QTL analysis of main agronomic traits in rice under low temperature stress

To identify cold tolerance at the reproductive stage in rice ( Oryza sativa L.), the cold susceptible accession, IAPAR-9 ( tropical japonica ) was crossed with the cold tolerant accessions Akihikari and Liaoyan241 ( temperate japonica ) to construct two recombinant inbred lines (RIL) to detected QTLs related to cold-tolerance of rice through analyze phenotypic variation. The two RILs and their parents were experimentally grown in natural conditions and cold water irrigation at one site, Gongzhuling Jilin (China), and at natural low temperature in another site, Kunming Yunnan (China). We measured plant height, panicle length, number of panicles per plant, grain number per panicle, seed setting rate and panicle exsertion of parents and RIL populations in the maturation stage. In the three treatment environments, the traits of the two RILs showed normal distributions, and both exhibited transgressive segregation. Low temperature stress had greater influence on number of panicles per plant and grain number per panicle and lower influence on plant height and panicle length. Seventeen quantitative trait locus (QTLs) were detected, distributed on chromosomes 1, 3-6, 8, 11 and 12. Among these, four QTLs had values of phenotypic variance explained that were greater than 10%. There were two QTLs, qPN12 - 2 E2 and qPN12 - 2 E3 , detected in the IAPAR-9/Akihikari RIL population in same region under cold water irrigation condition in Gongzhuling Jilin and natural low temperature in Kunming Yunnan. Major regions related to cold tolerance QTLs in these two populations was on chromosome 12 from RM511 to RM3739. The cold tolerance allele was from the Akihikari and Liaoyan241 in the respective populations for both QTL regions.