| Artemisia selengensis Turcz,also known as Artemisia rebaudiana,Artemisia vulgaris,Artemisia aquatica,etc.,belongs to Artemisia of Asteraceae Bercht and is a perennial herb.It is distributed in Poyang Lake,Jiangxi Province,Hunan Province,Hubei Province,and other places in China.It mainly grows on the shore of the lake grassland.The plant itself has a fragrant smell and contains protein,multiple trace elements,as well as chemical components such as polysaccharides,chlorogenic acid,volatile oil,and flavonoids.Therefore,it has edible,medicinal,and industrial value.At present,the research on Artemisia selengensis germplasm resources mainly focuses on the chemical substances and active components in Artemisia selengensis.The research on its genetic diversity and systematic evolution is relatively lagged,due to the uneven distribution of Artemisia selengensis germplasm resources in different regions in China,different growth environments,complex genetic background,and fuzzy system classification,which seriously limits the population genetics research,new variety selection and genetic improvement and utilization of Artemisia selengensis germplasm resources.In this study,ISSR and SSR methods were used to analyze the genetic diversity and genetic structure of different Artemisia selengensis germplasm resources;At the same time,complete chloroplast genome splicing,annotation,and genetic map visualization of 10 Artemisia selengensis germplasm resources were completed through the second-generation high-throughput sequencing technology,and chloroplast genome sequence alignment analysis,repeat sequence detection,and phylogenetic analysis were also carried out;It clarifies the genetic structure and genetic relationship of Artemisia selengensis,lays the foundation for the systematic development and classification research of Artemisia selengensis,and provides the basis for the protection and utilization of Artemisia selengensis germplasm resources,which is of great significance for the development of Artemisia selengensis industry.The main results are as follows:(1)In this study,ISSR primers published by Columbia University were selected for synthesis and screening.Finally,9 primers were used to analyze the genetic diversity of 117 Artemisia selengensis.The results showed that a total of 88 loci were amplified,with polymorphic loci accounting for 98.86%.The range of observed allele number(Na)was 1-1.9773,with an average of 1.3245.The range of effective allele number(Ne)was 1-1.3663,with an average of 1.1649.The average value of Shannon’s genetic diversity index was 0.1522,indicating that the selected primers had high polymorphism.The genetic differentiation coefficient Gst is 39.34%,which indicates that the genetic differentiation degree within the population is higher,the genetic flow degree between populations is higher,and the genetic variation is smaller.The genetic diversity of the Artemisia selengensis germplasm material population is more abundant.In ISSR cluster analysis,distance clustering,and model clustering all the materials are divided into three categories,showing the same classification trend,but the materials with the same geographical source in each group are not completely clustered together,and there is a certain degree of heterozygosity in classification,indicating that there is a certain degree of gene exchange between Artemisia selengensis species in different regions.(2)The SSR primers were selected from the transcriptome sequencing data of Artemisia selengensis and synthesized.Finally,six pairs of SSR primers were selected for genetic diversity analysis,cluster analysis,and genetic structure analysis of 117 Artemisia selengensis materials.The results showed that a total of 41 allele loci were amplified,the effective allele number(Ne)of all loci ranged from 2.1535 to 6.5876,and the observed heterozygosity(Ho)varied from 0.4615 to 0.6838,with an average of 0.5826,and the expected heterozygosity(He)varied from 0.5379 to 0.8518,with an average of 0.7070,indicating that the heterozygosity of Artemisia selengensis materials used in the experiment was high.The polymorphism information content(PIC)ranged from 0.4284 to 0.8321,with an average of 0.6503.All primers showed moderate and high polymorphism.At the population level,the results of the genetic variation coefficient showed that most genetic variation occurred within the population(74.7%),and a few occurred between populations(25.3%),which was consistent with the ISSR results.Cluster and population structure analyses divide all materials into 3 and 4 genetic differentiation populations,respectively.Clustering is relatively mixed,which is not completely consistent with the origin classification,and the genetic background is relatively complex.It also shows that the genetic diversity of Artemisia selengensis materials is relatively rich and the degree of gene exchange is high.(3)The whole chloroplast genome of 10 Artemisia selengensis germplasm resources was sequenced in the second generation,the assembly and annotation of the whole genome were completed,the chloroplast genome structure map was visualized,and the sequenced data were analyzed.The results showed that the length of the chloroplast genome of 10 Artemisia selengensis was between 151,148 and 151,257 bp,all of which were typical tetrad round structure,with 133 annotated genes,88 protein-coding genes,37 t RNA genes,and 8 r RNA genes.The boundary analysis showed that the chloroplast of Artemisia selengensis had a conservative genome structure with a highly similar gene sequence and GC percentage.The codon analysis results showed that the content of arginine,leucine,and serine was the highest,and the use rate of cysteine was the lowest.The common base at the third position of the codon was A/T.42-45 scattered repeats and 42-44 SSR repeats were detected.Genome comparison found that the variation in chloroplast genome occurred more in the non-coding region.Nucleotide diversity analysis of Artemisia selengensis and other Artemisia plants showed that a total of 8 mutation hotspots were detected.In the analysis of protein-coding gene Ka/Ks,most genes were subjected to purification and selection.The acc D,rps12,atp F,and pet B genes showed positive selection pressure,and no neutral selection was found.The phylogenetic analysis of 10 Artemisia selengensis and other 27 Asteraceae plants was carried out using the maximum likelihood method.All Artemisia genera were clustered into a large branch,forming a monophyletic group,and were sister genera to the Chrysanthemum genus. |
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