biostudies-literatureDing XZhejiang Science and Technology Major Program on Agricultural New Variety BreedingFundamental Research Funds of Chinese Forestry Academye1010017https://www.ebi.ac.uk/biostudies/studies/S-EPMC8843129biostudies-literatureUnknown18(2)Slash pine (Pinus elliottii Engelm.) is an important timber and resin species in the United States, China, Brazil and other countries. Understanding the genetic basis of these traits will accelerate its breeding progress. We carried out a genome-wide association study (GWAS), transcriptome-wide association study (TWAS) and weighted gene co-expression network analysis (WGCNA) for growth, wood quality, and oleoresin traits using 240 unrelated individuals from a Chinese slash pine breeding population. We developed high quality 53,229 single nucleotide polymorphisms (SNPs). Our analysis reveals three main results: (1) the Chinese breeding population can be divided into three genetic groups with a mean inbreeding coefficient of 0.137; (2) 32 SNPs significantly were associated with growth and olPLoS geneticsA transcriptome-based association study of  growth, wood quality, and oleoresin traits in a slash pine  breeding population.PMC88431292021C02070-8CAFYBB2017ZA001-2-1Jiang JDing XZhang YDiao SLuan QWu HXfalseA transcriptome-based association study of  growth, wood quality, and oleoresin traits in a slash pine  breeding population.Slash pine (Pinus elliottii Engelm.) is an important timber and resin species in the United States, China, Brazil and other countries. Understanding the genetic basis of these traits will accelerate its breeding progress. We carried out a genome-wide association study (GWAS), transcriptome-wide association study (TWAS) and weighted gene co-expression network analysis (WGCNA) for growth, wood quality, and oleoresin traits using 240 unrelated individuals from a Chinese slash pine breeding population. We developed high quality 53,229 single nucleotide polymorphisms (SNPs). Our analysis reveals three main results: (1) the Chinese breeding population can be divided into three genetic groups with a mean inbreeding coefficient of 0.137; (2) 32 SNPs significantly were associated with growth and ol2022-01-01T00:00:00Z2022 Feb2025-04-04T08:58:03.609Z2025-04-04T08:58:03.609ZS-EPMC88431293510826910.1371/journal.pgen.1010017