Landscape Genetic Of Cymbidium Kanran By Restriction-site-associated DNA Sequencing

Cymbidium kanran is a perennial orchid,which is distributed widely in southern China.The value of high economic and ornamental make it become more popular in China.With people’s awareness of orchid genus increased in recent years,more and more wild C.kanran populations faced a series of problems: the excavation of habitat loss,population quantity reducing and the original habitat destruction.Researching genetic diversity and genetic structure and the space distribution in an effective way to protect wild C.kanran populations resources,which can provide theoretical basis to the plan of C.kanran protection.In this study,simplified genome sequencing(dd-RAD)was used to sequence the wild C.kanran from 11 provinces of China,and the high-quality SNPs were analyzed in population genetics.Combined with climate data published on wordclim,the distribution of C.kanran in different periods in the future was predicted and the effects of environmental variables on the genetic variation of C.kanran population were studied.The main results are as follows:1.A total of 27405 high-quality SNP were identified from 463 C.kanran individuals with genotyping by sequencing and data screening.The range of observed heterozygosity,expected heterozygosity and nucleotide diversity of each population were 0.2872～0.4045,0.1871～0.2852,0.1936～0.2965,respectively,and the average were 0.2814,0.2627 and 0.2750.The observed heterozygosity higher than expected heterozygosity at the whole C.kanran population level based on genetic diversity analysis,and there was a heterozygosity selection advantage among the populations.There are high level of nucleotide polymorphism in C.kanran population.The highest nucleotide diversity(He=0.2866)was found in Shangyou Population of Jiangxi Province,and the lowest was found in Chongqing Youyang population(CQYY)(He=0.1871).AMOVA showed that 91.71% of genetic variation was mainly from within the population.C.kanran population genetic differentiation of the Fst range is 0.03-0.18,the whole populations have relatively low genetic differentiation,the location close to the group of similar degree of genetic differentiation,population genetic differentiation of high altitude higher than low altitude in the group,which showed that high altitude mountains is likely to be barriers in the group;BARRIER 2.0 software analysis also indicated that geographical isolation at high altitude was the main genetic barrier to gene flow between populations.2.Population structure analysis revealed that 4 gene pool 36 group most likely to be detected from 36 population,the first group in China’s southwest Yunnan,Sichuan province,the second group in the west of Guizhou,Hunan and Jiangxi in the group,the third group including Guangxi,Guangdong,Jiangxi and Fujian at the junction,south of Fujian and Zhejiang in the group,the fourth group is youyang group of Chongqing,which showed that genetic structure of C.kanran correlated with complex terrain.The population of Chongqing,Yunnan,and Sichuan were significantly separated by PCA from other provinces,and their genetic relationships were further than other provinces.3.Results of MaxEnt model prediction of C.kanran distribution in 2061-2080 and 2081-2100,the distribution of the suitable area of C.kanran will migrate to the south and show a large area of contraction in the future,and there will be a trend of temporary expansion than contraction only in the SSPs585 scenario in 2081-2100.The agglomeration pattern of C.kanran distribution based on Maxent model in spatial autocorrelation analysis.Mantel detected that geographical distance affected the genetic differentiation of C.kanran populations at large spatial scales.As geographical distance increases,there may be a stronger trend of genetic differentiation among populations.In the small scale,the change is not obvious.4.Annual precipitation(bio＿12),precipitation of driest month(bio＿14),precipitation of driest quarter(bio＿17),precipitation of coldest quarter(bio＿19)and temperature seasonality(bio＿4)had the same effect on population genetic structure from RDA.Precipitation in the wettest season and the warmest season had little effect on population structure data.According to the analysis of gradient forest(GF),among the eight environmental factors,precipitation of driest season(bio＿17)and precipitation of coldest quarter(bio＿19)had the most significant effect on genetic variation of C.kanran population.The allele frequency of the populations with precipitation greater than 50 changed significantly in the driest and coldest seasons.