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Dryad

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

Cite this dataset

Shu, Mengjun; Moran, Emily (2023). Data from: Identifying genetic variation associated with environmental variation and drought-tolerance phenotypes in ponderosa pine [Dataset]. Dryad. https://doi.org/10.6071/M3DQ1D

Abstract

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.

README: 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.

Funding

Office of the Director, Award: 1S10OD010786-01

National Science Foundation, Award: ACI-1548562