title: 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.
authors.affiliation: Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.|Beijing Key Laboratory for Forest Pest Control, College of Forestry, Beijing Forestry University, Beijing 100083, China.
authors.forename: Li-Jun
authors.initials: LJ
authors.lastname: Cao
authors.affiliation: Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
authors.forename: Ze-Min
authors.initials: ZM
authors.lastname: Li
authors.affiliation: Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
authors.forename: Ze-Hua
authors.initials: ZH
authors.lastname: Wang
authors.affiliation: Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
authors.forename: Liang
authors.initials: L
authors.lastname: Zhu
authors.affiliation: Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
authors.forename: Ya-Jun
authors.initials: YJ
authors.lastname: Gong
authors.affiliation: Beijing Key Laboratory for Forest Pest Control, College of Forestry, Beijing Forestry University, Beijing 100083, China.
authors.forename: Min
authors.initials: M
authors.lastname: Chen
authors.affiliation: Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
authors.forename: Shu-Jun
authors.initials: SJ
authors.lastname: Wei
mesh_terms: D000818:Animals; D017931:DNA Primers / Q000032:analysis; D005828:Genetics, Population; D059014:High-Throughput Nucleotide Sequencing; D015810:Linkage Disequilibrium; D018895:Microsatellite Repeats; D020641:Polymorphism, Single Nucleotide; D061149:Thysanoptera / Q000235:genetics*
chemical_list: D017931:DNA Primers