Study On Ecological Adaptation Based On Drought And Hypoxia Related Candidate Genes In Trees

Quercus aquifoliodes Rehd.Et Wils is an evergreen and sclerophyllous oak species belonging to Quercus Sect.Heterobalanus(Oerst.)Menits.It widely distribute in south-west China with a high altitude range and adapt to harsh ecological environments.In this study,landscape genomic was used to study the ecological adaptation of Q.aquifolioides based on drought and hypoxia related candidate genes.65 candidate genes were selected from the published database from other oak species and primers were designed,verified by Sanger sequencing in Q.aquifoliesuoides.Next-Generation pool Sequencing were used to genotyping all the candidate genes in 587 individuals from 60 populations of the species and 381 high-quality single nucleotide polymorphisms(SNPs)were identified.Firstly,three sets of genetic data including all SNP dataste,neutral SNP datasets and eight published Simple Sequence Repeat(SSR)loci were used to conduct comparative analysis on the genetic diversity and genetic structure of Q.aquifolioides.Results showed that the species can be divided into two lineages,which are Tibet lineage distributed in the eastern of Tibet and HDM-WSP lineage distributed in Hengduan Mountains and the western Sichuan Province.The genetic divergency of Tibet lineage and HDM-WSP lineage based on all SNP dataset is more obvious than the results based on other molecular markers,which may be caused by adaptation to different ecological environments.The genetic diversity of Tibet lineage was significantly smaller than HDM-WSP lineage based on analysis of neutral SNP and SSR datasets.Secondly,using two methoed based on FST outlier(BAYESCAN and FDIST2)and two method based on the correlations between allele frequency and environmental gradient correlation(BayEnv and LFMM),a total of 310 non-neutral SNPs were detected from 56 candidate genes.The specific or common SNPs detected in the two lineage will play a key role in the understanding of the ecological adaptation mechanism of the species.Finally,two linear methods,Mantel test and redundancy analysis(RDA)and two non-linear methods,Gradient Forests(GF)and Generalized Dissimilarity Modelling(GDM)were used to analyze the response pattern of genetic variation with environmental gradients of Q.aquifolioides.The results showed that geographical factors are the most significant factors that affects the genetic differentiation of Q.aquifolioides in all populations.However,compared with the large-scale spatial range(all populations),the role of climatic factors becomes larger in the small-scale spatial range(two lineages).In addition,the cumulative importance curve of GF indicates that allelic composition changes sharply within the extent of 96-98°E of longitude,12-14 mm of precipitation in January and 160-180mm of precipitation in June,whereas changes along other environmental variables occur gradually.In this study,based on SNPs detected from candidate genes and published SSR loci,we detected the genetic diversity and genetic structure of the species,investigated the adaptive SNPs and explored the response patterns to different environmental factors of Q.aquifolioides,all of which provides a basic theoretical basis for the ecological adaptation of Q.aquifolioides and new insights for the landscape genomic studies for other tree species.