Changes in the climate affect the survival and long-term viability of natural forests, therefore genomic information is key to understand the capacity of natural populations of tree species to adapt to new environmental conditions and diseases, and to develop effective conservation and management strategies. Research in our lab focuses on understanding the genomic and evolutionary basis of phenotypic trait variation, plant stress response, and adaptation to changing environments, using tools in genomics, transcriptomics, epigenomics and physiology.
Genomics of local adaptation to climate
Understanding the genomic basis of local adaptation is crucial to determine the potential of long lived woody species to withstand changes in their natural environments. Whole-genome studies were not feasible until very recently due to the absence of reference gymnosperm genomes, therefore previous studies were based on a small number of genes. Current studies in our research group aim to understand the genomic architectures of local adaptation in several conifer species. This data will allow comparative population genomic studies to test whether divergent or parallel evolution has occurred in different species; whether natural selection acts primarily on standing genetic variation or on new mutations; and how adaptive evolution has occurred in the different taxa. This work contributes to the study of local adaptation in ecologically important conifer species, and will inform conservation and management practices under climate change.
De La Torre AR, Wilhite B, DB Neale. 2019. Environmental genome-wide association reveals climate adaptation is shaped by subtle to moderate allele frequency shifts in loblolly pine. Genome Biology and Evolution 11(10): 2976-2989.
Hybridization and the maintenance of species barriers
When ecological divergence is driving the evolution of reproductive isolation in natural populations, identifying loci involved in local adaptation is the first step to understand the process of speciation and the maintainance of species identities. In our study in interior spruce, Genome-wide studies, as well as paleoclimatic and ecological niche modeling suggested that despite a long history of hybridization and introgression, dating to at least 21,000 years ago, species identity was maintained by a combination of strong environmental selection acting on a small number of widely distributed genes and reduced current interspecific gene flow (De La Torre et al. 2014 Mol Ecology). Current research in our group aims to understand how different hybridizing tree varieties have evolved different adaptations to contrasting environments (e.g. coastal vs. mountainous).
Genomics of complex traits
Most traits of interest in plant species have complex inheritance, meaning that a large number of genes of small effect contribute to the phenotype. The understanding of the genomic basis of complex traits is essential to mitigate the devastating effects of disease, drought and cold stress and to develop breeding strategies including genome selection, and marker-assisted breeding. Our recent studies in several conifers such as Loblolly pine, Douglas fir and Sugar pine have identified thousands of gene-trait associations, identifying important genes and pathways in different important traits.
De La Torre AR, Puiu D, Crepeau MW, Stevens K, Salzberg SL, Langley CH, Neale DB. 2019. Genomic architecture of complex traits in Loblolly pine (Pinus taeda). New Phytologist 221:1789-1801, doi: 10.1111/nph.15535.
De La Torre AR, Wilhite B, Puiu D, St. Clair JB, Crepeau MW, Salzberg SL, Langley CH, Allen B, Neale DB. 2021. Dissecting the polygenic basis of cold adaptation using genome-wide association of traits and environmental data in Douglas-fir. Genes, 12, 110.
De la Torre AR, Sekhwal MK, Puiu D, Salzberg SL, Scott AD, Allen B, Neale DB, Chin ARO, Buckley TN. 2021. Genome-wide association identifies candidate genes for drought tolerance in coast redwood and giant sequoia. The Plant Journal, doi:10.1111/tpj.15592
Epigenomics and genomics of disease resistance
Plants possess sophisticated immune responses to defend themselves against pathogens. Recent studies in model plant species suggest DNA methylation may contribute to plant immunity against biotrophic pathogens by regulating the expression of specific defense-related genes. In highly-repetitive, densely-methylated conifer genomes, DNA methylation may play an important role in the response to pathogens, as varying levels of resistance and high levels of phenotypic plasticity and local adaptation are usually observed in natural populations of conifer species, despite the very slow mutation rates (De La Torre et al. 2017). Due to the pervasive expansion of pests and pathogens in the Northern hemisphere as a consequence of climate change, genomic, transcriptomic and epigenomic analyses are key to ensure the trees’ future survival.
Weiss M, Sniezko R, Puiu D, Crepeau MW, Stevens K, Salzberg SL, Langley CH, Neale DB, De La Torre AR. 2020. Genomic basis of white pine blister rust quantitative disease resistance and its relationship with qualitative resistance. The Plant Journal, doi:10.1111/tpj.14928.
The recent sequencing of the enormous genomes (20-30 Gbp) of gymnosperms has opened a window to understand the evolution of seed plants. Gymnosperms separated from flowering plants 300 Mya. While flowering plants have gone through successive rounds of species radiations leading to a great diversity of species, gymnosperms have not changed much during evolutionary time (De la Torre et al. 2014 Plant Physiology). In contrast to this apparent “genome stasis”, numerous examples of local adaptation have been reported in gymnosperm species. To answer the question of whether gymnosperms genomes have evolved differently than their sister plant clade of flowering plants, we have studied the patterns of selection and molecular evolution across the genomes of 61 plant species. We found that gymnosperms evolve slower than angiosperms, but present higher substitution rate ratios that may suggest a higher potential for adaptive evolution (De La Torre et al. 2017 Mol Biol Evol). More recently, our group was involved in large collaborative projects to sequence the reference genomes of Populus tremula and P. tremuloides (Li et al. 2018 PNAS), Sequoia sempervirens (Neale et al. 2022) and Pinus pinaster (Sterck et al. 2022).
De La Torre AR, Piot A, Liu B, Wilhite B, Weiss M, Porth I. 2020. Functional and morphological evolution in gymnosperms: a portrait of implicated gene families. Evolutionary Applications 13(1): 210-227.
De La Torre AR, Li Z, Van de Peer Y, Ingvarsson PK. 2017. Contrasting rates of molecular evolution and patterns of selection among gymnosperms and flowering plants. Molecular Biology and Evolution 34(6): 1363-1377.
Genomic approaches can be used to help develop long-term conservation and restoration plans for species threatened by fragmentation, overexploitation, invasive species, habitat loss, and climate change. Recent projects in our group, aim to assess the levels of genome-wide diversity in isolated and endangered populations of whitebark pine (Pinus albicaulis) that will inform conservation and restoration of the species. In addition, our group is also assessing the levels of genomic diversity, fine-scale population structure, and salinity resistance in mangrove populations in the Caribbean.