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

Citation

Shu, Mengjun; Moran, Emily (2021), Data from: Identifying genetic variation associated with environmental variation and drought-tolerance phenotypes in ponderosa pine, Dryad, Dataset, https://doi.org/10.6071/M3DQ1D

Abstract

Background

Genotype-to-environment (G2E) association analysis coupled with genotype-to-phenotype (G2P) association analysis promises exciting advances towards discovering genes responsible for local adaptation. We combine G2E and G2P analysis with gene annotation in Pinus ponderosa (ponderosa pine), an ecologically and economically important conifer that lacks a sequenced genome, to identify genetic variants and gene functions that may be associated with local adaptation to drought.

Results

We identified SNP markers in 223 genotypes from across the Sierra Nevada by aligning GBS sequence fragments to the reference genome of Pinus taeda (loblolly pine). Focusing on SNPs in or near coding regions, we found 1458 associated with 5 largely-uncorrelated climate variables, with the largest number (1151) associated with April 1st snow pack. We also planted seeds from a subset of these trees in the greenhouse, subjected half of the seedlings to a drought treatment, and measured phenotypes thought to be associated with drought tolerance, including root length and stomatal density. 817 SNPs were associated with the control-condition values of six traits, while 1154 were associated with responsiveness of these traits to drought.

Conclusions

While no individual SNPs were associated with both the environmental variables and the measured traits, several categories of genes were associated with both, particularly those involved in cell wall formation, biotic and abiotic stress responses, and ubiquitination. However, functions of many of the associated genes have not yet been determined due to the lack of gene annotation information for trees and future studies are needed.

Usage Notes

ponderosa_pine_SNPs_delintergenic_4.1million.vcf.gz

Genotypic data were obtained by the authors for 223 ponderosa pine trees. We called SNPs using the Stack v.2.2 pipeline with reference genome. In this study, the raw SNPs were filtered by removing the intergenic SNPs, which likely have no direct effect on gene expression or function. A total of 4,155,896 SNPs were retained.

Funding

National Institutes of Health, Award: 1S10OD010786-01

National Science Foundation, Award: ACI-1548562