A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome
Abstract
Polyploid species have long been thought to be recalcitrant to whole-genome assembly. By combining high-throughput sequencing, recent developments in parallel computing, and genetic mapping, we derive, de novo, a sequence assembly representing 9.1 Gbp of the highly repetitive 16 Gbp genome of hexaploid wheat, Triticum aestivum, and assign 7.1 Gb of this assembly to chromosomal locations. The genome representation and accuracy of our assembly is comparable or even exceeds that of a chromosome-by-chromosome shotgun assembly. Our assembly and mapping strategy uses only short read sequencing technology and is applicable to any species where it is possible to construct a mapping population.
- Authors:
-
- Department of Energy Joint Genome Institute, Walnut Creek, CA (United States)
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben (Germany)
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)
- Univ. of California, Berkeley, CA (United States)
- Department of Energy Joint Genome Institute, Walnut Creek, CA (United States); HudsonAlpha Institute of Biotechnology, Huntsville, AL (United States)
- Kansas State Univ., Manhattan, KS (United States); South Dakota State Univ., Brookings, SD (United States)
- Univ. of Dundee & The James Hutton Institute, Dundee (United Kingdom)
- Kansas State Univ., Manhattan, KS (United States)
- Univ. of Minnesota, St. Paul, MN (United States)
- Department of Energy Joint Genome Institute, Walnut Creek, CA (United States); Univ. of California, Berkeley, CA (United States)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1256489
- Alternate Identifier(s):
- OSTI ID: 1524013
- Grant/Contract Number:
- AC02-05CH11231; SC0008700
- Resource Type:
- Accepted Manuscript
- Journal Name:
- GenomeBiology.com
- Additional Journal Information:
- Journal Volume: 16; Journal Issue: 1; Journal ID: ISSN 1465-6906
- Publisher:
- BioMed Central
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Chapman, Jarrod A., Mascher, Martin, Buluc, Aydin, Barry, Kerrie, Georganas, Evangelos, Session, Adam, Strnadova, Veronika, Jenkins, Jerry, Sehgal, Sunish, Oliker, Leonid, Schmutz, Jeremy, Yelick, Katherine A., Scholz, Uwe, Waugh, Robbie, Poland, Jesse A., Muehlbauer, Gary J., Stein, Nils, and Rokhsar, Daniel S. A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome. United States: N. p., 2015.
Web. doi:10.1186/s13059-015-0582-8.
Chapman, Jarrod A., Mascher, Martin, Buluc, Aydin, Barry, Kerrie, Georganas, Evangelos, Session, Adam, Strnadova, Veronika, Jenkins, Jerry, Sehgal, Sunish, Oliker, Leonid, Schmutz, Jeremy, Yelick, Katherine A., Scholz, Uwe, Waugh, Robbie, Poland, Jesse A., Muehlbauer, Gary J., Stein, Nils, & Rokhsar, Daniel S. A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome. United States. https://doi.org/10.1186/s13059-015-0582-8
Chapman, Jarrod A., Mascher, Martin, Buluc, Aydin, Barry, Kerrie, Georganas, Evangelos, Session, Adam, Strnadova, Veronika, Jenkins, Jerry, Sehgal, Sunish, Oliker, Leonid, Schmutz, Jeremy, Yelick, Katherine A., Scholz, Uwe, Waugh, Robbie, Poland, Jesse A., Muehlbauer, Gary J., Stein, Nils, and Rokhsar, Daniel S. Sat .
"A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome". United States. https://doi.org/10.1186/s13059-015-0582-8. https://www.osti.gov/servlets/purl/1256489.
