Transcriptome analysis reveals plasticity in gene regulation due to environmental cues in Primula sikkimensis, a high altitude plant species

Priya Darshini Gurung,Uma Ramakrishnan,Ramanathan Sowdhamini,Atul Kumar Upadhyay,Pardeep Kumar Bhardwaj

doi:10.1186/s12864-019-6354-1

Abstract

BackgroundStudying plasticity in gene expression in natural systems is crucial, for predicting and managing the effects of climate change on plant species. To understand the contribution of gene expression level variations to abiotic stress compensation in a Himalaya plant (Primula sikkimensis), we carried out a transplant experiment within (Ambient), and beyond (Below Ambient and Above Ambient) the altitudinal range limit of species. We sequenced nine transcriptomes (three each from each altitudinal range condition) using Illumina sequencing technology. We compared the fitness variation of transplants among three transplant conditions.ResultsA large number of significantly differentially expressed genes (DEGs) between below ambient versus ambient (109) and above ambient versus ambient (85) were identified. Transcripts involved in plant growth and development were mostly up-regulated in below ambient conditions. Transcripts involved in signalling, defence, and membrane transport were mostly up-regulated in above ambient condition. Pathway analysis revealed that most of the genes involved in metabolic processes, secondary metabolism, and flavonoid biosynthesis were differentially expressed in below ambient conditions, whereas most of the genes involved in photosynthesis and plant hormone signalling were differentially expressed in above ambient conditions. In addition, we observed higher reproductive fitness in transplant individuals at below ambient condition compared to above ambient conditions; contrary to what we expect from the cold adaptive P. sikkimensis plants.ConclusionsWe reveal P. sikkimensis’s capacity for rapid adaptation to climate change through transcriptome variation, which may facilitate the phenotypic plasticity observed in morphological and life history traits. The genes and pathways identified provide a genetic resource for understanding the temperature stress (both the hot and cold stress) tolerance mechanism of P. sikkimensis in their natural environment.

Highlights

Studying plasticity in gene expression in natural systems is crucial, for predicting and managing the effects of climate change on plant species
We compared the significant Differentially expressed gene (DEG) of P. sikkimensis from the Below Ambient (BA) vs. A comparison with heat stress genes of Arabidopsis thaliana using Gene Expression Omnibus (GEO), at National Center for Biotechnology Information (NCBI)
The higher reproductive fitness of the BA transplants compared to Above Ambient (AA) transplants was contrary to what we expect from the cold adaptive P. sikkimensis plants

Summary

Introduction

Studying plasticity in gene expression in natural systems is crucial, for predicting and managing the effects of climate change on plant species. Given the current rate at which the climate is changing [3], concerns are rising about the capacity of species to adapt. Sessile organisms such as plants have to be considerably more adaptable to stressful environments and must acquire greater tolerance to multiple stresses than animals. Understanding plasticity in gene expression in natural systems is crucial, for predicting and managing the effects of climate change on plant species

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