Identifying heat shock-responsive lncRNAs in wheat during grain filling

Abstract Background Heat stress (HS) during the grain-filling stage severely threatens wheat yield. While long non-coding RNAs (lncRNAs) are known to regulate plant stress responses, their specific roles in wheat grain filling under HS remain poorly understood. Results In this study, we integrated population-scale transcriptomics to explore lncRNA-associated thermotolerance networks. Analysis of 41 diverse wheat genotypes under control and HS conditions identified 9,463 high-confidence lncRNA loci and thousands of differentially expressed transcripts. Weighted gene co-expression network analysis (WGCNA) uncovered modules closely linked to thousand-grain weight (TGW), highlighting 79 hub lncRNAs. Association analysis revealed 22 lncRNAs with haplotypes significantly correlated with TGW. Field phenotyping demonstrated that under HS, wheat genotypes the high expression of MSTRG.64082 exhibited significantly higher TGW than those with medium or low expression. A positive correlation between TGW and the expression level of MSTRG.64082 was also observed in the 2025 field trials. Furthermore, the heat-induced expression of MSTRG.64082 was accompanied by the specific upregulation of key heat-responsive genes. Genetic analysis indicated that MSTRG.64082 harbors a favorable haplotype (HapC) associated precisely with enhanced TGW under HS. Notably the HapC allele displays a temperature-associated latitudinal cline, with its frequency increasing significantly in warmer regions. These findings suggest that MSTRG.64082 potentially acts as a positive regulator of heat tolerance and may have been subjected to selection pressure in warm climates. Conclusions This study provides a comprehensive population-level atlas of heat-responsive lncRNAs during wheat grain filling and highlights MSTRG.64082 as a promising candidate locus for breeding heat-tolerant wheat varieties.