Genetic Diversity of the 4th-Cycle Breeding Population of Cunninghamia lanceolata (Lamb.) Hook. Using SSR Markers

Abstract

: Cunninghamia lanceolata (Lamb.) Hook., a fast-growing timber species endemic to China, has been constrained in genetic improvement and marker-assisted breeding programs by the paucity of molecular-level genetic diversity information. In this study, 22 pairs of highly polymorphic SSR molecular markers were designed and developed based on transcriptome sequencing and public data, and subsequently employed for genetic diversity analysis of 258 germplasm accessions. These primers amplified 235 alleles across all accessions, averaging 10.682 alleles per marker. The mean observed heterozygosity (Ho) and expected heterozygosity (He) were 0.543 and 0.668, respectively, and the polymorphic information content (PIC) values ranged from 0.237 to 0.947, with a mean of 0.627, indicating substantial genetic diversity within the tested germplasm panel. Bayesian population structure analysis resolved the 258 accessions into 11 distinct genetic groups, with group 11 comprising 155 individuals and exhibiting the most complex provenance composition—a pattern independently corroborated by phylogenetic reconstruction and Principal Coordinate Analysis (PCoA). Among 11% of the genetic variation originated between populations and 89% from within populations. Pairwise estimates of Nei’s genetic distance and pairwise FST indicated frequent historical gene flow and close genetic relatedness among most groups. These findings provide a valuable empirical reference for germplasm evaluation and marker-assisted breeding in C. lanceolata .