Identification of Chaperonin10 as a gene necessary for tolerance to root heat stress in rice

Due to global warming, crops are exposed to heat stress more frequently. This may reduce yields, hence heat-tolerant varieties are needed. For this, it is important to identify genes governing heat tolerance. In this study we identified a line that is sensitive to high temperature in roots, and through QTL analysis we identified a gene associated with heat tolerance in rice. Utilizing a water temperature of 33-34°C, we observed that the effect of root heat stress (RHS) in Koshihikari (KH) growth is more severe compared to Nipponbare (NB). To identify the chromosome region associated with RHS tolerance, we performed QTL-seq and identified a QTL on chromosome 7, between 24.5 and 26.5 Mb. Within this QTL, a 10-bp deletion in the second exon of Os07g0641700 (Chaperonin10, CPN10) was detected in KH. To assess the association between the RHS sensitivity and the mutation on CPN10, we created several cpn10-knockout (ko) lines using CRISPR-Cas9 in the NB background. Phenotypes of four cpn10-ko lines under RHS conditions were similar to those of KH, which strongly suggest that the mutation observed in KH CPN10 is the cause of the high sensitivity to RHS. We also found that the disruption of CPN10 negatively affects biomass accumulation for both the short- and long-term exposure to RHS conditions. This study establishes the necessity of CPN10 in root heat tolerance in rice.