Development Of Chloroplast Microsatellite Marker And Phylogeography Of Cryptomeria

Cryptomeria is an evergreen tree with beautiful shape and excellent material,which is a good timber forest and landscape tree species.It can be divided into two groups:Cryptomeria fortunei and Cryptomeria japonica,but their origins and taxonomic relationship are unclear,which is controversial.In this paper,the phylogenetic relationship of Cryptomeria was analyzed and determined by using the chloroplast microsatellite（cpSSR）loci developed independently.The genetic diversity level and genetic differentiation of natural populations of Cryptomeria（China and Japan）were analyzed,the populations’dynamic history was understood,and the ice shelters and populations diffusion route were speculated.The related research can provide theoretical basis for the resource protection and long-term breeding of Cryptomeria.The main results are as follows:1.Development of cpSSR loci in C.fortuneiBased on the chloroplast genome sequence of C.fortunei,11 polymorphic cpSSR loci were developed and 18 haplotypes were detected in 3 populations.The average diversity index of the loci was 0.917,among which the highest polymorphism was found in Cf＿cp＿22.Eleven loci were effectively amplified in C.fortunei and its four related species.2.Phylogenetic analysis of Cryptomeria in TaxodiaceaeThe phylogenetic relationships of 11 species of 8 genus of the Taxodiaceae show that the Cryptomeria had a relatively early developmental status in the Taxodiaceae,11 species can be divided into 2 clusters,among which the Cryptomeria and Cunninghamia lanceolata are one cluster,and other species of Taxodiaceae are one large cluster.Cryptomeria and Cunninghamia lanceolata,Glyptostrobus pensilis and Taxodiumare closely related to each other.3.The phylogeography of Cryptomeria populationThe Cryptomeria has obvious phylogeography structure in East Asia.At the level of species,the total genetic diversity（H_T）of Cryptomeria population was 0.983,the genetic diversity（H_S）within the population was 0.859,genetic differentiation coefficient R_STbetween populations（0.274）Significantly greater than G_ST（0.126）。The results of molecular variance analysis（AMOVA）showed that the genetic variation of Cryptomeria population mainly came from within the population（59.71%）.The populations of Cryptomeria had obvious phylogeography structure.216 haplotypes were detected in 21 populations of Cryptomeria in East Asia.There was no shared haplotype between C.fortunei and C.japonica,and the number of private haplotypes in each group was significantly higher than that of shared haplotypes.The results of STRUCTURE and DAPC analysis were consistent that 21populations were mainly divided into two clusters.C.fortunei and C.japonica gather in an independent branch,and Lushan（LS）population was more closely related to C.japonica.4.Evolution history of Cryptomeria populationAccording to the results of STRUCTURE,9 populations of C.fortunei were used as gene bank 1（Pop 1）,Lushan（LS）population and C.japonica population as gene bank 2（Pop 2）.DIY ABC analysis showed that C.japonica separated from the C.fortunei about 84,800 years ago and evolved independently.There were two main ice age refuges of Cryptomeria in East Asia,one in central and southeast China and the other in southwest Japan.