Genome-wide association study and KASP development for growth and leaf traits in Populus deltoides

BACKGROUND: Populus deltoides is a valuable timber species of considerable importance in the study of forest genetic breeding. However, its genetic improvement continues to rely predominantly on conventional selection and hybridization strategies hampered by long breeding cycles and limited efficiency. RESULTS: A total of 209 P. deltoides accessions were genotyped using a 60K SNP (Single nucleotide polymorphism) liquid array. Following quality control, 46,031 high-quality SNPs were screened and analyzed alongside 15 phenotypic traits in a genome-wide association study (GWAS), which identified 219 SNPs significantly associated with the traits. After further screening and annotation, a final set of 57 target SNPs and 77 candidate genes was obtained. Using kompetitive allele-specific PCR (KASP) assays, we successfully developed 48 polymorphic KASP markers. Of these, 25 markers exhibited significant phenotypic differences (p < 0.05) across genotype groups. CONCLUSIONS: These 25 KASP markers can serve as reliable and practical tools for phenotype-assisted selection, providing efficient molecular resources for accelerating genetic improvement and marker-assisted breeding in poplar.