Population Genetic Structure And Its Influencing Factors Or Mechanism Of The Oriental Fruit Moth,Grapholita Molesta(Lepidoptera Tortricidae) In China

The oriental fruit moth(OFM),Grapholita molesta(Lepidoptera:Tortricidae),is one of the most globally destructive orchared pests,including Asia,Australia,South America,North America,Europe and South Africa.In China,it has been reported in every province except Tibet,and caused serious economic loss in the northern,median and southern China.At present,many studies indicated that Austrial and Japanese populations clusters consistent with Chinese populations.Using mitochondrial DNA and microsatellite markers,the population genetic structure of OFM has been explored.However,it is unknown about the influencing factors and mechanism of such population structure.So,in this study,we utilized ddRAD to obtain thousands of SNPs,detailedly describe population structure and explore environmental adaptation of the OFM.The main results and conclusions were as follows:1.The best combination of restriction endonucleases for ddRAD projects of OFMFor OFM without reference genome,it is difficult to filter the best combination of restriction endonucleases(REs)through computer programs.Different combinations of REs may produce varying size distributions of digested fragments,which affect the number of genotyped loci.To evaluate profiles of the combinations of REs more accurately,we made use of genome sequences to compare the in silico digestion profile of 26 combinations in 131 insect species with two simulation programs.The number of digested fragments in the 300-450 bp range increases linearly with the size of the genome.Different insect species and orders showed similar profiles when digested by different combinations of REs in silico,indicating the conservation of digestion by double enzymes in insect genomes.Combinations with NlaIII or Taq?I usually produced higher number of fragments in the range of 300-450 bp,while combinations with EcoRI or MLuCI produced fewer fragments.The two four-base enzyme pairs produced more fragments than pairs of four-base+six-base enzymes.Experimental digestion of three species from Hymenoptera,Lepidoptera and Thysanoptera showed profiles congruent with in silico expectations.Our results shed light on understanding the digestion profiles of insect genomes,that combinations with NlaIII or Taq~?I are more suitable.In this study,we chose NlaIII+AciI for ddRAD project of OFM.2.Population genetic structure of OFMWe collected 684 OFM larvaes at 19 locations across China.In total,24,267biallelic SNPs were identified by ddRAD method,including 3,219 unlinkaged neutral SNPs and 3,549 SNPs putatively under selection.Based on neutral loci,ADMIXTURE and DAPC indicated that the nineteen populations were clustered into six sub-groups,including YN,SC,NE(northern and eatern popualtions),NW(northwest),MIX and GD.3.The influencing factors of population structure and the environmental adaptation of OFMIn this study,we firstly explored the effect of Wolbachia for population genetic structure.Through mapping of Bowtie,the sequences of Wolbachia were exported from each samples.In northern and eastern China,there were no infected individuals,that was not consistent with the population structure obtained by mitochondrial DNA.So,the strains of Wolbachia in OFM did not result in a selective sweep.Secondly,a significant association between genetic distance and geographic distance was confirmed among 19 populations,while it was no association between genetic distance and geographic distance among NE group.Moreover,we found 72 outliers and 427 genes around these SNPs ranging up to 200 Kb.After the analysis of KEGG,40 metabolism pathways were enriched,including energy metabolism,environment stimulus regulation,insect growth and development regulation,cell proliferation and differentiation regulation.Finally,we downloaded nineteen bioclimatic variables from WorldClim database for correlative analysis.219 SNPs were related to isothermality(BIO3)that was the largest.In summary,based on the results of conserved profiles about digestion by double restriction endonucleases in insect genomes,we chose NlaIII+AciI for ddRAD projects of OFM.Using ddRAD,we obtained thousands of SNPs,and rebuild population genetic structure of OFM.We did not found a selective sweep caused by Wolbachia.The form of population structure among OFM populations may be influenced by isolation of geographic distance and isothermality.The results indicated the current geographic distribution and population structure of OFM.The structure was complicatedly influenced by isothermality,geographic distance and human activities.The finding of this study might shed light on the evolution history of OFM and provide a successful example of uncovering the genetic structure and the influencing factors or mechanism for other insects.