Characterization And Isolation Of Microsatellites From The Plutella Xylostella Transcriptome

The diamondback moth (DBM), Plutella xylostella, which is well-known for its migratory capacity and resistance to almost all applicable insecticides, has caused tremendous social and economic losses and become one of the most difficult pests to eliminate or control around the world. Thus, obtaining comprehensive knowledge of the genetic variations and mechanisms of resistance present in this species is of great importance for the development of cost-effective management strategies for this pest. Here, we characterized and isolated simple sequence repeats (SSRs) based on transcriptome data of P. xylostella. We identified 11,280 SSRs from a total of 171,262 non-redundant sequences, with an average density of one SSR in every 8.9 kb of the EST sequence being observed. Mono-nucleotide motifs were the most abundant type of SSR, accounting for 56% of the identified SSRs, followed by tri-and di-nucleotide repeats, accounting for 30% and 11%, respectively. Mapping analysis showed that 424 of the SSR loci were located in CDS regions, while 390 and 374 loci were located at the 3’-UTR and 5’-UTR, respectively.35 microsatellite loci isolated from a total of 281 SSR primer pairs and 27 (11%) successfully amplified SSR markers showed polymorphism, while none of which showed cross-species amplification. Nine of the polymorphic loci were used in population genetic analysis, in which 8 polymorphic markers were found to be in Hardy-Weinberg equilibrium with a wild population and showed numbers of alleles ranging from 4 to 8. For the null alleles commonly observed in our analysis as well as for SNPs in flanking regions, the low isolation efficiency can be explained, at least in part, by the polymorphic nature of Lepidopteran genomes. The obtained set of polymorphic EST-SSRs will be used in gene mapping and population genetic analyses, which are vital to understand the resistance and migration of the diamondback moth.