Selection of Tolerant Rice Germplasm Through Phenotypic and Genotypic Evaluation for Germination Under Low Temperatures

Low temperature germinability (LTG) is an important trait for stand establishment in the direct-seeding method of rice cultivation. In temperate growing regions, water temperature during sowing season is frequently below 15°C resulting in poor crop establishment. The objective of this study was to select enhanced rice germplasm for low temperature germinability. Association of the phenotype for LTG with the genotype for qLTG3-1, a major QTL for LTG, in japonica rice accessions (n = 180) from East Asia was conducted. A highly significant association was observed between qLTG3-1 alleles and tolerant (χ² = 56.617, P = 5.08E-13) or sensitive (χ² = 32.844, P = 7.38E-08) accessions. Association of genotype and phenotype suggested the germplasm panel used in this study were closely associated with cold environment at the germination stage. Genotypic data from 32 SNP markers derived from previously reported LTG QTLs showed a mean polymorphism information content (PIC) of 0.248 and an average gene diversity of 0.307. A neighbor-joining tree clustered 23 tolerant accessions into one group and the genotypic data for four of the markers revealed that all of these accessions had the alternative allele for the qLTG3-1 and qLTG2-6 markers and the reference allele at the qLTG11-1 marker. Sensitive accessions clustered into one group and harbored the reference allele at the qLTG4-3 marker. Finally, ten accessions were selected after phenotypic and genotypic evaluation for LTG and these temperate japonica cultivars or breeding lines may contribute to the breeding of rice varieties for direct-seeding systems.