Fine mapping a QTL qCTB7 for cold tolerance at the booting stage on rice chromosome 7 using a near-isogenic line

Abstract

Low temperature at the booting stage is a serious abiotic stress in rice, and cold tolerance is a complex trait controlled by many quantitative trait loci (QTL). A QTL for cold tolerance at the booting stage in cold-tolerant near-isogenic rice line ZL1929-4 was analyzed. A total of 647 simple sequence repeat (SSR) markers distributed across 12 chromosomes were used to survey for polymorphisms between ZL1929-4 and the cold-sensitive japonica cultivar Towada, and nine were polymorphic. Single marker analysis revealed that markers on chromosome 7 were associated with cold tolerance. By interval mapping using an F(2) population from ZL1929-4 x Towada, a QTL for cold tolerance was detected on the long arm of chromosome 7. The QTL explained 9 and 21% of the phenotypic variances in the F(2) and F(3) generations, respectively. Recombinant plants were screened for two flanking markers, RM182 and RM1132, in an F(2) population with 2,810 plants. Two-step substitution mapping suggested that the QTL was located in a 92-kb interval between markers RI02905 and RM21862. This interval was present in BAC clone AP003804. We designated the QTL as qCTB7 (quantitative trait locus for cold tolerance at the booting stage on chromosome 7), and identified 12 putative candidate genes.

Reduction of Gibberellin by Low Temperature Disrupts Pollen Development in Rice

“…However, identification of the factors underlying temperature tolerance poses particular challenges. Cool-temperature tolerance in rice appears to be a highly complex trait that involves divergent loci in different rice lines (Takeuchi et al, 2001;Saito et al, 2001;Andaya and Mackill, 2003;Kuroki et al, 2007;Zeng et al, 2009;Saito et al, 2010;Zhou et al, 2010). These quantitative trait loci have been mapped on all twelve chromosomes.…”

Comparative analysis of microRNA profiles of rice anthers between cool-sensitive and cool-tolerant cultivars under cool-temperature stress

“…Genetic systems for conferring cool tolerance in rice are not clear, although many quantitative trait loci (QTLs) for cool tolerance at the booting stage have been detected (Takeuchi et al, 2001;Andaya and Mackill, 2003;Ye et al, 2010;Zhou et al, 2010;Kuroi et al, 2011). Saito and his colleagues (2001,2004,2010) have explored QTLs that correlated with cold tolerance of spikelet fertility at the booting stage in rice, and they indicated that an F-box protein gene, located on chromosome 4, is one of the genes conferring cold tolerance based on results from map-based cloning.…”

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).…”

“…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). Breeding for water-logging tolerance is complicated and needs to focus mainly on survival of the below-ground and vegetative plant parts, because the effects on reproductive development are secondary.…”