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We fine mapped the Xa4 locus and developed a pyramided rice line containing Xa3 and Xa4 R - alleles and a cold-tolerance QTL. This line will be valuable in rice breeding. Bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is a destructive disease of cultivated rice. Pyramiding BB resistance genes is an essential approach for increasing the resistance level of rice varieties. We selected an advanced backcross recombinant inbred line 132 (ABL132) from the BC3F7 population derived from a cross between cultivars Junam and IR72 by K3a inoculation and constructed the mapping population (BC4F6) to locate the Xa4 locus. The Xa4 locus was found to be delimited within a 60-kb interval between InDel markers InDel1 and InDel2 and tightly linked with the Xa3 gene on chromosome 11. After cold (4 °C) treatment, ABL132 with introgressions of IR72 in chromosome 11 showed lower survival rate, chlorophyll content, and relative water content compared to Junam. Genetic analysis showed that the cold stress-related quantitative trait locus (QTL) qCT11 was located in a 1.3-Mb interval close to the Xa4 locus. One line, ABL132-36, containing the Xa3 resistance allele from Junam, the Xa4 resistance allele from IR72, and the cold-tolerance QTL from Junam (qCT11), was developed from a BC4F6 population of 250 plants. This is the first report on the pyramiding of Xa3 and Xa4 genes with a cold-tolerance QTL. This region could provide a potential tool for improving resistance against BB and low-temperature stress in rice-breeding programs.

Bacterial blight (BB) of rice (Oryza sativa L.) caused by Xanthomonas oryzae pv. oryzae (Xoo) is a destructive disease in rice worldwide. Xa3, a gene conferring resistance to BB at the booting stage of the rice plant, has been characterized previously using map-based cloning. We cloned and sequenced the Xa3/xa3 gene in the Korean cultivars Hwayeong, Ilmi, and Goun and conferred resistance or susceptibility to BB. We detected polymorphisms, and polymerase chain reaction-based functional markers were developed based on the single nucleotide polymorphism from the Xa3 and xa3 nucleotide sequence. Susceptible or resistant individuals from an F2 population developed from a cross between Milyang 244 and Ilmi, near-isogenic lines carrying BB resistance genes, were screened with functional markers. The BB3-RF and BB3-RR primers consistently amplified a resistance-specific fragment of 255 bp only in resistant plants, whereas the BB3-SF and BB3-SR primers were specific to susceptible plants. Genotyping results were co-segregated with phenotype by conducting the BB resistance test with the K3 race. These markers could be effective for marker-assisted selection of the Xa3 gene in rice breeding programs.

Green rice leafhopper (GRH) is a major sap-sucking insect pest that causes large annual yield losses in rice by transmitting the rice dwarf virus or spreading sooty mold fungi. Genetic resistance is the most effective approach to control GRH as well as the spread of diseases. We performed a genetic analysis to detect the GRH resistant region in rice cv. ‘Cheongnam’ using bulk segregant analysis of the F2 population derived from a cross between GRH-resistant cv. ‘Cheongnam’ and GRH-susceptible cv. ‘Junam’. Two simple sequence repeat (SSR) markers, RM6818 and RM20142, demonstrated polymorphism between the parents, and between the resistant and susceptible bulks, and were located at the same region of GRH3 on chromosome 6. GRH3 was narrowed down to an interval between the RM20132 and RM20152 SSR markers, covering a 435-kb region of the ‘Nipponbare’ genome. We tested 1,000 individuals of the F2 population and 20 germplasm accessions and determined that GRH resistance co-segregated with SSR markers RM20142 and RM20145, which reside within the 435-kb region. This result demonstrates that these closely linked SSR markers are a convenient tool for the selection of GRH-resistant lines and cultivars.