Molecular signatures of local adaptation to light in Norway spruce

Abstract

Main conclusion Transcriptomic and exome capture analysis reveal an adaptive cline for shade tolerance in Norway spruce. Genes involved in the lignin pathway and immunity seem to play a potential role in contributing towards local adaptation to light. Abstract The study of natural variation is an efficient method to elucidate how plants adapt to local climatic conditions, a key process for the evolution of a species. Norway spruce is a shade-tolerant conifer in which the requirement of far-red light for growth increases latitudinally northwards. The objective of the study is to characterize the genetic control of local adaptation to light enriched in far-red in Norway spruce, motivated by a latitudinal gradient for the Red:Far-red (R:FR) ratio to which Norway spruce has been proven to be genetically adapted. We have established the genomic signatures of local adaptation by conducting transcriptomic (total RNA-sequencing) and genomic analyses (exome capture), for the identification of genes differentially regulated along the cline. RNA-sequencing revealed 274 differentially expressed genes in response to SHADE (low R:FR light), between the southern and northern natural populations in Sweden. Exome capture included analysis of a uniquely large data set (1654 trees) that revealed missense variations in coding regions of nine differentially expressed candidate genes, which followed a latitudinal cline in allele and genotype frequencies. These genes included five transcription factors involved in vital processes like bud-set/bud-flush, lignin pathway, and cold acclimation and other genes that take part in cell-wall remodeling, secondary cell-wall thickening, response to starvation, and immunity. Based on these results, we suggest that the northern populations might not only be able to adjust their growing season in response to low R:FR light, but they may also be better adapted towards disease resistance by up-regulation of the lignin pathway that is linked to immunity. This forms a concrete basis for local adaptation to light quality in Norway spruce, one of the most economically important conifer tree species in Sweden.

Enhanced lignin synthesis and ecotypic variation in defense‐related gene expression in response to shade in Norway spruce

“…A higher requirement of FR to maintain growth northwards in Norway spruce has been reported previously (Clapham et al, 1998;Ranade & García-Gil, 2021). This has been populations' adaptation to the local light quality conditions.…”

“…Norway spruce ( Picea abies [L.] H. Harst) is shade‐tolerant and it is one of the most economically important conifers in Boreal forests. Norway spruce shows ecotypic variation in response to twilight, which is characterized by a northward increase in the requirement for additional FR light to maintain growth (Clapham et al, 1998; Ranade & García‐Gil, 2021). This character could be interpreted as an adaptive response that allows trees to leave dormancy, grow and survive during the growing season when the northern latitudes are daily exposed to longer hours of twilight.…”

Norway spruce deploys tissue‐specific responses during acclimation to cold

“…These data demonstrate that early response TFs and COR genes can be induced by ICE1 homologs under cold in several plant species such as Zea mays (Lu et al, 2017), rice (Zhang et al, 2017), tomato (Feng et al, 2013), Vitis amurensis (Xu et al, 2014), Pyrus ussuriensis (Huang, Li, et al, 2015) and Poncirus trifoliata (Huang, Zhang, et al, 2015), in line with our finding that in Norway spruce this ICE1‐like protein is an important potential regulator of many COR genes, where 150 of these genes appear as targets of ICE1 in our regulatory network (Table ), and whose progressive late induction suggests that its role may become even stronger following freezing (Figure ). The recent finding that an ICE2 homolog has been associated with local adaptions to shade and cold at northern latitudes in Norway spruce (Ranade & García‐Gil, 2021) further supports a key role for ICE‐like proteins in cold tolerance in Norway spruce.…”

Adaptation insights from comparative transcriptome analysis of two Opisthopappus species in the Taihang mountains

“…When different populations experience heterogeneous environments, natural selection can drive phenotypic divergence while modulating underlying genomic architectures, which induces populations to adapt to their habitats [ 3 , 5 ]. Adaptative divergence has been well verified as a major mechanism that initiates evolutionary diversification and speciation [ 6 , 7 ]. There are myriad variations in the combination of phenotypic traits and environmental factors [ 8 ].…”