Development of a 50 K liquid-phased array for Chinese fir and its application in genomic selection

Chinese fir ( Cunninghamia lanceolata (Lamb.) Hook.) is the most commercially important conifer species for artificial plantations in China and has been subject to genetic improvement since the 1950s. Conventional breeding programs for this species are constrained by long generation cycles, therefore low genetic improvement per year. Genomic selection (GS) offers a novel and effective strategy for the genetic improvement of Chinese fir. However, the large size and complex genomic structure of Chinese fir make whole-genome resequencing (WGRS) costly for large breeding populations. Therefore, there is an urgent need to develop a cost-effective, efficient, and stable genotyping platform to facilitate genomic improvement in this species. In this study, the CunLa50K SNP array was developed based on WGRS data from 548 Chinese fir individuals spanning the species range. The array comprises 49,861 high-quality, uniformly distributed SNPs and 715 functional SNPs that are significantly associated with growth, wood properties, and bioclimatic traits. Performance evaluation showed an average coverage rate of 98.14%, an average sequencing depth of 93.16 × , and a technical replicate concordance rate of 99.24%. The array accurately identified kinship relationships and mismatched samples during pedigree verification. The genomic based best linear unbiased prediction (GBLUP) model achieved 100% and 94.5% of the prediction accuracy demonstrated by the conventional ABLUP model for the traits of diameter at breast height (DBH) and wood density (WD), respectively. This study provides a key technological tool for high-throughput genotyping and establishes a foundation for a GS breeding system in Chinese fir, facilitating a paradigm shift in its breeding strategy from phenotypic-based selection towards DNA-based selection.