Near-Isogenic Lines of Japonica Rice Revealed New QTLs for Cold Tolerance at Booting Stage

Low temperature stress severely hampers rice productivity, and hence elaborating chilling-mediated physiochemical alterations and unravelling cold tolerance pathways will facilitate cold resilient rice breeding. Various cold tolerant Near-isogenic lines (NILs) selected at the booting stage through backcrossing of a japonica landrace Lijing2 (cold tolerant) with cold sensitive Towada (a japonica cultivar). The cold tolerance attributes of NILs was validated over two years by evaluating the spikelet fertility followed by correlation of nineteen morphological traits with the rate of seed setting (RSS). Results revealed BG, FG, 1-2IL, RSLL, and UIL were significantly correlated with RSS and had nearer marker interval distance with cold tolerance in QTL analysis. Two QTLs, qCTB-7-a and qCTB-7-b, were found for RSS based on a mixed linear model. Alleles of two QTLs were contributed by Lijing2 and genetic distances between the peaks were 0.00 and 0.06cM, which explained 5.70% and 8.36% variation, respectively, One QTL for 1-2IL, RSLL, and ILBS, while two QTLs for FG, BG, and UIL were also identified. These findings can be exploited to engineer low temperature stress tolerant rice in times of climate change.