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 PtoRSZ21hap2 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.

中文翻译：

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富含丝氨酸/精氨酸的剪接因子 PtoRSZ21 内的罕见变异调节气孔大小以确定杨树的耐旱性


摘要 稀有变异对数量性状的“遗传性缺失”有显着影响。稀有变异的全基因组特征及其在木本植物环境适应中的作用仍有待探索。利用全基因组稀有变异关联研究（RVAS）、表达数量性状位点（eQTL）作图、遗传转化和分子实验，我们探索了稀有变异对杨属气孔形态和干旱适应的影响。通过对世界范围内五种杨树的比较分析，我们观察了突变偏差和适应性选择对稀有变异分布的影响。 RVAS 鉴定了 75 个与气孔大小 (SS)/气孔密度 (SD) 相关的候选基因，富含丝氨酸/精氨酸的剪接因子 PtoRSZ21 启动子中的罕见单倍型成为控制 SS 的最重要的关联信号。作为耐旱性的正调节因子，PtoRSZ21 可以招募核心剪接因子 PtoU1-70K 来调节 PtoATG2b（自噬相关 2）的选择性剪接（AS）。罕见的单倍型PtoRSZ21hap2削弱了与PtoMYB61的结合亲和力，从而影响PtoRSZ21的表达和SS，最终导致杨属材料在干旱和潮湿气候中的差异分布。这项研究增强了对罕见变异诱导的 AS 调控机制的理解，并可能为杨树耐旱品种育种提供目标。