@article{osti_1256489,
title = {A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome},
author = {Chapman, Jarrod A. and Mascher, Martin and Buluc, Aydin and Barry, Kerrie and Georganas, Evangelos and Session, Adam and Strnadova, Veronika and Jenkins, Jerry and Sehgal, Sunish and Oliker, Leonid and Schmutz, Jeremy and Yelick, Katherine A. and Scholz, Uwe and Waugh, Robbie and Poland, Jesse A. and Muehlbauer, Gary J. and Stein, Nils and Rokhsar, Daniel S.},
abstractNote = {Polyploid species have long been thought to be recalcitrant to whole-genome assembly. By combining high-throughput sequencing, recent developments in parallel computing, and genetic mapping, we derive, de novo, a sequence assembly representing 9.1 Gbp of the highly repetitive 16 Gbp genome of hexaploid wheat, Triticum aestivum, and assign 7.1 Gb of this assembly to chromosomal locations. The genome representation and accuracy of our assembly is comparable or even exceeds that of a chromosome-by-chromosome shotgun assembly. Our assembly and mapping strategy uses only short read sequencing technology and is applicable to any species where it is possible to construct a mapping population.},
doi = {10.1186/s13059-015-0582-8},
journal = {GenomeBiology.com},
number = 1,
volume = 16,
place = {United States},
year = {Sat Jan 31 00:00:00 EST 2015},
month = {Sat Jan 31 00:00:00 EST 2015}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 184 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:
Reconstruction of the Synthetic W7984 × Opata M85 wheat reference population
journal, November 2011
- Sorrells, Mark E.; Gustafson, J. Perry; Somers, Daryl
- Genome, Vol. 54, Issue 11
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
RefSeq: an update on mammalian reference sequences
journal, November 2013
- Pruitt, Kim D.; Brown, Garth R.; Hiatt, Susan M.
- Nucleic Acids Research, Vol. 42, Issue D1
The Sequence of the Human Genome
journal, February 2001
- Venter, J. Craig; Adams, Mark D.; Myers, Eugene W.
- Science, Vol. 291, Issue 5507
Fast and accurate short read alignment with Burrows-Wheeler transform
journal, May 2009
- Li, H.; Durbin, R.
- Bioinformatics, Vol. 25, Issue 14
Nuclear DNA content of some important plant species
journal, August 1991
- Arumuganathan, K.; Earle, E. D.
- Plant Molecular Biology Reporter, Vol. 9, Issue 3
Sequence Polymorphism in Polyploid Wheat and Their D-Genome Diploid Ancestor
journal, June 2004
- Caldwell, Katherine S.; Dvorak, Jan; Lagudah, Evans S.
- Genetics, Vol. 167, Issue 2
The map-based sequence of the rice genome
journal, August 2005
- ,
- Nature, Vol. 436, Issue 7052, p. 793-800
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
journal, September 1997
- Altschul, Stephen F.; Madden, Thomas L.; Schäffer, Alejandro A.
- Nucleic Acids Research, Vol. 25, Issue 17, p. 3389-3402
Structural evolution of wheat chromosomes 4A, 5A, and 7B and its impact on recombination
journal, July 1995
- Devos, K. M.; Dubcovsky, J.; Dvořák, J.
- Theoretical and Applied Genetics, Vol. 91, Issue 2
A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome
journal, July 2014
- Mayer, K. F. X.; Rogers, J.; Dole el, J.
- Science, Vol. 345, Issue 6194
A Physical Map of the 1-Gigabase Bread Wheat Chromosome 3B
journal, October 2008
- Paux, E.; Sourdille, P.; Salse, J.
- Science, Vol. 322, Issue 5898
A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data
journal, September 2011
- Li, H.
- Bioinformatics, Vol. 27, Issue 21
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
Ent-kaurenoic acid oxidase genes in wheat
journal, August 2009
- Khlestkina, Elena K.; Kumar, Uttam; Röder, Marion S.
- Molecular Breeding, Vol. 25, Issue 2
Efficient and accurate clustering for large-scale genetic mapping
conference, November 2014
- Strnadova, Veronika; Buluc, Aydin; Chapman, Jarrod
- 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
The Norway spruce genome sequence and conifer genome evolution
journal, May 2013
- Nystedt, Björn; Street, Nathaniel R.; Wetterbom, Anna
- Nature, Vol. 497, Issue 7451
Genic regions of a large salamander genome contain long introns and novel genes
journal, January 2009
- Smith, Jeramiah J.; Putta, Srikrishna; Zhu, Wei
- BMC Genomics, Vol. 10, Issue 1
Basic local alignment search tool
journal, October 1990
- Altschul, Stephen F.; Gish, Warren; Miller, Webb
- Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410
Joint assembly and genetic mapping of the Atlantic horseshoe crab genome reveals ancient whole genome duplication
journal, May 2014
- Nossa, Carlos W.; Havlak, Paul; Yue, Jia-Xing
- GigaScience, Vol. 3, Issue 1
Development of High-Density Genetic Maps for Barley and Wheat Using a Novel Two-Enzyme Genotyping-by-Sequencing Approach
journal, February 2012
- Poland, Jesse A.; Brown, Patrick J.; Sorrells, Mark E.
