Association between simple sequence repeat markers and tree height variation in Pinus yunnanensis

Abstract Tree height is an important phenotypic trait influencing tree growth, closely related to timber volume, and therefore an important variable driving the economic value of forest trees. Pinus yunnanensis plays a vital role in the ecological and economic development of southwestern China; however, the progress of its breeding work has not met the actual needs. In this study, we compared the heights of 6892 7-year-old trees from nine provenances planted in a common garden. We evaluated the capacity of 17 polymorphic microsatellite [simple sequence repeat (SSR)] markers to construct genetic fingerprints, and employed these markers to analyze genetic diversity, population structure, and the association between SSR markers and height in 139 tall trees (height ≥ 300 cm) and 196 dwarf trees (height ≤ 100 cm) from 17 populations across the nine provenances. Our results revealed significant differences in tree height among the nine provenances and within four provenances (P < 0.001). The combined PIc and PIsibsc values for the 17 SSR markers were 1.1 × 10−11 and 1.1 × 10−5, respectively, indicating robust fingerprinting capability. Genetic diversity in P. yunnanensis was moderate, with no significant differences observed between tall tree (He = 0.574) and dwarf tree populations (He = 0.613), likely due to the predominantly wind-pollinated nature of P. yunnanensis (Fis = −0.112; Nm = 11.133; Fst = 0.041). Cluster analysis divided tall and dwarf trees into two distinct groups. Both the general linear model and mixed linear model supported a significant correlation between the PyTr06 and PK827 loci and tree height. Genotype analyses further identified unique alleles of 126 bp and 202 bp at the PyTr06 and PY827 loci for tall and dwarf trees, respectively. The DNA fingerprints generated in this study have important implications for the efficient and rapid selection of superior germplasm and the genetic improvement of this species.