Genome-wide association analysis of ecologically essential traits in Picea crassifolia

Picea crassifolia is a unique evergreen tree species native to China and plays a crucial role in regulating the regional ecological balance. However, the extent of variation in key traits and the genetic mechanisms underlying this variation remain unclear, limiting the development of P. crassifolia seed orchards. In this study, we evaluated essential wood, needle and growth traits and conducted a genome-wide association analysis to elucidate the genetic basis of these traits using clonal means from 106 clones of P. crassifolia collected from the Qilian Mountains, ensuring the representativeness of the germplasm. Substantial phenotypic variation was observed among clones for wood and needle properties, with an average coefficient of variation of 20.79% across phenotypic traits. Significant (P < 0.05) and highly significant (P < 0.01) correlations were observed among most pairs of wood traits and among most pairs of needle traits, whereas correlations between most wood and needle traits were generally not significant. Eighty-four single-nucleotide polymorphism (SNP) molecular markers were significantly (P < 0.05) associated with nine phenotypic traits using the general linear model (GLM). The proportion of phenotypic variation explained by each marker locus ranged within 24.34%–50.30%. Thirteen SNP markers were associated with two or more traits, and eighteen SNP markers were consistently detected using both the GLM and mixed linear model approaches; ten corresponding candidate genes were identified. This study identified candidate genes—some of which are involved in the regulation of plant morphology—and genetic markers that could serve as valuable tools for future P. crassifolia breeding programmes.