- PLoS ONE, Vol. 7, Issue 2
The genome of the mesopolyploid crop species Brassica rapa
journal, August 2011
- Wang, Xiaowu; Wang, Hanzhong; Wang, Jun
- Nature Genetics, Vol. 43, Issue 10
The oyster genome reveals stress adaptation and complexity of shell formation
journal, September 2012
- Zhang, Guofan; Fang, Xiaodong; Guo, Ximing
- Nature, Vol. 490, Issue 7418
Analysis of the bread wheat genome using whole-genome shotgun sequencing
journal, November 2012
- Brenchley, Rachel; Spannagl, Manuel; Pfeifer, Matthias
- Nature, Vol. 491, Issue 7426
Crop genome sequencing: lessons and rationales
journal, February 2011
- Feuillet, Catherine; Leach, Jan E.; Rogers, Jane
- Trends in Plant Science, Vol. 16, Issue 2
Chromosome-based genomics in the cereals
journal, January 2007
- Doležel, Jaroslav; Kubaláková, Marie; Paux, Etienne
- Chromosome Research, Vol. 15, Issue 1
The B73 Maize Genome: Complexity, Diversity, and Dynamics
journal, November 2009
- Schnable, P. S.; Ware, D.; Fulton, R. S.
- Science, Vol. 326, Issue 5956, p. 1112-1115
The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences
journal, January 2010
- Kovach, Allen; Wegrzyn, Jill L.; Parra, Genis
- BMC Genomics, Vol. 11, Issue 1
The Sequence of the Human Genome
journal, September 2015
- Venter, J. Craig; Smith, Hamilton O.; Adams, Mark D.
- Clinical Chemistry, Vol. 61, Issue 9
Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars
journal, April 2013
- Cavanagh, C. R.; Chao, S.; Wang, S.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 20
Human Whole-Genome Shotgun Sequencing
journal, May 1997
- Weber, James L.; Myers, Eugene W.
- Genome Research, Vol. 7, Issue 5
Repbase Update, a database of eukaryotic repetitive elements
journal, January 2005
- Jurka, J.; Kapitonov, V. V.; Pavlicek, A.
- Cytogenetic and Genome Research, Vol. 110, Issue 1-4
Initial sequencing and comparative analysis of the mouse genome
journal, January 2002
- Consortium, Mouse Genome Sequencing
- Nature, Vol. 420, Issue 6915, p. 520-562
Mapping-by-sequencing accelerates forward genetics in barley
journal, January 2014
- Mascher, Martin; Jost, Matthias; Kuon, Joel-Elias
- Genome Biology, Vol. 15, Issue 6
TriFLDB: A Database of Clustered Full-Length Coding Sequences from Triticeae with Applications to Comparative Grass Genomics
journal, May 2009
- Mochida, Keiichi; Yoshida, Takuhiro; Sakurai, Tetsuya
- Plant Physiology, Vol. 150, Issue 3
Integration of mate pair sequences to improve shotgun assemblies of flow-sorted chromosome arms of hexaploid wheat
journal, January 2013
- Belova, Tatiana; Zhan, Bujie; Wright, Jonathan
- BMC Genomics, Vol. 14, Issue 1
Rapid Genome Mapping in Nanochannel Arrays for Highly Complete and Accurate De Novo Sequence Assembly of the Complex Aegilops tauschii Genome
journal, February 2013
- Hastie, Alex R.; Dong, Lingli; Smith, Alexis
- PLoS ONE, Vol. 8, Issue 2
Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome
journal, January 2011
- Saintenac, Cyrille; Jiang, Dayou; Akhunov, Eduard D.
- Genome Biology, Vol. 12, Issue 9
Sequence-based physical mapping of complex genomes by whole genome profiling
journal, February 2011
- van Oeveren, J.; de Ruiter, M.; Jesse, T.
