Genetic diversity study and molecular marker development for economic traits in Korean pine based on RAD-Seq

To reveal the genetic status of Korean pine germplasm resources, explore SNP loci associated with important economic traits of Korean pine, and develop breeding markers, the economic traits of 100 clones from 7 populations (planted in 6 seed orchards) were observed and reduced genome sequencing on the basis of Restriction-site associated DNA sequencing (RAD-Seq) was performed. Three models from the R software package "rMVP" were used for genome-wide association studies (GWAS). A total of 14,463,334 Single nucleotide polymorphisms (SNP) markers were obtained by variant detection and used for subsequent genetic analysis and GWAS. The average linkage disequilibrium- decay (LD- decay) of the SNP pairs varied from 3.383 (Weihe) to 96.245 (Lushuihe). The population with the highest Shannon index was Weihe (0.377) and the lowest was Lushuihe (0.331). The Fst between populations ranged from 0.0183 to 0.0516. A total of 16 traits were associated with 1692 SNP loci. On the basis of the GWAS results, Kompetitive allele-specific PCR (KASP) markers were developed and validated using 119 natural Korean pine plus trees. A total of 4 KASP markers were developed for cone number and cone weight. The genetic diversity of Korean pine populations is similar, and there is little differentiation between populations. Several SNPs related to economic traits, such as CN, have been obtained through GWAS. The developed KASP markers promote molecular marker-assisted selection (MAS) in breeding programs, improving the efficiency and accuracy of genetic improvement in Korean pine.