TSPmap, a tool making use of traveling salesperson problem solvers in the efficient and accurate construction of high-density genetic linkage maps
Abstract
Recent advances in nucleic acid sequencing technologies have led to a dramatic increase in the number of markers available to generate genetic linkage maps. This increased marker density can be used to improve genome assemblies as well as add much needed resolution for loci controlling variation in ecologically and agriculturally important traits. However, traditional genetic map construction methods from these large marker datasets can be computationally prohibitive and highly error prone. We present TSPmap, a method which implements both approximate and exact Traveling Salesperson Problem solvers to generate linkage maps. We demonstrate that for datasets with large numbers of genomic markers (e.g. 10,000) and in multiple population types generated from inbred parents, TSPmap can rapidly produce high quality linkage maps with low sensitivity to missing and erroneous genotyping data compared to two other benchmark methods, JoinMap and MSTmap. TSPmap is open source and freely available as an R package. With the advancement of low cost sequencing technologies, the number of markers used in the generation of genetic maps is expected to continue to rise. TSPmap will be a useful tool to handle such large datasets into the future, quickly producing high quality maps using a large number of genomic markers.
- Authors:
- Publication Date:
- Research Org.:
- Colorado State Univ., Fort Collins, CO (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); National Science Foundation (NSF); USDA National Inst. of Food and Agriculture (NIFA)
- OSTI Identifier:
- 1618579
- Alternate Identifier(s):
- OSTI ID: 1502978
- Grant/Contract Number:
- SC0012459; FG02-08ER64629; DEB-1556262; 2014–38420-21801
- Resource Type:
- Published Article
- Journal Name:
- BioData Mining
- Additional Journal Information:
- Journal Name: BioData Mining Journal Volume: 10 Journal Issue: 1; Journal ID: ISSN 1756-0381
- Publisher:
- Springer Science + Business Media
- Country of Publication:
- United Kingdom
- Language:
- English
- Subject:
- 97 MATHEMATICS AND COMPUTING; 59 BASIC BIOLOGICAL SCIENCES; genetic mapping; linkage; travelling salesperson problem; genomic markers; next generation sequencing; genotyping by sequencing
Citation Formats
Monroe, J. Grey, Allen, Zachariah A., Tanger, Paul, Mullen, Jack L., Lovell, John T., Moyers, Brook T., Whitley, Darrell, and McKay, John K. TSPmap, a tool making use of traveling salesperson problem solvers in the efficient and accurate construction of high-density genetic linkage maps. United Kingdom: N. p., 2017.
Web. doi:10.1186/s13040-017-0158-0.
Monroe, J. Grey, Allen, Zachariah A., Tanger, Paul, Mullen, Jack L., Lovell, John T., Moyers, Brook T., Whitley, Darrell, & McKay, John K. TSPmap, a tool making use of traveling salesperson problem solvers in the efficient and accurate construction of high-density genetic linkage maps. United Kingdom. https://doi.org/10.1186/s13040-017-0158-0
Monroe, J. Grey, Allen, Zachariah A., Tanger, Paul, Mullen, Jack L., Lovell, John T., Moyers, Brook T., Whitley, Darrell, and McKay, John K. Tue .
"TSPmap, a tool making use of traveling salesperson problem solvers in the efficient and accurate construction of high-density genetic linkage maps". United Kingdom. https://doi.org/10.1186/s13040-017-0158-0.
@article{osti_1618579,
title = {TSPmap, a tool making use of traveling salesperson problem solvers in the efficient and accurate construction of high-density genetic linkage maps},
author = {Monroe, J. Grey and Allen, Zachariah A. and Tanger, Paul and Mullen, Jack L. and Lovell, John T. and Moyers, Brook T. and Whitley, Darrell and McKay, John K.},
abstractNote = {Recent advances in nucleic acid sequencing technologies have led to a dramatic increase in the number of markers available to generate genetic linkage maps. This increased marker density can be used to improve genome assemblies as well as add much needed resolution for loci controlling variation in ecologically and agriculturally important traits. However, traditional genetic map construction methods from these large marker datasets can be computationally prohibitive and highly error prone. We present TSPmap, a method which implements both approximate and exact Traveling Salesperson Problem solvers to generate linkage maps. We demonstrate that for datasets with large numbers of genomic markers (e.g. 10,000) and in multiple population types generated from inbred parents, TSPmap can rapidly produce high quality linkage maps with low sensitivity to missing and erroneous genotyping data compared to two other benchmark methods, JoinMap and MSTmap. TSPmap is open source and freely available as an R package. With the advancement of low cost sequencing technologies, the number of markers used in the generation of genetic maps is expected to continue to rise. TSPmap will be a useful tool to handle such large datasets into the future, quickly producing high quality maps using a large number of genomic markers.},
doi = {10.1186/s13040-017-0158-0},
journal = {BioData Mining},
number = 1,
volume = 10,
place = {United Kingdom},
year = {Tue Dec 19 00:00:00 EST 2017},
month = {Tue Dec 19 00:00:00 EST 2017}
}
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1186/s13040-017-0158-0
https://doi.org/10.1186/s13040-017-0158-0
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 13 works
Citation information provided by
Web of Science
Web of Science
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Construction of integrated genetic linkage maps by means of a new computer package: Join Map
journal, May 1993
- Stam, Piet
- The Plant Journal, Vol. 3, Issue 5
A successful algorithm for the undirected Hamiltonian path problem
journal, February 1985
- Thompson, Gerald L.; Singhal, Sharad
- Discrete Applied Mathematics, Vol. 10, Issue 2
Single nucleotide polymorphism genotyping using Kompetitive Allele Specific PCR (KASP): overview of the technology and its application in crop improvement
journal, July 2013
- Semagn, Kassa; Babu, Raman; Hearne, Sarah
- Molecular Breeding, Vol. 33, Issue 1
An Ultra-High-Density, Transcript-Based, Genetic Map of Lettuce
journal, March 2013
- Truco, Maria José; Ashrafi, Hamid; Kozik, Alexander
- G3: Genes|Genomes|Genetics, Vol. 3, Issue 4
R/qtl: QTL mapping in experimental crosses
journal, May 2003
- Broman, K. W.; Wu, H.; Sen, S.
