Identifying genetic variation associated with environmental gradients and drought-tolerance phenotypes in ponderosa pine

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. We found 1458 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 seedlings grown in control and drought treatments. 817 SNPs were associated with control-condition trait values, while 1154 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.

Identifying genetic variation associated with environmental gradients and drought‐tolerance phenotypes in ponderosa pine

“…Furthermore, the P. taeda reference genome was successfully used to design probes for sequence capture in P. contorta (Suren et al., 2016 ; Yeaman et al., 2016 ), a distant relative. Based on preliminary analyses, we selected the Stacks v.2.2 pipeline (Rochette & Catchen, 2017 ) with this reference genome ( https://treegenesdb.org/FTP/Genomes/Pita/ ) for SNP calling (Shu, 2020 ). Each step in the Stacks reference pipeline was performed internally in Stacks algorithms except alignment with BWA v.0.7.17 (Li & Durbin, 2009 ) and the Samtools v.1.9 (Li, 2011 ) step used to get read position.…”