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.)

Abstract

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.

Genome-wide association study of cold tolerance of Chinese indica rice varieties at the bud burst stage

“…Low temperature is one of the most common environmental stress factors; it can affect rice architecture and seed germination, slow the growth rate, delay seed maturation, cause male sterility, decrease the seed setting rate, and ultimately reduce the rice yield (Fujino and Matsuda 2010;Fujino et al 2008;Ma et al 2015;Saito et al 2004Saito et al , 2010Suh et al 2010). Cold stress is a major factor contributing to reduced rice yield in temperate and high-altitude regions.…”

Physiological and Molecular-Genetic Evaluation of Rice Breeding Resources on Cold Tolerance for Creating New Varieties for the Northern Zone of Rice Cultivation

“…After hybridization with domestic and foreign varieties, the obtained F 1 hybrids in various combinations were analyzed with the use of microsatellite markers that are closely related to the cold tolerance trait RM 24545, RM 1377, RM 231, RM 569 (Suh et al, 2010). The nucleotide sequence of primer pairs of cold tolerance markers is shown in Table 4.…”

“…The effect of low temperatures is manifested at various stages of rice plant growth (Suh et al, 2010). In this regard, in the programs of breeding rice tolerant to cold stress, the first and the most important stage is initial screening of selection samples to identify donors of tolerance to this stress factor.…”

“…In addition, the authors identified SSR markers RM569, RM1377, RM24545, which were closely related to these loci. The phenotypic test for cold tolerance was the calculation of the percentage of germinated seeds in the irrigation water at 18-19°C and at the controlled temperature (17°C) in a greenhouse (Suh et al, 2010).…”

Yield stability for cereals in a changing climate

“…In the case of cold-tolerance in rice breeding efforts have focussed on improving seedling vigour, shortening the growth season, and improving cold-tolerance at the booting stage Mackill 2003a, 2003b). Genetic variability has been identified for reproductive stage cold tolerance and this material has made it possible to identify cold-tolerance QTL (Saito et al 2004;Oliver et al 2005;Kuroki et al 2009;Suh et al 2010;Zhou et al 2010). Two cold tolerance loci, Ctb-1 and qCTB7, have been fine-mapped (Saito et al 2004;Zhou et al 2010).…”