Data from: Association genetics of growth and adaptive traits in loblolly pine (Pinus taeda L.) using whole-exome-discovered polymorphisms

In the United States, forest genetics research began over 100 years ago
and loblolly pine breeding programs were established in the 1950s.
However, the genetics underlying complex traits of loblolly pine remains
to be discovered. To address this, adaptive and growth traits were
measured and analyzed in a clonally tested loblolly pine (Pinus taeda L.)
population. Over 2.8 million single nucleotide polymorphism (SNP) markers
detected from exome sequencing were used to test for single locus
associations, SNP-SNP interactions and correlation of individual
heterozygosity with phenotypic traits. A total of 36 SNP-trait
associations were found for specific leaf area (5 SNPs), branch angle (2),
crown width (3), stem diameter (4), total height (9), carbon isotope
discrimination (4), nitrogen concentration (2), and pitch canker
resistance traits (7). Eleven SNP-SNP interactions were found to be
associated with branch angle (1 SNP-SNP interaction), crown width (2),
total height (2), carbon isotope discrimination (2), nitrogen
concentration (1), and pitch canker resistance (3). Non-additive effects
imposed by dominance and epistasis account for a large fraction of the
genetic variance for the quantitative traits. Genes that contain the
identified SNPs have a wide spectrum of functions. Individual
heterozygosity positively correlated with water use efficiency and
nitrogen concentration. In conclusion, multiple effects identified in this
study influence the performance of loblolly pines, provide resources for
understanding the genetic control of complex traits, and have potential
value for assessing with breeding through marker assisted selection and
genomic selection.