Allelic variation in the coumarate 3-hydroxylase gene associated with wood properties of Catalpa fargesii Bur.

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; r 2 ≥ 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.