DOI: 10.6071/m3dq1d
title: Data from: Identifying genetic variation associated with environmental variation and drought-tolerance phenotypes in ponderosa pine

description: 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.
description: # Data from: Identifying genetic variation associated with environmental
 variation and drought-tolerance phenotypes in ponderosa pine ### 4.1
 Million SNPs Dataset for 223 Ponderosa Pine Genotypes #### File name:
 ponderosa\_pine\_SNPs\_delintergenic\_4.1million.vcf.gz #### Description
 of the data and file structure This VCF (Variant Call Format) file
 contains genetic data for 223 Ponderosa Pine genotypes. All intergenic
 SNPs have been filtered out, leaving a total of 4.1 million SNPs that are
 being utilized for our association analysis. ### annotation file for 1374
 significantly associated SNPs in Genotype-Environment Association (GEA)
 analysis #### File name: GEA\_1374SNPs\_annotation.xlsx #### Description
 of the data and file structure This Excel file contains annotation for the
 1374 significantly associated SNPs in GEA analysis. GO terms involved in
 cell wall formation, biotic and abiotic stress responses, and
 ubiquitination are highlighted as yellow. ### annotation file for 796
 significantly associated SNPs in Genotype-Phenotype Association (GPA)
 analysis with traits in control condition #### File name:
 GPA\_control\_796SNPs\_annotation.xlsx #### Description of the data and
 file structure This Excel file contains annotation for the 796
 significantly associated SNPs in GPA analysis with traits measured in
 control condition. GO terms involved in cell wall formation, biotic and
 abiotic stress responses, and ubiquitination are highlighted as yellow.
 ### annotation file for 1149 significantly associated SNPs in
 Genotype-Phenotype Association (GPA) analysis with drought responsiveness
 traits #### File name:
 GPA\_droughtresponsiveness\_1149SNPs\_annotation.xlsx #### Description of
 the data and file structure This Excel file contains annotation for the
 1149 significantly associated SNPs in GPA analysis with drought
 responsiveness traits. GO terms involved in cell wall formation, biotic
 and abiotic stress responses, and ubiquitination are highlighted as
 yellow.