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 ...