Data from: Identifying genetic variation associated with environmental variation and drought-tolerance phenotypes in ponderosa pine

As climate changes, understanding the genetic basis of local adaptation in
plants becomes an ever more pressing issue. Combining Genotype-Environment
Association (GEA) with Genotype-Phenotype Association (GPA) analysis has
an exciting potential to uncover the genetic basis of environmental
responses. We use these approaches to identify genetic variants linked to
local adaptation to drought in Pinus ponderosa. Over 4 million SNPs were
identified using 223 individuals from across the Sierra Nevada of
California and 927,740 (22.3%) Single Nucleotide Polymorphisms (SNPs) were
retained after filtering and used in our association analyses. We found
1374 associated with five largely uncorrelated climate variables, with the
largest number (1151) associated with April 1st snowpack. We also
conducted a greenhouse study with various drought-tolerance traits
measured in first-year seedlings grown in control and drought treatments.
796 SNPs were associated with control-condition trait values, while 1149
were associated with responsiveness of these traits to drought. While no
individual SNPs were associated with both the environmental variables and
the measured traits, several annotated genes were associated with both,
particularly those involved in cell wall formation, biotic and abiotic
stress responses, and ubiquitination. However, the functions of many of
the associated genes have not yet been determined due to the lack of gene
annotation information for conifers. Future studies are needed to assess
the developmental roles and ecological significance of these unknown
genes.