Multi-Approach Analysis Reveals Local Adaptation in a Widespread Forest Tree of Reunion Island

Abstract

Detecting processes of local adaptation in forest trees and identifying environmental selective drivers are of primary importance for forest management and conservation. Transplant experiments, functional genomics and population genomics are complementary tools to efficiently characterize heritable phenotypic traits and to decipher the genetic bases of adaptive traits. Using an integrative approach combining phenotypic assessment in common garden, transcriptomics and landscape genomics, we investigated leaf adaptive traits in Coffea mauritiana, a forest tree endemic to Reunion Island. Eight populations of C. mauritiana originating from sites with contrasted environmental conditions were sampled in common garden to assess several leaf morphological traits, to analyze the leaf transcriptome and leaf cuticular wax composition. The relative alkane content of cuticular waxes was significantly correlated with major climatic gradients, paving the way for further transcriptome-based analyses. The expression pattern of cuticle biosynthetic genes was consistent with a modulation of alkane accumulation across the population studied, supporting the hypothesis that the composition of cuticular wax is involved in the local adaptation of C. mauritiana. Association tests in landscape genomics performed using RNA-seq-derived single-nucleotide polymorphisms revealed that genes associated with cell wall remodeling also likely play an adaptive role. By combining these different approaches, this study efficiently identified local adaptation processes in a non-model species. Our results provide the first evidence for local adaptation in trees endemic to Reunion Island and highlight the importance of cuticle composition for the adaptation of trees to the high evaporative demand in warm climates.

Studies on genetic diversity, gene flow and landscape genetic in Avicennia marina: Spatial PCA, Random Forest, and phylogeography approaches

“…Presence of heterogenous environmental conditions bring about changes in the genetic diversity of plant species, which in turn results in local adaptations [ 15 , 40 , 41 ]. Therefore, the studies concerned with the genetic basis of local adaptation and identifying adaptive genetic loci or SNPs can improve the knowledge of the genetic mechanism of local adaptation and probably species diversification within a genus [ 15 ].…”

Multi-Approach Analysis Reveals Pathways of Cold Tolerance Divergence in Camellia japonica

“…Gene expression must change to modify physiological status and adapt to local environmental change; however, little is known regarding the molecular mechanism. Differences between populations of forsythia and Coffea mauritiana have been explored by transcriptome analyses (Garot et al, 2021;Li et al, 2021)Garot.…”

Putative Local Adaptive SNPs in the Genus Avicennia

“…Several studies have been carried out to identify the putative adaptive SNPs in different plant species (see for example Abebe et al 2015;Garot et al 2021). These landscape genetic studies screen the genomes to identify differentiated regions (i.e.…”

“…SNPs) and environmental variables of the species habitat while accounting for neutral patterns that affect allelic frequencies such as genetic structure and demographic history. Therefore, these studies not only identify the candidate loci for adaptation but also identify the ecological selective pressures responsible for local adaptation (Garot et al 2021).…”

“…Landscape genetic studies utilize different statistical and bioinformatics methods. For example, MDS (Multidimentional scaling), and PCA (Principal components analysis), have been used for the population divergence, while a combination of RDA (Redundancy analysis), and LFMM (Latent factor mixed model) have been used for identifying the adaptive genetic regions (see for example, Abebe et al 2015;Garot et al 2021). To our knowledge, there has been no report on putative local adaptive SNPs in The genus Avicennia, therefore, the present study was performed with the following tasks: 1-To Identify the nucleotides which can differentiate Avicennia species and geographical populations from each other, 2-To reveal association between DNA sequences and geographical coordinates, and 3-To identify the SNPs which halve phylogenetic signal.…”