- Genome Research, Vol. 21, Issue 4
Meraculous: De Novo Genome Assembly with Short Paired-End Reads
journal, August 2011
- Chapman, Jarrod A.; Ho, Isaac; Sunkara, Sirisha
- PLoS ONE, Vol. 6, Issue 8
A Whole-Genome Assembly of Drosophila
journal, March 2000
- Myers, E. W.
- Science, Vol. 287, Issue 5461
Genome size and the proportion of repeated nucleotide sequence DNA in plants
journal, October 1974
- Flavell, R. B.; Bennett, M. D.; Smith, J. B.
- Biochemical Genetics, Vol. 12, Issue 4
Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data
journal, May 2013
- Birol, Inanc; Raymond, Anthony; Jackman, Shaun D.
- Bioinformatics, Vol. 29, Issue 12
A Greedy Algorithm for Aligning DNA Sequences
journal, February 2000
- Zhang, Zheng; Schwartz, Scott; Wagner, Lukas
- Journal of Computational Biology, Vol. 7, Issue 1-2
Draft genome of the wheat A-genome progenitor Triticum urartu
journal, March 2013
- Ling, Hong-Qing; Zhao, Shancen; Liu, Dongcheng
- Nature, Vol. 496, Issue 7443
e!DAL - a framework to store, share and publish research data
journal, June 2014
- Arend, Daniel; Lange, Matthias; Chen, Jinbo
- BMC Bioinformatics, Vol. 15, Issue 1
Haplotype dictionary for the Rht-1 loci in wheat
journal, April 2013
- Wilhelm, Edward P.; Mackay, Ian J.; Saville, Robert J.
- Theoretical and Applied Genetics, Vol. 126, Issue 7
w7984_meraculous_scaffolds
collection, January 2014
- Mascher, Martin
- e!DAL - Plant Genomics and Phenomics Research Data Repository (PGP), IPK Gatersleben, Seeland OT Gatersleben, Corrensstraße 3, 06466, Germany
Cereal breeding takes a walk on the wild side
journal, January 2008
- Feuillet, Catherine; Langridge, Peter; Waugh, Robbie
- Trends in Genetics, Vol. 24, Issue 1
Paired-end sequencing of Fosmid libraries by Illumina
journal, July 2012
- Williams, L. J. S.; Tabbaa, D. G.; Li, N.
- Genome Research, Vol. 22, Issue 11
A High-Density Gene Map of Loblolly Pine ( Pinus taeda L.) Based on Exome Sequence Capture Genotyping
journal, November 2013
- Neves, Leandro Gomide; Davis, John M.; Barbazuk, William B.
- G3: Genes|Genomes|Genetics, Vol. 4, Issue 1
Whole-genome profiling and shotgun sequencing delivers an anchored, gene-decorated, physical map assembly of bread wheat chromosome 6A
journal, June 2014
- Poursarebani, Naser; Nussbaumer, Thomas; Šimková, Hana
- The Plant Journal, Vol. 79, Issue 2
Limitations of next-generation genome sequence assembly
journal, November 2010
- Alkan, Can; Sajjadian, Saba; Eichler, Evan E.
- Nature Methods, Vol. 8, Issue 1
Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ)
journal, October 2013
- Mascher, Martin; Muehlbauer, Gary J.; Rokhsar, Daniel S.
- The Plant Journal, Vol. 76, Issue 4
BEDTools: a flexible suite of utilities for comparing genomic features
journal, January 2010
- Quinlan, Aaron R.; Hall, Ira M.
- Bioinformatics, Vol. 26, Issue 6
A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor
journal, April 2013
- Luo, M. -C.; Gu, Y. Q.; You, F. M.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 19
Structural and functional partitioning of bread wheat chromosome 3B
journal, July 2014
- Choulet, F.; Alberti, A.; Theil, S.
- Science, Vol. 345, Issue 6194
Sequencing and Assembly of the 22-Gb Loblolly Pine Genome
journal, March 2014
- Zimin, Aleksey; Stevens, Kristian A.; Crepeau, Marc W.
- Genetics, Vol. 196, Issue 3
Sequencing, Assembling, and Correcting Draft Genomes Using Recombinant Populations
journal, February 2014
- Hahn, Matthew W.; Zhang, Simo V.; Moyle, Leonie C.
