Genetic Variation Related to High Elevation Adaptation Revealed by Common Garden Experiments in Pinus yunnanensis

Abstract

Local adaptation, adaptation to specialized niches and environmental clines have been extensively reported for forest trees. Investigation of the adaptive genetic variation is crucial for forest resource management and breeding, especially in the context of global climate change. Here, we utilized a Pinus yunnanensis common garden experiments established at high and low elevation sites to assess the differences in growth and survival among populations and between the two common garden sites. The studied traits showed significant variation between the two test sites and among populations, suggesting adaptive divergence. To detect genetic variation related to environment, we captured 103,608 high quality SNPs based on RNA sequencing, and used them to assess the genetic diversity and population structure. We identified 321 outlier SNPs from 131 genes showing significant divergence in allelic frequency between survival populations of two sites. Functional categories associated with adaptation to high elevation were found to be related to flavonoid biosynthesis, response to UV, DNA repair, response to reactive oxygen species, and membrane lipid metabolic process. Further investigation of the outlier genes showed overrepresentation of the flavonoid biosynthesis pathway, suggesting that this pathway may play a key role in P. yunnanensis adaptation to high elevation environments. The outlier genes identified, and their variants, provide a basic reference for advanced investigations.

Dissecting the Polygenic Basis of Cold Adaptation Using Genome-Wide Association of Traits and Environmental Data in Douglas-fir

“…Previous studies have shown strong evidence of steep phenotypic and environmental clines within the coastal variety [ 17 , 18 , 19 , 32 , 56 ]. Significant divergence in allele frequency was also found in genome-wide studies comparing high and low elevation populations of Pinus yunnanensis [ 57 ]. In contrast, studies in this and other forest tree species suggested small to moderate shifts in allele frequency of adaptive alleles [ 6 , 58 , 59 ], and the presence of intermediate-frequency polymorphisms characteristic of recurrent selective sweeps [ 60 ].…”

Population transcriptomic sequencing reveals allopatric divergence and local adaptation in Pseudotaxus chienii (Taxaceae)

“…a RDA1 and RDA2 axes of an RDA based on all loci. b RDA1 and RDA2 axes of an RDA based on outlier loci associated with the most outlier SNPs (36), followed by soil Cu content (29), soil Zn content (25), percent tree cover (21), aspect (18), and precipitation of the driest month (16).…”

“…For example, Yan et al (2017) [15] sequenced the transcriptomes of 78 Miscanthus lutarioriparius individuals from 10 populations and found genes related to photosynthetic processes and responses to environmental stimuli such as temperature and reactive oxygen species. Sun et al (2020) [16] compared the transcriptomes of Pinus yunnanensis from high-and low-elevation sites and identified 103,608 high-quality SNPs and 321 outlier SNPs based on RNA-Seq to investigate adaptive genetic variation. The 321 outlier SNPs from 131 genes displayed significant divergence in terms of allelic frequency between high-and low-elevation populations and indicated that the flavonoid biosynthesis pathway may play a crucial role in the adaptation of P. yunnanensis to high-elevation environments.…”

A Chromosome-level Assembly of a Wild Castor Genome Provides New Insights into the Adaptive Evolution in a Tropical Desert

“…In rice, two of the key amino acid natural variations in the CPD photolyase gene, among the major DNA lesions induced by UV-B radiation, appear to decrease activity in response to UV radiation [61]. SNP variation in Pinus yunnanensis occurs in response to ultraviolet radiation at high altitudes [62].…”