Genetic analysis of germinating ability and seedling vigor under cold stress in US weedy rice

Low temperature stress is a major constraint for rice production in temperate and high altitude areas of the world. Delayed germination coupled with reduced seedling vigor hinders crop establishment and crop growth resulting in reduced rice productivity. Mapping of the chromosomal regions controlling cold tolerance will accelerate marker-assisted breeding of cold tolerant rice varieties. A recombinant inbred line mapping population involving a US weedy rice accession ‘PSRR-1’ and a rice cultivar ‘Bengal’ was evaluated for germinating ability and seedling vigor under low temperature (13 °C) and optimum temperature (28 °C). ‘PSRR-1’ performed better than ‘Bengal’ under cold stress. Forty-nine QTL distributed over ten chromosomes were identified for 11 traits. The number of QTL varied from one to nine with phenotypic variability of each QTL ranging from 3.5 to 12.7 %. For 18 QTL, ‘Bengal’ alleles were desirable, whereas ‘PSRR-1’ allele improved germination and seedling vigor under cold stress in 31 QTL. Three major QTL were observed for coleoptile length and seedling shoot length. The QTL were clustered in six chromosomal regions. The congruency of QTL cluster on chromosome 11 with earlier studies suggests a potential target for cloning cold tolerance genes at germination and seedling stages. This study demonstrated that weedy rice can be a valuable donor for desirable alleles to improve germination and seedling stage cold tolerance in rice.