High Genetic Diversity and Structured Populations of the Oriental Fruit Moth in Its Range of Origin

The oriental fruit moth Grapholita ( = Cydia) molesta is a key fruit pest globally. Despite its economic importance, little is known about its population genetics in its putative native range that includes China. We used five polymorphic microsatellite loci and two mitochondrial gene sequences to characterize the population genetic diversity and genetic structure of G. molesta from nine sublocations in three regions of a major fruit growing area of China. Larval samples were collected throughout the season from peach, and in late season, after host switch by the moth to pome fruit, also from apple and pear. We found high numbers of microsatellite alleles and mitochondrial DNA haplotypes in all regions, together with a high number of private alleles and of haplotypes at all sublocations, providing strong evidence that the sampled area belongs to the origin of this species. Samples collected from peach at all sublocations were geographically structured, and a significant albeit weak pattern of isolation-by-distance was found among populations, likely reflecting the low flight capacity of this moth. Interestingly, populations sampled from apple and pear in the late season showed a structure differing from that of populations sampled from peach throughout the season, indicating a selective host switch of a certain part of the population only. The recently detected various olfactory genotypes in G. molesta may underly this selective host switch. These genetic data yield, for the first time, an understanding of population dynamics of G. molesta in its native range, and of a selective host switch from peach to pome fruit, which may have a broad applicability to other global fruit production areas for designing suitable pest management strategies.     

Microsatellite analysis revealed a different approach of control of olive fly population (Bactrocera oleae) in Slovenia

The olive fruit fly (Bactrocera oleae Gmelin) is the most important olive pest in the north‐eastern Adriatic coast region. Despite the importance of olive production in the region, and the significance of the olive fruit fly, no information with respect to genetic diversity, population structure or dispersion patterns of this pest is available. The aims of this study were to investigate the genetic structure of the olive fly population in the Slovenian Istria region using microsatellite markers to determine olive fruit fly migration between locations and to establish an appropriate and effective strategy for controlling the pest population. Analysis was performed on a sample of 117 flies, collected from attacked olive fruits at three different locations. Olive fruit flies were genotyped using eight microsatellite loci. Sixty‐six alleles were identified over all microsatellite loci with an average of 8.25 alleles per locus. The population structure was determined with methods based on Bayesian principles using the BAPS 6.0 and STRUCTURE 2.3 programs. Genetic analysis confirmed unlimited migration and random mating between individuals of different microlocations, which suggests time‐coordinated first treatment in the region would be the best solution.     

Isolation and characterization of eight polymorphic microsatellite loci for the coconut pest, Brontispa longissima (Coleoptera: Hispidae)

Brontispa longissima is one of the most serious insect pests of coconut in Southeast Asia; it was first discovered on Hainan Island in June 2002. Despite the economic risk associated with this pest, genetic aspects of the invasion process have remained relatively unexplored. Using microsatellite markers, we investigated the population structure, genetic variability and pattern of invasion in various geographic populations. The methodology was based on a modified biotin-capture method. Eight polymorphic microsatellite loci were isolated and characterized for the pest. The allele number per locus varied from 2 to 3 (N = 30). The expected and observed heterozygosities of the eight loci ranged from 0.042 to 0.509 and from 0.042 to 0.963, respectively. Although the frequency of polymorphisms was not very high in this population, the microsatellite loci that were isolated will be useful for investigating the genetic diversity and migration routes of B. longissima populations.     

Genetic structure of a phytophagous mite species affected by crop practices: the case of Tetranychus urticae in clementine mandarins

Tetranychus urticae Koch is a cosmopolitan mite considered as the most polyphagous species among spider mites. This mite is a key pest of clementine mandarins in Eastern Spain, where Spanish clementine production concentrates. Crop management practices can affect the population dynamics of this mite and, consequently, its impact on the orchard. Microsatellite markers were used to study mite population genetics from two commercial orchards which had been managed differently following Integrated Pest Management (IPM) or Organic Pest Management (OPM) schemes during four consecutive years. A multiplex system including 20 microsatellite loci was designed specifically and allowed an efficient and inexpensive genotyping of individual mites. We found that the IPM population had a stronger fluctuation of population structure and higher genetic diversity compared to OPM population. Thus, our study concludes that crop management has an impact on the population genetics of T. urticae which may be related to the alternation of some acaricides under IPM.     

