Identification and analysis of QTLs controlling cold tolerance at the reproductive stage and validation of effective QTLs in cold-tolerant genotypes of rice (Oryza sativa L.)

Low temperature or cold stress is one of the major constraints of rice production and productivity in temperate rice-growing countries and high-altitude areas in the tropics. Even though low temperature affects the rice plant in all stages of growth, the percent seed set is damaged severely by cold and this reduces the yield potential of cultivars significantly. In this study, a new source of cold-tolerant line, IR66160-121-4-4-2, was used as a donor parent with a cold-sensitive cultivar, Geumobyeo, to produce 153 F(8) recombinant inbred lines (RILs) for quantitative trait locus (QTL) analysis. QTL analysis with 175 polymorphic simple sequence repeat (SSR) markers and composite interval mapping identified three main-effect QTLs (qPSST-3, qPSST-7, and qPSST-9) on chromosomes 3, 7, and 9. The SSR markers RM569, RM1377, and RM24545 were linked to the identified QTLs for cold tolerance with respect to percent seed set using cold-water (18-19 degrees C) irrigation in the field and controlled air temperature (17 degrees C) in the greenhouse. The total phenotypic variation for cold tolerance contributed by the three QTLs was 27.4%. RILs with high percent seed set under cold stress were validated with linked DNA markers and by haplotype analysis that revealed the contribution of progenitor genomes from the tropical japonica cultivar Jimbrug (Javanica) and temperate japonica cultivar Shen-Nung89-366. Three QTLs contributed by the cold-tolerant parent were identified which showed additive effect on percent seed set under cold treatment. This study demonstrated the utility of a new phenotyping method as well as the identification of SSR markers associated with QTLs for selection of cold-tolerant genotypes to improve temperate rice production.

The pi40 gene for durable resistance to rice blast and molecular analysis of pi40-advanced backcross breeding lines

Rice blast severely reduces production in both irrigated and water-stressed upland ecosystems of tropical and temperate countries. Nearly 50 blast resistance genes have been identified and some of those are incorporated into several rice cultivars. However, most of the resistance genes break down in a few years because of their race specificity and the rapid change in pathogenicity of the blast fungus (Magnaporthe grisea). The objective of this study was to analyze advanced backcross breeding lines (ABL) possessing the gene Pi40 for durable rice blast resistance. In all, 4 resistant genotypes, 4 japonica cultivars, and 10 monogenic differential rice genotypes with some known resistance genes were bioassayed in the greenhouse using seven sequential plantings and 29 virulent M. grisea isolates of Korea. The genotypes with the Pi40 gene had <3% diseased leaf area, which was significantly below the disease threshold level of 40% considered for durable blast resistance. Moreover, the genotypes with the Pi40 gene expressed compatibility with only two to three virulent M. grisea isolates supporting durability of resistance, in contrast to susceptible cultivars with >50% diseased leaf area and 10 compatible isolates. Of the 10 known resistance genes tested, Piz-t, Piz-5, and Pi9 showed differential reactions to the pathogen isolates in seven plantings. Genotyping of the ABL with 260 simple sequence repeat (SSR) markers revealed rapid conversion toward recurrent parent genotypes with fewer donor chromosomal segments (5.3 to 14.5%). Our study based on a sequential testing and background selection of breeding lines with the resistance gene Pi40 provided valuable information for durable blast resistance breeding in rice.