Coumarate 3-hydroxylase (C3h) genes participate in the synthesis of lignin and may affect the properties of wood that are important for its commercial value. A better understanding of the natural variation in C3h genes and their associations to wood properties is required to effectively improve wood quality. We used a candidate gene-based association mapping approach to identify CfC3h allelic variants associated with traits that affect the wood properties of Catalpa fargesii. We first isolated the full-length CfC3h cDNA (1825 bp), which was expressed at relatively high levels in xylem according to real time-polymerase chain reaction. In totally, 17 common single-nucleotide polymorphisms (minor allele frequency > 5%) were identified through cloning and sequencing the CfC3h locus from a mapping population (including 88 unrelated natural C. fargesii individuals collected from main distribution area). Nucleotide diversity and linkage disequilibrium (LD) in CfC3h indicate that CfC3h has low nucleotide diversity (π_t = 0.0031 and θ_w = 0.0103) and relatively low LD (within 1800 bp; r² ≥ 0.1). An association analysis identified eight common single-nucleotide polymorphisms (SNPs) (false discovery rate, Q < 0.10) and ten haplotypes (Q < 0.10) associated with wood properties, explaining 4.92–12.09% of the phenotypic variance in an association population consisted of 125 unrelated natural individuals (The 88 individuals from the mapping population were comprised in the association population). Our study would provide new insight into C3h gene affecting wood quality, and the SNP markers identified would have potential applications in marker-assisted breeding in the future.

香豆酸盐3-羟化酶（C3h）基因参与木质素的合成，并可能影响木材的特性，这对于其商业价值至关重要。为了有效地改善木材质量，需要更好地了解C3h基因的自然变异及其与木材特性的关联。我们使用了基于候选基因的关联作图方法来鉴定与影响Catalpa fargesii木材特性的性状相关的CfC3h等位基因变体。我们首先隔离了全长CfC3hcDNA（1825 bp），根据实时聚合酶链反应在木质部中以相对较高的水平表达。通过克隆和测序来自一个作图种群（包括从主要分布地区收集的88个无亲缘天然C. fargesii个体）的CfC3h基因座，总共鉴定出17种常见的单核苷酸多态性（次要等位基因频率> 5％）。核苷酸多样性和处于连锁不平衡（LD）CfC3h表明CfC3h具有低核苷酸多样性（π_吨 = 0.0031和θ_瓦特 = 0.0103）和相对低的LD（内1800个碱基; - [R ² ≥0.1）。关联分析确定了八种常见的单核苷酸多态性（SNP）（错误发现率，Q  <0.10）和十种 与木材特性相关的单倍型（Q <0.10），解释了关联种群中4.92–12.09％的表型变异包括125个不相关的自然个体（测绘种群中的88个个体包含在关联种群中）。我们的研究将提供有关影响木材质量的C3h基因的新见识，并且鉴定出的SNP标记将在将来的标记辅助育种中具有潜在的应用。