Differential alternative polyadenylation of homoeologous genes of allohexaploid wheat ABD subgenomes during drought stress response

• Published in: The Plant journal : for cell and molecular biology 2023-05, Vol.114 (3), p.499-518
• Main Authors: Ma, Hui, Lin, Juncheng, Mei, Fangming, Mao, Hude, Li, Qingshun Q.
• Format: Article
• Language: English
• Subjects: 3' Untranslated regions; Adaptability; allohexaploid; alternative polyadenylation; Annotations; Crop yield; Divergence; Drought; drought stress; Droughts; Gene expression; Gene Expression Regulation; Gene Expression Regulation, Plant - genetics; Gene regulation; Genes; Genomes; homoeologous genes; Isoforms; Polyadenylation; Polyadenylation - genetics; Transcriptome - genetics; Transcriptomes; Triticum - genetics; Triticum - metabolism; Triticum aestivum; Wheat
• ISSN: 0960-7412; 1365-313X
• DOI: 10.1111/tpj.16150

SUMMARY Because allohexaploid wheat genome contains ABD subgenomes, how the expression of homoeologous genes is coordinated remains largely unknown, particularly at the co‐transcriptional level. Alternative polyadenylation (APA) is an important part of co‐transcriptional regulation, which is crucial in developmental processes and stress responses. Drought stress is a major threat to the stable yield of wheat. Focusing on APA, we used poly(A) tag sequencing to track poly(A) site dynamics in wheat under drought stress. The results showed that drought stress led to extensive APA involving 37–47% of differentially expressed genes in wheat. Significant poly(A) site switching was found in stress‐responsive genes. Interestingly, homoeologous genes exhibit unequal numbers of poly(A) sites, divergent APA patterns with tissue specificity and time‐course dynamics, and distinct 3′‐UTR length changes. Moreover, differentially expressed transcripts in leaves and roots used different poly(A) signals, the up‐ and downregulated isoforms had distinct preferences for non‐canonical poly(A) sites. Genes that encode key polyadenylation factors showed differential expression patterns under drought stress. In summary, poly(A) signals and the changes in core poly(A) factors may widely affect the selection of poly(A) sites and gene expression levels during the response to drought stress, and divergent APA patterns among homoeologous genes add extensive plasticity to this responsive network. These results not only reveal the significant role of APA in drought stress response, but also provide a fresh perspective on how homoeologous genes contribute to adaptability through transcriptome diversity. In addition, this work provides information about the ends of transcripts for a better annotation of the wheat genome. Significance Statement The functional conservation and divergence in a polyploidy genome across the subgenomes of wheat have always been intriguing. From the angle of APA, this work not only reveals the widespread occurrence of APA in the allohexaploid wheat and the important role it plays, but also broadens the knowledge of how homoeologous genes contribute to the adaptability and transcriptional plasticity in a polyploidy genome through RNA processing.