Combining Genotype, Phenotype, and Environment to Infer Potential Candidate Genes

Area of Science:

• Ecology
• Genetics
• Plant Science

Background:

• Population genomic analysis is crucial for understanding local adaptation.
• Identifying adaptive loci typically involves genomic data and environmental variables.
• Incorporating phenotypic data alongside genomic scans enhances insights into adaptation.

Purpose of the Study:

• To identify loci in Loblolly pine (Pinus taeda) potentially involved in adaptation to climate.
• To analyze associations between molecular, phenotypic, and environmental variables in Loblolly pine.
• To improve confidence in identifying candidate genes for local adaptation.

Main Methods:

• Analyzed 283 Loblolly pine samples across the southeastern United States.
• Utilized 3082 single nucleotide polymorphism (SNP) loci and three categories of phenotypic traits (gene expression, metabolites, whole-plant traits).
• Correlated candidate genes with environmental variables.

Main Results:

• Identified 6 SNP loci showing potential signals of local adaptation.
• Five of the six SNPs are linked to gene expression traits for lignin development.
• One SNP is associated with whole-plant traits; three candidate genes showed high correlation with environmental variables.

Conclusions:

• A combination of genotypes, phenotypes, and environmental variables is essential for robust adaptation studies.
• Appropriate sampling schemes and study designs are critical for reliable identification of adaptive loci.
• This study provides candidate genes for Loblolly pine adaptation to climate.