Genetic Mapping of Cold Tolerance Roots of Rice (Oryza sativa L.) Seedling

Mechanical transplanting commonly used in rice (Oryza sativa L.) cultivation usually caused systematic damages to the root system of rice seedlings. The retarded regrowth of adventitious roots may occur as the result of cold current between January and March in Taiwan, and limit nutrient uptake of the seedlings to a point that the seedling leaves become discolored. In this study, a genome-wide association study (GWAS) was conducted on the 44K panel to identify QTLs associated with seedling root regrowth under low temperature treatment. P model was used to reduce the possibility of false positive caused by population structure. We have found a significant region of 18.10 to 18.44 Mb on Chromosome 2, and simplified the significant SNPs in this region into 7 haplotypes. Accessions possessing haplotype 2 performed better than others, and most of them are temperate japonica. A set of 10 cold tolerant and 5 cold sensitive accessions were selected based on both phenotypic and genotypic data, and their root growth difference were verified by subject them to the same cold treatment with extended repeats. However, bi-parental mapping on the F2 population derived from the cross between cold tolerant “Kon Suito” and cold sensitive “Taichung Sen 10” did not reveal any QTL related to the root growth characteristic under cold treatment. It is speculated that while P model was used in the GWAS, the population structure was still not fully corrected. In light of the result of this study, we recommend to conduct bi-parental mapping as a verification measure after GWAS.