Isolation and characterization of microsatellite markers in Chinese herb of Dendrobium loddigesii

As an invaluable herb, Dendrobium loddigesii is widely used in Chinese medicinal field. In order to develop a convenient and efficient identification method and investigate the genetic diversity and structure of this species, twelve microsatellite loci were isolated from two microsatellite-enriched libraries. Twenty-six individuals from Baise population were analysed. The observed and expected heterozygosities ranged from 0.174 to 0.617 and from 0.182 to 0.608, respectively. These microsatellite loci characterized from D. loddigesii will contribute to research on the individual authentication, population structure, genetic diversity and conservation of this species and its similar species.     

Genetic Diversity of Sitobion avenae (Homoptera: Aphididae) Populations from Different Geographic Regions in China

Sitobion avenae is a major agricultural pest of wheat in China. Using microsatellite markers, we studied the potential gene flow, genetic diversity, genetic differentiation, and genetic structure of seven S. avenae populations from different regions of China (Beijing, Hebei, Henan, Hubei, Jiangsu, Shandong, and Shanxi provinces). The populations from Henan, Shandong, and Jiangsu showed high levels of genic and genotypic diversity. By contrast, the genic diversity in the Beijing and Hebei populations was much lower. Despite this low genic diversity, the genotypic diversity of the Beijing population was higher than that of all of the other populations, except those from Jiangsu and Shandong. Overall, the genetic divergence among the seven S. avenae populations tested was high, though there was almost no differentiation between the Shandong and Henan populations. We observed significant negative correlation between the strength of gene flow and the geographic distances among populations. Based on genetic analysis, the seven S. avenae populations studied can be divided into four distinct clusters; (i) Hubei, (ii) Shanxi, (iii) Beijing and Hebei, and (iv) Shandong, Henan, and Jiangsu. The present results provide a basis for potentially optimizing integrated pest management (IPM) programs in China, through adapting control methods that target biological traits shared by various populations of the same genotype.     

Microsatellite markers for Lycium ruthenicum (Solananeae)

We developed microsatellite markers in Lycium ruthenicum, a desert plant widely distributed in northwestern China. In order to investigate its population genetic structure, genetic diversity, and its evolutionary history, we have isolated 11 novel microsatellite loci primers and characterized them in 24 individuals from 3 populations of L. ruthenicum using the combined biotin capture technique. For these microsatellites, one to seven alleles per locus were identified. The observed heterozygosities ranged from 0 to 0.958, meanwhile the expected heterozygosities ranged from 0 to 0.841. These microsatellite markers could be first useful for population level studies like genetic diversity and structure in this species.     

Genetic diversity of native and introduced populations of the invasive house crow (<Emphasis Type="Italic">Corvus splendens</Emphasis>) in Asia and Africa

The common house crow (Corvus splendens) is one of the best known and most wide spread species of the family Corvidae. It is a successful invasive species able to exploit urban environments, well removed from its natural distribution. It is considered a pest as it attains high population densities, can cause serious economic losses and has many adverse effects on native fauna and flora, including predation, competitive displacement and disease transmission. Little genetic research on the house crow has been undertaken so we have only a limited understanding of its natural genetic population structure and invasion history. In this study, we employ microsatellite and mitochondrial DNA markers to assess genetic diversity, phylogeography and population structure of C. splendens within its native range represented by Sri Lanka and Bangladesh and introduced range represented by Malaysia, Singapore, Kenya and South Africa. We found high levels of genetic diversity in some of the invasive populations for which multiple invasions are proposed. The lowest genetic diversity was found for the intentionally introduced population in Selangor, Malaysia. Sri Lanka is a possible source population for Malaysia Selangor consistent with a documented introduction over 100 years ago, with port cities within the introduced range revealing possible presence of migrants from other unsampled locations. We demonstrate the power of the approach of using multiple molecular markers to untangle patterns of invasion, provide insights into population structure and phylogeographic relationships and illustrate how historical processes may have contributed to making this species such a successful invader.     

