Molecular signatures of local adaptation to light in Norway spruce

Sonali Sachin Ranade,María Rosario García-Gil

doi:10.1007/s00425-020-03517-9

Sonali Sachin Ranade, María Rosario García-Gil

Open Access

https://doi.org/10.1007/s00425-020-03517-9

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Abstract

Main conclusionTranscriptomic 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.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.

Highlights

Research indicates that local adaptation in conifer populations will be affected by major disturbances due to an increase in average temperature, change in precipitation regimes and rise in new biotic stresses, which could compromise forest survival and sustainability at their present locations (Leinonen 1996; Millar and Stephenson 2015)
We aimed to identify the genomic signals of local adaptation in response to low Red:Far-red (R:FR) ratio (SHADE) in Norway spruce which is shade tolerant
This study aims to answer the following specific questions: (i) Do we observe a phenotypic cline in the Norway spruce seedlings in response to low R:FR or SHADE?—this will be answered by comparing the hypocotyl elongation under SHADE and SUN conditions across the latitudes. (ii) Knowing that Norway spruce seems to be adapted to the local light quality conditions (Clapham et al 1998), what are the genomic signs of local adaptation for the exposure to SHADE?—this will be answered by RNA-Seq and exome capture methodologies

Summary

Introduction

Research indicates that local adaptation in conifer populations will be affected by major disturbances due to an increase in average temperature, change in precipitation regimes and rise in new biotic stresses, which could compromise forest survival and sustainability at their present locations (Leinonen 1996; Millar and Stephenson 2015). Given the prognosis of a rapid climatic change (IPCC 2019), forest breeders and conservationists are urging for a better understanding of the genetic and genomic basis underlying local adaptation This aspect is crucial to design effective spatial migration actions to transfer forest trees into their optimal ecological niches or to assist the trees to adapt to the new conditions at their current location (Aitken et al 2008). A similar latitudinal response has been described in Salix pentandra L. and Scots pine (Pinus sylvestris L.) (Juntilla and Kaurin 1985; Clapham et al 2002; Mølmann et al 2006) This latitudinal variation has been suggested to be an adaptive response to the prolonged end-of-day (EOD) FR-enriched light condition (twilight) (Juntilla and Kaurin 1985), which characterizes the northern latitudes during the summer solstice (Nilsen 1985). EOD FR-enriched tolerance and shade tolerance are both triggered by low R:FR ratio and by the existence of common molecular components regulating both mechanisms (Johnson et al 1994; Muller-Moule et al 2016)

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