- Bioinformatics, Vol. 19, Issue 7
Genetic mapping of adaptation reveals fitness tradeoffs in Arabidopsis thaliana
journal, December 2013
- Agren, J.; Oakley, C. G.; McKay, J. K.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 52
An ultradense genetic recombination map for Brassica napus, consisting of 13551 SRAP markers
journal, April 2007
- Sun, Zudong; Wang, Zining; Tu, Jinxing
- Theoretical and Applied Genetics, Vol. 114, Issue 8
An Effective Heuristic Algorithm for the Traveling-Salesman Problem
journal, April 1973
- Lin, S.; Kernighan, B. W.
- Operations Research, Vol. 21, Issue 2
The linear arrangement of six sex-linked factors in Drosophila, as shown by their mode of association
journal, January 1913
- Sturtevant, A. H.
- Journal of Experimental Zoology, Vol. 14, Issue 1
A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species
journal, May 2011
- Elshire, Robert J.; Glaubitz, Jeffrey C.; Sun, Qi
- PLoS ONE, Vol. 6, Issue 5, Article No. e19379
A rapid marker ordering approach for high-density genetic linkage maps in experimental autotetraploid populations using multidimensional scaling
journal, August 2016
- Preedy, K. F.; Hackett, C. A.
- Theoretical and Applied Genetics, Vol. 129, Issue 11
Field-based high throughput phenotyping rapidly identifies genomic regions controlling yield components in rice
journal, February 2017
- Tanger, Paul; Klassen, Stephen; Mojica, Julius P.
- Scientific Reports, Vol. 7, Issue 1
AntMap: Constructing Genetic Linkage Maps Using an Ant Colony Optimization Algorithm
journal, January 2006
- Iwata, Hiroyoshi; Ninomiya, Seishi
- Breeding Science, Vol. 56, Issue 4
A second generation SNP and SSR integrated linkage map and QTL mapping for the Chinese mitten crab Eriocheir sinensis
journal, January 2017
- Qiu, Gao-Feng; Xiong, Liang-Wei; Han, Zhi-Ke
- Scientific Reports, Vol. 7, Issue 1
Efficient and Accurate Construction of Genetic Linkage Maps from the Minimum Spanning Tree of a Graph
journal, October 2008
- Wu, Yonghui; Bhat, Prasanna R.; Close, Timothy J.
- PLoS Genetics, Vol. 4, Issue 10
Computational approaches and software tools for genetic linkage map estimation in plants
journal, November 2009
- Cheema, J.; Dicks, J.
- Briefings in Bioinformatics, Vol. 10, Issue 6
Development of a 10,000 Locus Genetic Map of the Sunflower Genome Based on Multiple Crosses
journal, July 2012
- Bowers, John E.; Bachlava, Eleni; Brunick, Robert L.
- G3: Genes|Genomes|Genetics, Vol. 2, Issue 7
Construction of multilocus genetic linkage maps in humans.
journal, April 1987
- Lander, E. S.; Green, P.
- Proceedings of the National Academy of Sciences, Vol. 84, Issue 8
Integration of Solexa sequences on an ultradense genetic map in Brassica rapa L.
journal, May 2011
- Li, Wei; Zhang, Jiefu; Mou, Yanglong
- BMC Genomics, Vol. 12, Issue 1
High-throughput SNP genotyping with the GoldenGate assay in maize
journal, October 2009
- Yan, Jianbing; Yang, Xiaohong; Shah, Trushar
- Molecular Breeding, Vol. 25, Issue 3
Works referencing / citing this record:
QTL × environment interactions underlie adaptive divergence in switchgrass across a large latitudinal gradient
journal, June 2019
- Lowry, David B.; Lovell, John T.; Zhang, Li
- Proceedings of the National Academy of Sciences, Vol. 116, Issue 26
De Novo Genome Assembly of Populus simonii Further Supports That Populus simonii and Populus trichocarpa Belong to Different Sections
journal, December 2019
- Wu, Hainan; Yao, Dan; Chen, Yuhua
- G3: Genes|Genomes|Genetics, Vol. 10, Issue 2
Tools for Genetic Studies in Experimental Populations of Polyploids
journal, April 2018
- Bourke, Peter M.; Voorrips, Roeland E.; Visser, Richard G. F.
- Frontiers in Plant Science, Vol. 9