Development of Microsatellite Markers and Analysis of Genetic Diversity and Population Structure of Colletotrichum gloeosporioides from Ethiopia

Twenty three polymorphic microsatellite markers were developed for citrus plant pathogenic fungus, Colletotrichum gloeosporioides, and were used to analyze genetic diversity and population structure of 163 isolates from four different geographical regions of Ethiopia. These loci produced a total of 118 alleles with an average of 5.13 alleles per microsatellite marker. The polymorphic information content values ranged from 0.104 to 0.597 with an average of 0.371. The average observed heterozygosity across all loci varied from 0.046 to 0.058. The gene diversity among the loci ranged from 0.106 to 0.664. Unweighted Neighbor-joining and population structure analysis grouped these 163 isolates into three major groups. The clusters were not according to the geographic origin of the isolates. Analysis of molecular variance showed 85% of the total variation within populations and only 5% among populations. There was low genetic differentiation in the total populations (F_ST = 0.049) as evidenced by high level of gene flow estimate (N_m = 4.8 per generation) among populations. The results show that Ethiopian C. gloeosporioides populations are generally characterized by a low level of genetic diversity. The newly developed microsatellite markers were useful in analyzing the genetic diversity and population structure of the C. gloeosporioides populations. Information obtained from this study could be useful as a base to design strategies for better management of leaf and fruit spot disease of citrus in Ethiopia.     

Characterization of 11 novel polymorphic microsatellite loci in the threatened Korean loach,Iksookimia koreensis,isolated using a next-generation sequencing method

To investigate the genetic diversity and population structure of Iksookimia koreensis, we characterized 11 novel polymorphic microsatellite markers developed using next-generation sequencing. The number of alleles per locus ranged from 4 to 10 (average = 6.26). Observed and expected heterozygosities ranged from 0.333 to 0.866 and from 0.375 to 0.866, respectively. No loci showed significant deviation from Hardy–Weinberg equilibrium (HWE). These loci were also used successfully to study the genetic diversity of a closely related species, Iksookimia longicorpa. Four of the 11 loci amplified in the two species showed different allele frequency and distribution, indicating deep genetic divergence between I. koreensis and I. longicorpa. The newly developed microsatellite markers reported here will provide a useful tool for examining gene flow, population genetic structure, and genetic diversity of these species.     

Genetic variation and phylogeographic structure of Laodelphax striatellus in China based on microsatellite markers

The small brown planthopper (SBPH), Laodelphax striatellus (Fallén) (Hemiptera: Delphacidae), is an important agricultural pest that has caused serious economic losses in the major rice-producing areas of China. To effectively manage this insect pest, we analysed its genetic variation, genetic structure and population demographic history. We used nine nuclear microsatellite loci to investigate the genetic diversity and population genetic structure of SBPH at 43 sampling sites in China. High levels of genetic diversity and genetic differentiation among most populations were detected. Overall, neighbour-joining dendrograms, STRUCTURE and principal coordinate analysis (PCoA) revealed no genetically distinct groups and exhibited an admixed phylogeographic structure in China. Isolation by distance (IBD) and spatial autocorrelation analyses demonstrated no correlation between genetic distance and geographic distance. On the other hand, bottleneck analysis indicated that SBPH populations had not undergone severe bottleneck effects in these regions. This study provides useful data for resolving the genetic relationships and migration patterns of SBPH and thus contributes to developing effective management strategies for this pest.     

Genetic Diversity and Population Structure of Sitodiplosis mosellana in Northern China

The wheat midge, Sitodiplosis mosellana, is an important pest in Northern China. We tested the hypothesis that the population structure of this species arises during a range expansion over the past 30 years. This study used microsatellite and mitochondrial loci to conduct population genetic analysis of S. mosellana across its distribution range in China. We found strong genetic structure among the 16 studied populations, including two genetically distinct groups (the eastern and western groups), broadly consistent with the geography and habitat fragmentation. These results underline the importance of natural barriers in impeding dispersal and gene flow of S. mosellana populations. Low to moderate genetic diversity among the populations and moderate genetic differentiation (F _ST = 0.117) between the two groups were also found. The populations in the western group had lower genetic diversity, higher genetic differentiation and lower gene flow (F _ST = 0.116, Nm = 1.89) than those in the eastern group (F _ST = 0.049, Nm = 4.91). Genetic distance between populations was positively and significantly correlated with geographic distance (r = 0.56, P<0.001). The population history of this species provided no evidence for population expansion or bottlenecks in any of these populations. Our data suggest that the distribution of genetic diversity, genetic differentiation and population structure of S. mosellana have resulted from a historical event, reflecting its adaptation to diverse habitats and forming two different gene pools. These results may be the outcome of a combination of restricted gene flow due to geographical and environmental factors, population history, random processes of genetic drift and individual dispersal patterns. Given the current risk status of this species in China, this study can offer useful information for forecasting outbreaks and designing effective pest management programs.     

