Transcriptome sequencing, and rapid development and application of SNP markers for the legume pod borer Maruca vitrata (Lepidoptera: Crambidae)

Authors: MARGAM, VENU - Purdue University; Coates, Brad; Bayles, Darrell; Hellmich Ii, Richard; AGUNBIADE, TOLULOPE - University Of Illinois; SEUFFERHELD, MANFREDO - University Of Illinois; SUN, WEILIN - University Of Illinois; Kroemer, Jeremy; BA, MALICK - Institute Of Environmental And Agricultural Research - Burkina Faso (FORMERLY: UPPER VOLTA); BINSO-DABIRE, CLEMENTINE - Institute Of Environmental And Agricultural Research - Burkina Faso (FORMERLY: UPPER VOLTA); BAOUA, IBRAHIM - Institut National De La Recherche Agronomique Du Niger (INRAN); ISHIYAKU, MOHAMMAD - Ahmadu Bello University; COVAS, FERNANDO - University Of Puerto Rico; SRINIVASAN, RAMASAMY - The World Vegetable Center (AVRDC) - Taiwan; ARMSTRONG, JOEL - Commonwealth Scientific And Industrial Research Organisation (CSIRO); MURDOCK, LARRY - Purdue University; PITTENDRIGH, BARRY - University Of Illinois

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/26/2011
Publication Date: 7/6/2011
Citation: Margam, V.M., Coates, B.S., Bayles, D.O., Hellmich II, R.L., Agunbiade, T., Seufferheld, M.J., Sun, W., Kroemer, J.A., Ba, M.N., Binso-Dabire, C.L., Baoua, I., Ishiyaku, M.F., Covas, F.G., Srinivasan, R., Armstrong, J., Murdock, L.L., Pittendrigh, B.R. 2011. Transcriptome sequencing, and rapid development and application of SNP markers for the legume pod borer Maruca vitrata (Lepidoptera: Crambidae). PLoS One. 6(7):e21388.

Interpretive Summary: The moth larvae that are pests of fruit- and seed-bearing crops threaten producer viability and contribute to food shortages worldwide. Controlling these pest insects in developing nations and within sub-tropical regions of the United States is especially difficult due to long crop growing seasons and multiple generations of the pests. Understanding insect pest biology and ecology will help scientists to develop ecologically sound methods for managing insect resistance to transgenic crops. This includes cowpea that expresses insecticidal toxins from Bacillus thuringiensis (Bt). We developed genetic markers from random mutations at single nucleotide positions within the genome of the legume pod borer, and applied these markers to estimate the level of genetic differences between populations. These results will be useful to all scientists, particularly in developing countries, interested in understanding insect population genetics before using transgenic crops to control pests.

Technical Abstract: The legume pod borer, Maruca vitrata (Lepidoptera: Crambidae), is an insect pest species that is destructive to crops grown by subsistence farmers in tropical regions of West Africa. We present the de novo assembly of 3729 contigs from 454- and Sanger-derived sequencing reads for midgut, salivary, and whole adult tissues of this non-model species. Functional annotation predicted that 1320 M. vitrata protein coding genes are present, of which 631 were shown to have orthologs within the Bombyx mori gene model. A homology-based analysis initially resulted in assignment of M. vitrata genes into group of paralogs, but were subsequently partitioned into putative orthologs following phylogenetic analyses. Following sequence quality filtering, a total of 1542 putative single nucleotide polymorphisms (SNPs) were predicted within M. vitrata contig assemblies. Seventy-one of 1078 designed molecular genetic markers were used to screen M. vitrata samples from five collection sites in West Africa, and results indicated that population substructure may be present, which has important implications for managing this insect’s resistance to transgenic cowpea that express Bacillus thuringiensis crystalline toxins. This study shows that mutation data derived from transcriptome sequencing data is an expeditious and economical source for genetic marker development that allows evaluation of ecological differentiation.