Development Of EST-SSR Markers And Research Of Genetic Diversity In Natural Populations Of Phoebe Chekiangensis C.B. Shang

Phoebe chekiangensis C.B. Shang is an important timber and ornamental tree,which considers as endangered species and lists as secondary national protection plant.In this study, we investigated the status of natural resources at all distributional region,and several typical communities were selected, which was used to study thecommunity structure and biodiversity of P. chekiangensis. The transcriptome of P.chekiangensis was sequenced by Solexa high-throughput sequencing, and the SSRloci were searched. The polymorphicprimers were selected to the analysis of geneticdiversity among seven natural populations of P.chekiangensis, including190individuals. The main results as below:1. The analysis of natural community structure showed that the similarity among6natural communities of P. chekiangensises were0.0606-0.4000, of which theminimum similarity was between Zhejiang Yongjia and Jiangxi Wuyuan?while themaximum was between Zhejiang Songyang and Jiangxi Wuyuan. The important valueof P. chekiangensises in6natural communities were16.27%-43.09%, of which thecommunity of Zhejiang TaiShun had the lowest important values, while thecommunity of JiangXi LiChuan had the highest important values. We predicted thatthe structural differences might be related to the protection of the community. Sevencommunities were clustered into five classes, based on leaf phenotype.2. A total of0.53million RNA-seq sequences were obtained by transcriptomesequencing, and the average length was94.31bp. After DE NOVO splicing,111250Unigenes were obtained and the total length of Unigenes were79126921bp.In thetranscript of gene function annotation and classification,47525Unegenes matched thehomologous protein library of information on NR and accounted for a proportion42.72%;16135Unigenes homology with KEEG library information and annotated thenumber of984enzymes, metabolic pathways for the298;There were25kinds KOGsand15605Unigenes specific protein function defined;Among GO functionalclassification, a total of36,370Unigenes from60categories of Annotation weredefined specific functions.3.Using MISA software searched the sequence with SSR locis were19259and thetotal number of SSRs were22985and had a frequency of17.31%.The main types ofSSRs were dinucleotides and trinucleotides an accounted for56.14%and42.11%respectively.41pairs of primers could amplify polymorphic bands.4.88alleles were detected by41pairs of polymorphisms primers?the averagenumber of alleles na*observed was2.00and the average effective number of allelesne*was1.73;Shannon diversity index I*with an average of0.41,Nei genetic diversity index h*is0.5911.Coefficient of gene differentiation Fst was0.20, geneflow Nm was1.99.Polymorphic information content PIC of41microsatellite markerswas0.0452-0.5896, with an average of0.32.5.NTS clustering showed that190P.chekiangensises were divided into fivecommunities significantly when selected the genetic distance of0.68.The Nei'sgenetic distance UPGMA cluster analysis showed that7P.chekiangensis'communities could be divided into four categories:Zhejiang Hangzhou and ZhejiangSongyang wereclustered together; Zhejiang Taishun and Zhejiang Yongjia wereclustered together;Jiangxi Yanshan and Jiangxi Wuyuan were clusteredtogether;Jiangxi Lichuan as a single group.Population genetic structure analysissoftware Structure2.3divided190P. chekiangensises froom seven naturalpopulations into five subgroups which was similar to the NTS clustering results.6.Mantel test results showed that The genetic distance between populations andgeographic distance was significantly positively correlated(r=0.616?P=0.005);Thegenetic distance between populations correlated with the temperature difference wasnot significant(r=0.192?P=0.394);The genetic distance between populationscorrelated highly with precipitation difference was not significant(r=0.012, P=0.958).The results showed that genetic variation within populations was far greaterthan the genetic variation between populations of natural P.chekiangensis. Existinggene exchange among certain populations that it can rich genetic diversity ofP.chekiangensis. Obviously we can conclude that geographical distance is animportant factor which is affecting genetic distance populations of P.chekiangensis.