Variability of allozyme and cpSSR markers in the populations of Siberian spruce

The variability of 21 allozyme and three microsatellite loci of chloroplast DNA (cpDNA) was studied in the populations of Siberian spruce (Picea obovata Ledeb.) from Irkutsk oblast, Magadan oblast, Buryatia, and Mongolia. It was demonstrated that the highest level of genetic diversity among the examined populations at both allozyme and microsatellite loci was observed in the Tulyushka population from Irkutsk oblast. The lowest level of genetic diversity was observed in marginal isolated populations of Bogd Uul and Magadan. In the relict spruce population from Olkhon Island, differing from the other populations in the lowest allelic diversity of both types of markers, no expected decline of expected heterozygosity and haplotype diversity was observed. In this population, the variability parameters mentioned were close to the population mean. The obtained intrapopulation and intraspecific variability parameters of allozyme and microsatellite loci of chloroplast DNA and the data on the population differentiation at these loci indicate that the given markers can be used for the analysis of the population structure of Siberian spruce.     

烟粉虱生物型的监测及其遗传结构研究

烟粉虱Bemisia tabaci(Gennadius)是一种重要的农业害虫并包括许多生物型,其中B型和Q型是入侵性较强的2种生物型。文章着重介绍近年来在烟粉虱生物型的监测及其遗传结构方面的研究进展。B型烟粉虱和Q型烟粉虱这2个生物型均已入侵我国,其中多数地区烟粉虱是B型烟粉虱,局部地区有Q型烟粉虱并呈现不断蔓延趋势。微卫星(SSR)分子标记分析结果表明我国B型烟粉虱的入侵来源具有多元化,而云南地区Q型烟粉虱来源比较单一。化学农药的使用能够影响室内种群的遗传结构,降低种群的遗传多样性。基于RAPD、ISSR分子标记的分析结果表明,Q型烟粉虱种群各项遗传多样性指数均比B型烟粉虱的高。今后加强烟粉虱入侵生物型的遗传结构及其种群动态关系等方面的研究,对于揭示烟粉虱的灾变机制及其控制具有重要的意义。     

Population Genetic Structuring in Opisthorchis viverrini over Various Spatial Scales in Thailand and Lao PDR

Khon Kaen Province in northeast Thailand is known as a hot spot for opisthorchiasis in Southeast Asia. Preliminary allozyme and mitochondrial DNA haplotype data from within one endemic district in this Province (Ban Phai), indicated substantial genetic variability within Opisthorchis viverrini. Here, we used microsatellite DNA analyses to examine the genetic diversity and population structure of O. viverrini from four geographically close localities in Khon Kaen Province. Genotyping based on 12 microsatellite loci yielded a mean number of alleles per locus that ranged from 2.83 to 3.7 with an expected heterozygosity in Hardy–Weinberg equilibrium of 0.44–0.56. Assessment of population structure by pairwise F_ST analysis showed inter-population differentiation (P<0.05) which indicates population substructuring between these localities. Unique alleles were found in three of four localities with the highest number observed per locality being three. Our results highlight the existence of genetic diversity and population substructuring in O. viverrini over a small spatial scale which is similar to that found at a larger scale. This provides the basis for the investigation of the role of parasite genetic diversity and differentiation in transmission dynamics and control of O. viverrini.     

