From common gardens to candidate genes: exploring local adaptation to climate in red spruce

Abstract

Summary Local adaptation to climate is common in plant species and has been studied in a range of contexts, from improving crop yields to predicting population maladaptation to future conditions. The genomic era has brought new tools to study this process, which was historically explored through common garden experiments. In this study, we combine genomic methods and common gardens to investigate local adaptation in red spruce and identify environmental gradients and loci involved in climate adaptation. We first use climate transfer functions to estimate the impact of climate change on seedling performance in three common gardens. We then explore the use of multivariate gene–environment association methods to identify genes underlying climate adaptation, with particular attention to the implications of conducting genome scans with and without correction for neutral population structure. This integrative approach uncovered phenotypic evidence of local adaptation to climate and identified a set of putatively adaptive genes, some of which are involved in three main adaptive pathways found in other temperate and boreal coniferous species: drought tolerance, cold hardiness, and phenology. These putatively adaptive genes segregated into two ‘modules’ associated with different environmental gradients. This study nicely exemplifies the multivariate dimension of adaptation to climate in trees.

Probing the dark matter of environmental associations yields novel insights into the architecture of adaptation

“…In this issue of New Phytologist, Capblancq et al . (2023; pp. 1590–1605) take a combined approach for red spruce ( Picea rubens Sarg.)…”

“…Thus, the use of both types of frameworks is recommended for best inference (Sork et al, 2013). In this issue of New Phytologist, Capblancq et al (2023;pp. 1590-1605) take a combined approach for red spruce (Picea rubens Sarg.)…”

Novel genomic offset metrics integrate local adaptation into habitat suitability forecasts and inform assisted migration

“…Red spruce is anticipated to face high risk from climate change (Hamburg & Cogbill, 1988; Ribbons, 2014; Taylor et al, 2017) and ENMs forecast significant loss of suitable habitat, especially for the United States (Beane & Rentch, 2015; Koo et al, 2015; Peters et al, 2019). Several recent studies have reported evidence for local adaptation to climate in red spruce (Butnor et al, 2019; Capblancq et al, 2023; Prakash et al, 2022), and established that populations cluster into three distinct geographic regions at low, mid and high latitude across the species range that are also differentiated in their climate‐associated genetic variation (Capblancq et al, 2023; Capblancq, Butnor, et al, 2020). In particular, genetically distinct populations occur within the fragmented southern range edge (Capblancq, Butnor, et al, 2020), which might serve as crucial reservoirs for preadaptations to future climates.…”

Using landscape genomics to assess local adaptation and genomic vulnerability of a perennial herb Tetrastigma hemsleyanum (Vitaceae) in subtropical China

“…Local adaptation is ubiquitous in plants, which can result in the genetic divergence of populations cross the landscape ( Sork et al, 2016 ; Cao et al, 2020 ; Shen et al, 2022 ). Climate is a major driver of such variation ( Rehfeldt et al, 2014 ; Jia et al, 2020 ; Capblancq et al, 2022 ), whereas the primary climatic agents of selection and targets remain unknown for many species. The widely distributed species can span multiple climatic and topographic gradients whereby both adaptive and neutral processes can both affect their genome-wide variations ( Savolainen et al, 2013 ; Wang et al, 2015 ; Nadeau et al, 2016 ).…”

“…Advances in evolutionary and landscape genomics approaches and the increasing accessibility of large genomic and climate datasets enabled the characterization of the independent contributions of climate and space to explaining patterns of genetic variation ( Feng and Du, 2022 ). These strategies serve as a complement to traditional approaches uncovering evidence for local adaptation (i.e., common garden experiments and/or reciprocal transplant), and aid efforts to identify agents of selection acting in natural populations and their possible genetic targets ( Lasky et al, 2012 ; Lu et al, 2019 ; Capblancq et al, 2022 ).…”