Landscape genomic analysis of candidate genes for climate adaptation in a California endemic oak, Quercus lobata

PREMISE OF THE STUDY: The ability of California tree populations to survive anthropogenic climate change will be shaped by the geographic structure of adaptive genetic variation. Our goal is to test whether climate-associated candidate genes show evidence of spatially divergent selection in natural...

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Published inAmerican journal of botany Vol. 103; no. 1; pp. 33 - 46
Main Authors Sork, Victoria L., Squire, Kevin, Gugger, Paul F., Steele, Stephanie E., Levy, Eric D., Eckert, Andrew J.
Format Journal Article
LanguageEnglish
Published United States Botanical Society of America, Inc 01.01.2016
Botanical Society of America
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Summary:PREMISE OF THE STUDY: The ability of California tree populations to survive anthropogenic climate change will be shaped by the geographic structure of adaptive genetic variation. Our goal is to test whether climate-associated candidate genes show evidence of spatially divergent selection in natural populations of valley oak, Quercus lobata, as preliminary indication of local adaptation. METHODS: Using DNA from 45 individuals from 13 localities across the species' range, we sequenced portions of 40 candidate genes related to budburst/flowering, growth, osmotic stress, and temperature stress. Using 195 single nucleotide polymorphisms (SNPs), we estimated genetic differentiation across populations and correlated alíele frequencies with climate gradients using single-locus and multivariate models. RESULTS: The top 5% of FST estimates ranged from 0.25 to 0.68, yielding loci potentially under spatially divergent selection. Environmental analyses of SNP frequencies with climate gradients revealed three significantly correlated SNPs within budburst/flowering genes and two SNPs within temperature stress genes with mean annual precipitation, after controlling for multiple testing. A redundancy model showed a significant association between SNPs and climate variables and revealed a similar set of SNPs with high loadings on the first axis. In the RDA, climate accounted for 67% of the explained variation, when holding climate constant, in contrast to a putatively neutral SSR data set where climate accounted for only 33%. CONCLUSIONS: Population differentiation and geographic gradients of allele frequencies in climate-associated functional genes in Q. lobata provide initial evidence of adaptive genetic variation and background for predicting population response to climate change.
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ISSN:0002-9122
1537-2197
DOI:10.3732/ajb.1500162