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Margam VM, Coates BS, Bayles DO, Hellmich RL, Agunbiade T, Seufferheld MJ, Sun W, Kroemer JA, Ba MN, Binso-Dabire CL, Baoua I, Ishiyaku MF, Covas FG, Srinivasan R, Armstrong J, Murdock LL, Pittendrigh BR. Transcriptome sequencing, and rapid development and application of SNP markers for the legume pod borer Maruca vitrata (Lepidoptera: Crambidae). PLoS One 2011; 6:e21388. [PMID: 21754987 PMCID: PMC3130784 DOI: 10.1371/journal.pone.0021388] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Accepted: 05/26/2011] [Indexed: 01/31/2023] Open
Abstract
The legume pod borer, Maruca vitrata (Lepidoptera: Crambidae), is an insect pest species of crops grown by subsistence farmers in tropical regions of 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 have orthologs within the Bombyx mori gene model. A homology-based analysis assigned M. vitrata genes into a group of paralogs, but these 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. Population substructure may be present with significant implications in the insect resistance management recommendations pertaining to the release of biological control agents or transgenic cowpea that express Bacillus thuringiensis crystal toxins. Mutation data derived from transcriptome sequencing is an expeditious and economical source for genetic markers that allow evaluation of ecological differentiation.
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Affiliation(s)
- Venu M. Margam
- Department of Entomology, Purdue University, West Lafayette, Indiana, United States of America
| | - Brad S. Coates
- United States Department of Agriculture – Agricultural Research Service, Corn Insect and Crop Genetics Research Unit, Genetics Laboratory, Iowa State University, Ames, Iowa, United States of America
| | - Darrell O. Bayles
- United States Department of Agriculture – Agricultural Research Service, Corn Insect and Crop Genetics Research Unit, Genetics Laboratory, Iowa State University, Ames, Iowa, United States of America
| | - Richard L. Hellmich
- United States Department of Agriculture – Agricultural Research Service, Corn Insect and Crop Genetics Research Unit, Genetics Laboratory, Iowa State University, Ames, Iowa, United States of America
| | - Tolulope Agunbiade
- Department of Entomology, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
| | - Manfredo J. Seufferheld
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
| | - Weilin Sun
- Department of Entomology, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
| | - Jeremy A. Kroemer
- United States Department of Agriculture – Agricultural Research Service, Corn Insect and Crop Genetics Research Unit, Genetics Laboratory, Iowa State University, Ames, Iowa, United States of America
| | - Malick N. Ba
- Institut de l'Environnement et de Recherches Agricoles (INERA), Station de Kamboinsé, Ouagadougou, Burkina Faso
| | - Clementine L. Binso-Dabire
- Institut de l'Environnement et de Recherches Agricoles (INERA), Station de Kamboinsé, Ouagadougou, Burkina Faso
| | - Ibrahim Baoua
- Institut National de Recherche Agronomique du Niger, Maradi, Niger
| | - Mohammad F. Ishiyaku
- Department of Plant Science, Institute for Agricultural Research, Ahmadu Bello University, Zaria, Nigeria
| | | | | | - Joel Armstrong
- Ecosystem Sciences, The Commonwealth Scientific and Industrial Research Organization, Black Mountain, Australian Capital Territory, Australia
| | - Larry L. Murdock
- Department of Entomology, Purdue University, West Lafayette, Indiana, United States of America
| | - Barry R. Pittendrigh
- Department of Entomology, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
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Weller JI, Ron M. Invited review: quantitative trait nucleotide determination in the era of genomic selection. J Dairy Sci 2011; 94:1082-90. [PMID: 21338774 DOI: 10.3168/jds.2010-3793] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Accepted: 11/09/2010] [Indexed: 12/24/2022]
Abstract
Genome-wide association studies based on tens of thousands of single nucleotide polymorphisms have been completed for several dairy cattle populations. Methods have been proposed to directly incorporate genome scan data into breeding programs, chiefly by selection of young sires based on their genotypes for the genetic markers and pedigree without progeny test. Thus, the rate of genetic gain is increased by reduction of the mean generation interval. The methods developed so far for application of genomic selection do not require identification of the actual quantitative trait nucleotides (QTN) responsible for the observed variation of quantitative trait loci (QTL). To date, 2 QTN affecting milk production traits have been detected in dairy cattle: DGAT1 and ABCG2. This review will attempt to address the following questions based on the current state of bovine genomics and statistics. What are the pros and cons for QTN determination? How can data obtained from high-density, genome-wide scans be used most efficiently for QTN determination? Can the genome scan results already available and next-generation sequencing data be used to determine QTN? Should QTN be treated differently than markers at linkage disequilibrium with QTL in genetic evaluation programs? Data obtained by genome-wide association studies can be used to deduce QTL genotypes of sires via application of the a posteriori granddaughter design for concordance testing of putative QTN. This, together with next-generation sequencing technology, will dramatically reduce costs for QTN determination. By complete genome sequencing of 21 sires with many artificial insemination sons, it should be possible to determine concordance for all potential QTN, thus establishing the field of QTNomics.
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Affiliation(s)
- J I Weller
- Institute of Animal Sciences, A.R.O., The Volcani Center, Bet Dagan 50250, Israel.
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