Isolation and characterization of microsatellite markers for Achyranthes bidentata (Amaranthaceae) using next-generation sequencing platform

Achyranthes bidentata Blume (Amaranthaceae) is a perennial herb that is widely distributed in India, Java, China, and Japan. The natural resources of A. bidentata in its geo-authentic product area have rapidly declined in recent years because of the over-collection of its roots. To devise adequate conservation and management strategies for this species, its genetic diversity and population structure should be characterized. Roche 454 pyrosequencing combined with magnetic bead enrichment was used to develop microsatellite markers for A. bidentata. A total of 903 microsatellite loci were identified from 42,004 individual sequence reads. One hundred microsatellite loci were selected to test the primer amplification efficiency across 16 individuals from two A. bidentata populations. Of these tested markers, 8 yielded polymorphic amplification products, 29 yielded single alleles. For polymorphic primer pairs, the number of alleles per locus ranged from 2 to 4, with an average of 2.75. The observed and expected heterozygosities ranged from 0.353 to 0.671 and 0.250 to 0.938, respectively. The inbreeding coefficient varied from −0.692 to 0.627. This set of markers will provide useful tools for examining genetic diversity and population structure, and aid in better understanding of the conservation of A. bidentata.     

Microsatellite variation in the pinewood nematode, Bursaphelenchus xylophilus (Steiner and Buhrer) Nickle in South Korea

The pinewood nematode Bursaphelenchus xylophilus is the causative agent of pine wilt disease, which has caused heavy economic losses to the South Korean forest industry. In this study, we investigated the genetic variation among South Korean pinewood nematodes using newly developed microsatellite loci. In order to ensure sufficient templates for the amplification of multiple loci required for individual identification, we employed an amplifying step of restricted fragments during the microsatellite development procedure. We found atypical genetic patterns in this non-native pest species: high allelic diversity and population structure. The large number of alleles may be the result of continuous and/or large-scaled introduction, which apparently went unnoticed before the first official report of pine wilt disease in Korea in 1998, or may come from gene pools of closely related species through genetic introgression after hybridization. Ecological properties of this species, such as a vector-mediated life cycle, may have contributed to its population structure, which may be enhanced by governmental efforts to prevent dispersal of this disease. As a geographic population structure was not observed, geographic patterns of genetic variation appear to be more affected by anthropogenic mediation than by natural dispersion through vector insects. And genotypes of Korean populations were compared to genotypes found in neighboring countries such as China and Japan.     

Isolation and characterization of microsatellite loci for the analysis of genetic diversity in Whitmania pigra

The objective of this study was to isolate microsatellite loci to analyze the genetic diversity of Whitmania pigra. Four new microsatellite markers of W. pigra were developed from an enriched library and ten from a modified SAMPL assay. A total of 127 alleles were detected, with an average of 9.1 alleles per locus. The expected heterozygosity (He) of each microsatellite locus varied from 0.451 to 0.857, with an average of 0.688. The polymorphism information content (PIC) of each microsatellite locus ranged from 0.361 to 0.838, with an average of 0.640. Analysis of molecular variance showed that the main variation component existed within the populations (81.64%) rather than among the populations (18.36%). Phylogenetic tree for 15 populations of Hirudo using the NJ method by MEGA 5.1 software were divided into two major clusters. These microsatellite markers will contribute to research on the individual identification, genetic diversity, population structure, genome mapping and conservation biology of Hirudo.     

Genetic diversity of Chinese giant salamander (Andrias davidianus) based on the novel microsatellite markers

Chinese giant salamander (Andrias davidianus) is a rare amphibian species in the world. Microsatellite markers are a promising tool for accurate estimation population structure and genetic diversity. In this paper, we isolated novel microsatellite marker for Chinese giant salamander using fast isolation by AFLP of sequences containing repeats (FIASCO) method. More than 50% sequences in 132 clones had repeat number over ten times with di or trinucleeotide repeat except of (GA)₁₂. Seventy pairs of primers were designed and eleven polymorphic microsatellite loci were characterized for wild and cultivated Chinese giant salamander populations. The allele number was from 3 to 9 in different loci. Polymorphism information content was from 0.544 to 0.702 in cultivated population. The results implied more alleles and PIC were in the wild population than cultivated population. The observed heterozygosities in two populations were higher than 0.553. The data analysis suggested that the cultivated population has lower genetic diversity than wild population, which it??s perhaps owing to inbreeding in artificial breeding. To our knowledge, it??s the first time to isolated microsatellite markers for Chinese giant salamander. The result indicated that the markers were suitable for the population genetic analysis of Chinese giant salamander.