Candidate Genes for the High-Altitude Adaptations of Two Mountain Pine Taxa.

Julia Zaborowska,Stephen Cavers,Annika Perry,Bartosz Łabiszak,Witold Wachowiak

doi:10.3390/ijms22073477

Abstract

Mountain plants, challenged by vegetation time contractions and dynamic changes in environmental conditions, developed adaptations that help them to balance their growth, reproduction, survival, and regeneration. However, knowledge regarding the genetic basis of species adaptation to higher altitudes remain scarce for most plant species. Here, we attempted to identify such corresponding genomic regions of high evolutionary importance in two closely related European pines, Pinus mugo and P. uncinata, contrasting them with a reference lowland relative—P. sylvestris. We genotyped 438 samples at thousands of single nucleotide polymorphism (SNP) markers, tested their genetic differentiation and population structure followed by outlier detection and gene ontology annotations. Markers clearly differentiated the species and uncovered patterns of population structure in two of them. In P. uncinata three Pyrenean sites were grouped together, while two outlying populations constituted a separate cluster. In P. sylvestris, Spanish population appeared distinct from the remaining four European sites. Between mountain pines and the reference species, 35 candidate genes for altitude-dependent selection were identified, including such encoding proteins responsible for photosynthesis, photorespiration and cell redox homeostasis, regulation of transcription, and mRNA processing. In comparison between two mountain pines, 75 outlier SNPs were found in proteins involved mainly in the gene expression and metabolism.

Highlights

The sessile lifestyle of plants forces them to develop adaptations, enabling them to quickly, reversibly, and often enduringly cope with environmental changes or colonize new niches to avoid competition
After quality filtering of single nucleotide polymorphism (SNP) and individuals following our criteria of genomic origin and potential linkage of markers, frequency of alleles (MAF), percentage of individuals properly genotyped per marker, and percentage of SNPs genotyped per individual, the data set consisted of 6003 polymorphisms and 438 samples: 79 dwarf pines, 182 Pyrenean pines, and 177 Scots pines, derived from 14 populations spread across Europe (Figure 1, Supplementary Table S1)
Our study provides a new example [40,41,42] of a successful application of a genomewide scan for delineation of phylogenetic relationships among taxonomically challenging plant groups which, in this study, were from the P. mugo complex [28,38]

Summary

Introduction

The sessile lifestyle of plants forces them to develop adaptations, enabling them to quickly, reversibly, and often enduringly cope with environmental changes or colonize new niches to avoid competition. Because photoperiod and temperature are important environmental factors for plants, long-lived trees must make trade-offs between survival, regeneration, development, and reproduction, fitting annual growth cycles in response to seasonal length variations [1]. In addition to usually strong contraction of the vegetation time, the most serious stressors include reduced atmospheric pressure, photooxidative stress, lowered temperatures, and demanding substrates [2,3,4]. Many tree species, including the pines on which the survey was conducted, maintain high fertility and enforce strong selection between recruited individuals, which facilitates adaptation to new environments. The populations are usually insular and are subjected to rapid changes in environmental factors along the elevation gradient

Methods

Results

Discussion

Conclusion