Rare variations within the serine/arginine‐rich splicing factor PtoRSZ21 modulate stomatal size to determine drought tolerance in Populus

Summary Rare variants contribute significantly to the ‘missing heritability’ of quantitative traits. The genome‐wide characteristics of rare variants and their roles in environmental adaptation of woody plants remain unexplored. Utilizing genome‐wide rare variant association study (RVAS), expression quantitative trait loci (eQTL) mapping, genetic transformation, and molecular experiments, we explored the impact of rare variants on stomatal morphology and drought adaptation in Populus . Through comparative analysis of five world‐wide Populus species, we observed the influence of mutational bias and adaptive selection on the distribution of rare variants. RVAS identified 75 candidate genes correlated with stomatal size (SS)/stomatal density (SD), and a rare haplotype in the promoter of serine/arginine‐rich splicing factor PtoRSZ21 emerged as the foremost association signal governing SS. As a positive regulator of drought tolerance, PtoRSZ21 can recruit the core splicing factor PtoU1‐70K to regulate alternative splicing (AS) of PtoATG2b (autophagy‐related 2). The rare haplotype PtoRSZ21 hap2 weakens binding affinity to PtoMYB61, consequently affecting PtoRSZ21 expression and SS, ultimately resulting in differential distribution of Populus accessions in arid and humid climates. This study enhances the understanding of regulatory mechanisms that underlie AS induced by rare variants and might provide targets for drought‐tolerant varieties breeding in Populus .