEVELOP SUSTAINABLE CROPPING SYSTEMS FOR THE GULF COAST
Title: The application of new markers for predicting blast resistance and cooking quality in rice
Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: December 1, 2003
Publication Date: June 1, 2004
Citation: McClung, A.M., Shank, A.R., Kanter, D., Jodari, F., Beighley, D., Chen, M., Fjellstrom, R.G. 2004. The application of new markers for predicting blast resistance and cooking quality in rice. In: Rice Technical Working Group Meeting Proceedings, February 29-March 4, 2004, New Orleans, LA. p. 59-60. 2004.
We have been developing DNA markers that are closely linked to traits that are important to the rice industry and can be used in the relatively narrow germplasm base that is commonly used by U.S. breeders. Marker assisted selection will facilitate breeding efforts to develop improved cultivars more efficiently and effectively. Our initial focus has been on simply inherited traits aspects of disease resistance and cooking quality. For any given trait, segregating mapping populations have been generated, chromosomal locations of candidate markers have been identified using public databases, polymorphic PCR-based markers have been developed, hundreds of progeny have been evaluated for phenotype and genotype, and associations between the marker alleles and trait variation have been determined. These markers have then been tested across diverse sets of germplasm (Uniform Rice Regional Nursery entries, historical U.S. rice cultivars, accessions from GRIN, etc.). As a result, we have developed DNA markers that are associated with all of the known major genes commonly found in U.S. germplasm that confer resistance to Pyricularia grisea which causes blast disease. The only exception is the pi-d gene which confers resistance only to race IB-1 and is associated with the Pi-k locus on chromosome 11. Marker RM 224 has been found to be closely linked to the Pi-k locus and can discern the presence of the Pi-kh (RM 224 = 140nt) and Pi-ks (RM 224 = 120nt) alleles. Pi- ks confers resistance only to the IB-54 race and is commonly found in southern U.S. medium grain cultivars but is also in a few long grain cultivars, eg. Cheniere, Drew, and Ahrent. In contrast, Pi-kh confers resistance to IB-54 and three other races of blast and is found in many southern U.S. long grains including Cypress, Wells, Kaybonnet, Saber, Lemont, and Cocodrie. Markers in this same region can discern the presence of another blast resistance gene, Pi-Leah, that conveys resistance to all of the same races as Pi-kh except for IB-54. The Pi-b gene is located on chromosome 2 and confers resistance to races IB-1, IB-45, IG-1, IC-17, IE-1, and IE-1k. Pi-b can be identified by the presence of the 177nt allele using marker RM 208 in cultivars Saber and Bolivar. We have used marker RM 7102 which is tightly linked to the Pi-ta2 gene located on chromosome 12 which conveys resistance to all predominant races of blast occurring in the U.S. except IE-1k. We are also using an unpublished marker from Dr. Yulin Jia (USDA-ARS) located within the Pita gene which confirms the presence of Pi-ta2 in cultivars like Kaybonnet, Drew, Madison, and Ahrent that had been previously identified by RM 7102. Developing markers associated with the Pi-z gene that are useful across a broad array of U.S. germplasm has been more difficult because this gene is located in an area of chromosome 6 that displays little polymorphism. The Pi-z gene is found in several medium grain cultivars like Bengal, Lafitte, Mars, and Orion and a few long grain cultivars like Jefferson and Cadet. We have identified markers AP 3540 and RM 527 which closely flank the Pi-z gene, but other markers are available in this region if these are not polymorphic in the breeder's cross of interest. AP 3540 is also closely linked to the Hd-1 gene that is associated with photoperiodism sensitivity in exotic germplasm. Flanking markers for the Pi-i gene on chromosome 9 conveying resistance to IH-1 were identified in a cross using L205 as the blast resistance donor. The 188nt allele of the RM 3855 marker and the 196nt allele of the AP 5128 marker identify the Pi-i resistance gene which is found in Dixiebelle, Cocodrie, and Francis, among others.
We have previously reported the identification of DNA markers associated with grain quality traits like amylose content (using marker RM 190 located on chromosome 6) as well as aroma (RG28, RM 223) and elongation (RM44) having markers on chromosome 8. We have recently identified additional markers within the Waxy gene that can differentiate between RVA pasting curves of L202 types (weak RVA) and Lemont types (strong RVA). We have developed markers associated with the Alk gene on chromosome 6 that can predict alkali spreading value (ASV) scores used to categorize rice cultivars for starch gelatinization temperature. It appears that cultivars categorized as intermediate ASV (values of 4-5) have the 90nt allele for the marker developed at this locus while cultivars with high ASV scores (values of 6-7) have the 92nt allele. ASV scores of 2-3 (high gelatinization temperature types) have the 90nt allele and an amylose content of less than 19 percent.
Development of DNA markers for these simply inherited traits are now being used on a routine basis in our rice breeding program and are available to the public. These markers can be analyzed using leaf tissue, brown rice or milled rice. Multiple traits can be determined following one DNA extraction of a sample and marker genotypes can be determined within a few days. All of the markers are co-dominant and thus, can discern homozygotes from heterozygotes. Once the line is fixed for the desired allele it may no longer require further evaluation of the trait. Markers can also identify genes that are masked by dominance (eg. aroma and semidwarfism) or the presence of other genes (eg. Pt-ta2 masks the presence of Pi- kh in Kaybonnet and Pi- ks in Drew). These examples demonstrate the tremendous savings in time, labor, equipment, and trained staff that marker technology can offer.