Genetic Diversity And Genetic Basis Of Local Adaptation In Pinus Yunnanensis

Local adaptation arise by differential selection pressures across heterogeneous environments.Local adaptation have been extensively reported for forest trees.Understanding the genetic basis of local adaptation is crucial for tree breeding,forest resource management and predicting the potential of long-lived woody species to withstand changes in their natural environment,especially in the context of global climate change.Although of widespread interest,the understanding of the genetic basis of local adaptation is still very limited.Pinus yunnanensis is the dominant pine in southwest China with a continuous distribution in the Yunnan-Guizhou region at elevations ranging from 700 to 3,000 m above sea level,and occupies very heterogeneous environments.The genetic and transcriptional basis underlaying this wide adaptation have not been studied to date.In this study,we used common garden experiments and transcriptome sequencing to investigate the patterns of adaptive differentiation among natural populations of P.yunnanensis,especially the genetic variation related to high elevation adaptation,the gene expression related to environments,and the polygenic regulation of adaptive differentiation.The main results are as follows:?1?Significant differences in growth and survival among populations and between the two common garden sites were observed.Two common gardens,one at low elevation?1890 M?and one at high elevation?2950 M?,were involved in this study.In the low elevation site?Kunming:KM?,significant differences in growth between populations were shown.The local population?KM?and two exotic populations from farthest Southwest?BS and GS?generally displayed the fastest growth.At the high elevation site?Linzhi:LZ?,the seedlings of all populations suffered heavy mortality.In the seventh year,only five individuals which originated from population KM survived at the high-elevation site?LZ?.In contrast,survival rates were comparatively high and constant at the low elevation site KM.?2?Continuous genetic differentiation over the majority of the species'range and discrete isolated local clusters were found.Transcriptome sequencing?RNA-seq?generated 103,608 high quality SNPs in the analyzed samples.Based on these SNPs,a clear population structure emerged with two distinct population clusters comprising,one consisting the southwestern corner population?BS?and another with all other populations in which continuous genetic differentiation was found.The later can be further divided into northwest group?ZD,LJ and GS?,central group?KM and YL?and south group?YX?.?3?Flavonoid biosynthesis pathway may play a key role in P.yunnanensis adaptation to high elevation environments.We identified 321 outlier SNPs from 131 genes showing significant divergence in allelic frequency between survival populations of the two common garden experiment 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.?4?This species showed population differentiation in gene expression that have been mainly shaped by source population site climate,and that are reflected in adaptive trait variations.We constructed gene co-expression network using gene expression data with a hierarchical clustering algorithm.The network consists of 18,694 genes,which were divided into 30 co-expression modules.According to GO enrichment analysis,21 modules showed enrichments for genes involved in specific biological processes.We found that nine modules were significantly associated with temperature-related variables,and eight modules with water availability.In addition,one module involved in cellular amino acid metabolism correlated with tree height.?5?The action of differential selection among populations is different among co-expression modules and drive genes in the co-expression modules to generate weak sequence differentiation.These small allele frequency shifts collectively may contribute to local adaptation.RNA-seq data analyses identified seven modules bear potential signatures of polygenic adaptation,with significant higher F_ST estimates than 99%of the permutated sampling of the genome,suggesting divergent selection.Importantly,the signal of selection was still significant when considering the cumulative effects of multiple genes,even though individual genes showed weak or no selective signal.This pattern corresponds to the hallmark of polygenic adaptation.?6?The gene expression variation and nucleotide diversity have a synergistic relationship within populations,while the gene expression variation between populations is basically not affected by genetic variation and geographic distance.At the gene level,significantly positive correlations were observed between the expression diversity?E_d?and nucleotide diversity across coding region(?_CDS)and full gene(?_gene)in each population.Among populations,pairwise expression similarity?E_p similarity?correlated with neither geographic nor genetic distance.In addition,isolation by distance?IBD?analysis,excluding the most geographic distant population,showed a significant association between population differentiation and geographic distance among the six populations.Based on common garden experiments and transcriptome sequencing,this study combined population genetics with gene expression analysis to systematically assess the adaptive phenotypic differentiation and genetic diversity.The investigations revealed polygenic basis and gene expression pattern of local adaptation in P.yunnanensis.The results are of great significance for understanding the genetic mechanism of adaptation,and have important implications for the management and utilization of germplasm resources and genetic improvement and breeding in P.yunnanensis.