ARS | Publication request: High-throughput transcriptome sequencing for SNP and gene discovery in a moth

Submitted to: Environmental Entomology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: May 24, 2012
Publication Date: August 1, 2012
Citation: Miller, N.J., Sun, J., Sappington, T.W. 2012. High-throughput transcriptome sequencing for SNP and gene discovery in a moth. Environmental Entomology. 41(4):997-1007.

Interpretive Summary: The western bean cutworm is a pest of corn and dry beans that used to be confined to the Great Plains. However, it underwent a dramatic range expansion in North America during the first decade of the 21st century, and is now a serious pest of corn throughout the Midwest. The reason for its spread are unknown, and other important aspects of its ecology and population dynamics are poorly understood. Population genetics research could provide important information to improve management of this species, but has been hindered by a lack of genetic markers. Identifying and developing traditional genetic markers for a species that has not been studied much previously, like the western bean cutworm, is time-consuming and expensive. In this study, relatively new sequencing-by-synthesis technology (so-called second generation sequencing) was used in a novel way to economically develop 71 genetic markers that are suitable for population studies. This work not only provides significant genetic resources for future research on western bean cutworm, but demonstrates the power of applying second-generation sequencing to previously under-studied species. This information will be used by university, government, and industry scientists who study western bean cutworm, and all researchers around the globe who face the same problem of needing to develop markers for a little-studied species, regardless of whether it is an insect or any other kind of organism.

Technical Abstract: The western bean cutworm, Striacosta albicosta (Smith) (Leptidoptera: Noctuidae) is a pest of corn and dry beans that underwent a dramatic range expansion in North America during the first decade of the 21st century. Research into the population genetics of this species has been hindered by a lack of genetic markers. The transcriptome of adult male S. albicosta was partially sequenced using Illumina sequencing-by-synthesis. Assembly of the sequence reads yielded 16,847 transcript sequences, of which 6,631 could be assigned a putative function. A search for single nucleotide polymorphisms (SNPs) identified 2,487 candidate SNPs distributed among 1,265 transcripts. A panel of 108 candidate SNPs was selected for empirical testing, of which 66% proved to be assayable polymorphisms that are suitable for population studies. This work provides significant genetic resources for studying S. albicosta and demonstrates the power of applying second-generation sequencing to previously under-studied species.