Prediction of environmental response in field-grown rice using expression-dynamics-QTL

Organisms respond to the fluctuations in field environments differently throughout their lives depending on their genetic variations. However, how such genetic variations affect environmental responses of organisms under field conditions, that is, the genotype × environment interaction (G×E), remains unclear. In the present study, we developed a method to identify the loci influencing gene expression dynamics (GED) in field-grown rice. We cultivated chromosome segment substitution lines (CSSLs) from Koshihikari and Takanari rice varieties1 in the field, and conducted approximately 900 time-series RNA sequencing (RNA-Seq) (bihourly-sampling for 16 d during 4 months). This novel analytical approach identified more than one thousand expression dynamics quantitative trait loci (edQTLs), which cause differences in GED between Koshihikari and Takanari. Based on the edQTLs, we successfully predicted the GED under environments different from training environments and in rice cultivars with more complex genotypes than the CSSLs. Results demonstrated that integrating genotype and environment information via the transcriptome can help predict the environmental response of GED under field conditions. We anticipate that edQTLs identification will help understand the G×E of organisms under natural conditions, which is difficult to assess with laboratory equipments2. As genetic variation and environmental conditions converge on transcriptome and transcriptome-based trait prediction functions effectively3,4, the prediction of GED based on genetic variations and environmental information will contribute to crop breeding by increasing the accuracy of trait prediction under diverse conditions.