Phenotypic Plasticity of Grain Size-Related Traits in Main-Crop and Ratoon Rice

Grain size and weight of main-crop are larger than those of ratoon rice, indicating that increasing grain size and weight of ratoon rice is an effective way to increase rice yield. Thus, grain length (GL), grain width (GW), and thousand-grain weight (TGW) of main-crop and ratoon rice in 159 indica rice accessions were used to associate with 2 017 495 SNP markers to detect quantitative trait nucleotides (QTNs) and their interactions with meteorological factors (QMIs), such as temperature and sunlight hours. Around 59 QMIs identified for temperature and 80 QMIs identified for sunlight hours, first, candidate gene LOC_Os02g40840 for GW and LOC_Os04g45480 for TGW were found to interact with temperature, while LOC_Os01g19970 for GL, LOC_Os02g39360 and LOC_Os07g05720 for GW, and LOC_Os07g49460 for TGW were found to interact with sunlight hours. Based on the results of previous studies, LOC_Os04g45480 exhibits high expression levels in the main-crop under higher temperature, thereby enhancing the accumulation of the auxin receptor TIR1. TIR1, in turn, promotes starch accumulation in the endosperm, explaining why TGW is heavier in main-crop than in ratoon rice. Finally, the analysis of best linear unbiased prediction values revealed 1 (LOC_Os08g10350) and 3 (LOC_Os02g50860, LOC_Os08g28680, and LOC_Os08g29160) candidate genes responsible for GW and TGW, respectively. In addition, we discussed the four available and six unavailable candidate genes in ratoon rice breeding. This study provides new method and genes for studying differences in grain size-related traits between main-crop and ratoon rice.