The impact of DNA-marker-assisted selection on breeding disease-resistant rice cultivar has been impressive as reflected by a number of studies. In lieu of RFLPs, PCR-based molecular tools in the form of STS and SSR have been developed to implement genotypic selection. Two important diseases, BLB and blast, were the prime targets for which a large number of genes have been identified and mapped in a wide range of germplasms. Rice lines with improved resistance against BLB and blast are being developed through successful pyramiding of multiple disease resistance genes. A number of STS and SSR markers linked to various BLB and blast genes and their primer sequences are listed in Table 11.
Among several STS markers generated from AFLP fragments linked to the rice bacterial blight resistance gene Xa7, M5 was found to be cosegregating with the gene (Porter et al. 2003). Gu et al. (2004) saturated the Xa27(t) genomic region with markers derived from the genomic sequence of O.sativa cv. Nipponbare and developed markers, viz., M631, M1230, and M449, that cosegregate with the gene. SSR and STS markers linked to BB resistance genes, xa5, xal3, Xa21, have been identified and developed (Ronald et al. 1992; Yoshimura et al. 1995; Zhang et al. 1996a; Blair and McCouch 1997).
In backcross breeding programs, DNA-marker-based selection can hasten the incorporation of desirable genes. Chen et al. (2000,2001) improved bacterial blight resistance of two elite restorer lines "6078" and "Minghui 63" by incorporating Xa21 from "IRBB21" through MAS. The hybrids developed using these improved restorer lines showed improvement in yield under disease infestation.
Mapping of many blast resistance genes followed by fine mapping and development of PCR-based markers have significantly accelerated the breeding of blast-resistant cultivars in rice. Analyzing the molecular profile and blast resistance data of the RIL population of Co 39 x Moroberekan (Wang et al. 1994b), three RI lines carrying different genes for complete resistance, and two RI lines with genes for partial resistance were identified for quick development of NILs
(Inukai et al. 1996). Liu et al. (2003) demonstrated the utility of MAS by improving the resistance of Zhen-shan 97 against rice blast. Selection was performed by using an SSR marker linked to Pi1 gene on chromosome 11.
For blast resistance gene Pi10, Naqvi and Chattoo (1996) developed SCAR markers from linked RAPD fragments. Hittalmani et al. (1995) developed an STS marker for a tightly linked RFLP marker RG64 and detected specific amplicon polymorphism (SAP) between the resistant and the susceptible genotypes upon digestion of the PCR products with a restriction enzyme HaeIII. Efficiency of selecting resistant plants with this STS marker was 95%, but use of flanking markers improved the selection efficiency to 100%. Pan et al. (2003) developed three RAPD markers, BAR 15486, BAR 15782, and BAR 15844, tightly flanking the Pi15 gene with recombination frequencies of 0.35%, 0.35%, and 1.1%, respectively, for marker-aided gene pyramiding. A pair of primers that specifically amplified a susceptible pi-ta allele was developed to verify the absence of Pi-ta gene (Jia et al. 2004).
Using sequence data found in public databases and degenerate primer pairs based on the P-loop, nucleotide binding sites, and kinase domain motifs of previously cloned resistance genes, Conaway-Bormans et al. (2003) developed PCR-based markers that cosegregate with the gene Pi-z that confers complete resistance to five races of blast and is located on theshort armofchromosome6. The abilitytoidentify polymorphism in a wide range of rice germplasms offers a valuable alternative to conventional pheno-typic screening for rapid introgression of genes into susceptible varieties as well as the incorporation of multiple genes into individual lines for more-durable blast resistance. Hayashi et al. (2004) surveyed SNPs and insertion-deletions (InDels) in the chromosomal region containing the blast resistance genes Piz and Piz-t and generated SNP markers to discriminate resistant and susceptible alleles.
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