Dataset Information

Bulk development and stringent selection of microsatellite markers in the western flower thrips Frankliniella occidentalis.

ABSTRACT: Recent improvements in next-generation sequencing technologies have enabled investigation of microsatellites on a genome-wide scale. Faced with a huge amount of candidates, the use of appropriate marker selection criteria is crucial. Here, we used the western flower thrips Frankliniella occidentalis for an empirical microsatellite survey and validation; 132,251 candidate microsatellites were identified, 92,102 of which were perfect. Dinucleotides were the most abundant category, while (AG)n was the most abundant motif. Sixty primer pairs were designed and validated in two natural populations, of which 30 loci were polymorphic, stable, and repeatable, but not all in Hardy-Weinberg equilibrium (HWE) and linkage equilibrium. Four marker panels were constructed to understand effect of marker selection on population genetic analyses: (i) only accept loci with single nucleotide insertions (SNI); (ii) only accept the most polymorphic loci (MP); (iii) only accept loci that did not deviate from HWE, did not show SNIs, and had unambiguous peaks (SS) and (iv) all developed markers (ALL). Although the MP panel resulted in microsatellites of highest genetic diversity followed by the SNI, the SS performed best in individual assignment. Our study proposes stringent criteria for selection of microsatellites from a large-scale number of genomic candidates for population genetic studies.

SUBMITTER: Cao LJ

PROVIDER: S-EPMC4873785 | biostudies-literature | 2016 May

REPOSITORIES: biostudies-literature

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Bulk development and stringent selection of microsatellite markers in the western flower thrips Frankliniella occidentalis.

Cao Li-Jun LJ Li Ze-Min ZM Wang Ze-Hua ZH Zhu Liang L Gong Ya-Jun YJ Chen Min M Wei Shu-Jun SJ

Scientific reports 20160520

Recent improvements in next-generation sequencing technologies have enabled investigation of microsatellites on a genome-wide scale. Faced with a huge amount of candidates, the use of appropriate marker selection criteria is crucial. Here, we used the western flower thrips Frankliniella occidentalis for an empirical microsatellite survey and validation; 132,251 candidate microsatellites were identified, 92,102 of which were perfect. Dinucleotides were the most abundant category, while (AG)n was ...[more]

PMID: 27197749

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Project description:Western flower thrips (WFT) is one of the most important pests of horticultural crops worldwide because it can damage many different crops and transmit various plant viruses. Given these significant impacts on plant production, novel methodologies are required to maximize regulation of WFT to minimize crop losses. One particular approach is to develop control strategies for the non-feeding, soil-dwelling stages of WFT. Control of these stages could be enhanced through the use of granules impregnated with entomopathogenic fungi mixed in the soil. The use of soil-applied fungi contrasts with existing approaches in which entomopathogenic fungi are formulated as oil-based suspensions or water-based wettable powders for foliar applications against the feeding stages of WFT. To examine the efficacy of this approach, we evaluated the effects of a granular formulation of Beauveria bassiana on the soil-dwelling, pupal phases of Frankliniella occidentalis in laboratory bioassays and greenhouse experiments. Based on micromorphological observations of fungal conidia during the infection process after treatment of WFT with a B. bassiana suspension, fungal conidia complete the process of surface attachment, germination, and penetration of the body wall of the WFT pupa and enter the host within 60 h of treatment. Given these results, we undertook a controlled greenhouse experiment and applied B. bassiana granules to soil used to cultivate eggplants. Populations of F. occidentalis on eggplants grown in treated soil were 70% lower than those on plants grown in the untreated soil after 8 weeks. Furthermore, when measuring the survival and growth of B. bassiana on granules under different soil moisture conditions, survival was greatest when the soil moisture content was kept at 20%. These results indicate that the application of B. bassiana-impregnated granules could prove to be an effective biological control strategy for use against F. occidentalis under greenhouse conditions.

Project description:Using RT-PCR and RACE-PCR strategies, we cloned and identified a new chemosensory protein (FoccCSP) from the Western flower thrips, Frankliniella occidentalis, a species for which no chemosensory protein (CSP) has yet been identified. The FoccCSP gene contains a 387 bp open-reading frame encoding a putative protein of 128 amino acids with a molecular weight of 14.51 kDa and an isoelectric point of 5.41. The deduced amino acid sequence contains a putative signal peptide of 19 amino acid residues at the N-terminus, as well as the typical four-cysteine signature found in other insect CSPs. As FoccCSP is from a different order of insect than other known CSPs, the GenBank FoccCSP homolog showed only 31-50% sequence identity with them. A neighbor-joining tree was constructed and revealed that FoccCSP is in a group with CSPs from Homopteran insects (e.g., AgosCSP4, AgosCSP10, ApisCSP, and NlugCSP9), suggesting that these genes likely developed from a common ancestral gene. The FoccCSP gene expression profile of different tissues and development stages was measured by quantitative real-time PCR. The results of this analysis revealed this gene is predominantly expressed in the antennae and also highly expressed in the first instar nymph, suggesting a function for FoccCSP in olfactory reception and in particular life activities during the first instar nymph stage. We expressed recombinant FoccCSP protein in a prokaryotic expression system and purified FoccCSP protein by affinity chromatography using a Ni-NTA-Sepharose column. Using N-phenyl-1-naphthylamine (1-NPN) as a fluorescent probe in fluorescence-based competitive binding assay, we determined the binding affinities of 19 volatile substances for FoccCSP protein. This analysis revealed that anisic aldehyde, geraniol and methyl salicylate have high binding affinities for FoccCSP, with KD values of 10.50, 15.35 and 35.24 μM, respectively. Thus, our study indicates that FoccCSP may play an important role in regulating the development of the first instar nymph and mediate F. occidentalis host recognition.

Dataset Information

Bulk development and stringent selection of microsatellite markers in the western flower thrips Frankliniella occidentalis.

Publications

Bulk development and stringent selection of microsatellite markers in the western flower thrips Frankliniella occidentalis.

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