- G3: Genes|Genomes|Genetics, Vol. 4, Issue 4
Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond
journal, August 2013
- Mascher, Martin; Richmond, Todd A.; Gerhardt, Daniel J.
- The Plant Journal, Vol. 76, Issue 3
Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation
journal, March 2013
- Jia, Jizeng; Zhao, Shancen; Kong, Xiuying
- Nature, Vol. 496, Issue 7443
Application of Genotyping-by-Sequencing on Semiconductor Sequencing Platforms: A Comparison of Genetic and Reference-Based Marker Ordering in Barley
journal, October 2013
- Mascher, Martin; Wu, Shuangye; Amand, Paul St.
- PLoS ONE, Vol. 8, Issue 10
Parallel De Bruijn Graph Construction and Traversal for De Novo Genome Assembly
conference, November 2014
- Georganas, Evangelos; Buluc, Aydin; Chapman, Jarrod
- SC14: International Conference for High Performance Computing, Networking, Storage and Analysis
Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome
journal, June 2013
- Muñoz-Amatriaín, María; Eichten, Steven R.; Wicker, Thomas
- Genome Biology, Vol. 14, Issue 6
Aegilops tauschii single nucleotide polymorphisms shed light on the origins of wheat D-genome genetic diversity and pinpoint the geographic origin of hexaploid wheat
journal, February 2013
- Wang, Jirui; Luo, Ming-Cheng; Chen, Zhongxu
- New Phytologist, Vol. 198, Issue 3
A Simple Sequence Repeat-Based Linkage Map of Barley
journal, December 2000
- Ramsay, L.; Macaulay, M.; Ivanissevich, S. degli
- Genetics, Vol. 156, Issue 4
Construction of an RFLP map of barley
journal, December 1991
- Graner, A.; Jahoor, A.; Schondelmaier, J.
- Theoretical and Applied Genetics, Vol. 83, Issue 2
Haplotype dictionary for the Rht-1 loci in wheat
journal, April 2013
- Wilhelm, Edward P.; Mackay, Ian J.; Saville, Robert J.
- Theoretical and Applied Genetics, Vol. 126, Issue 7
Chromosome-based genomics in the cereals
journal, January 2007
- Doležel, Jaroslav; Kubaláková, Marie; Paux, Etienne
- Chromosome Research, Vol. 15, Issue 1
Ent-kaurenoic acid oxidase genes in wheat
journal, August 2009
- Khlestkina, Elena K.; Kumar, Uttam; Röder, Marion S.
- Molecular Breeding, Vol. 25, Issue 2
Cereal breeding takes a walk on the wild side
journal, January 2008
- Feuillet, Catherine; Langridge, Peter; Waugh, Robbie
- Trends in Genetics, Vol. 24, Issue 1
The map-based sequence of the rice genome
journal, August 2005
- ,
- Nature, Vol. 436, Issue 7052, p. 793-800
Analysis of the bread wheat genome using whole-genome shotgun sequencing
journal, November 2012
- Brenchley, Rachel; Spannagl, Manuel; Pfeifer, Matthias
- Nature, Vol. 491, Issue 7426
Draft genome of the wheat A-genome progenitor Triticum urartu
journal, March 2013
- Ling, Hong-Qing; Zhao, Shancen; Liu, Dongcheng
- Nature, Vol. 496, Issue 7443
The Norway spruce genome sequence and conifer genome evolution
journal, May 2013
- Nystedt, Björn; Street, Nathaniel R.; Wetterbom, Anna
- Nature, Vol. 497, Issue 7451
Limitations of next-generation genome sequence assembly
journal, November 2010
- Alkan, Can; Sajjadian, Saba; Eichler, Evan E.
- Nature Methods, Vol. 8, Issue 1
Targeted A-to-G base editing of chloroplast DNA in plants
journal, December 2022
- Mok, Young Geun; Hong, Sunghyun; Bae, Su-Ji
- Nature Plants, Vol. 8, Issue 12
More on the sequencing of the human genome
journal, March 2003
- Waterston, Robert H.; Lander, Eric S.; Sulston, John E.
- Proceedings of the National Academy of Sciences, Vol. 100, Issue 6
Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars
journal, April 2013
- Cavanagh, C. R.; Chao, S.; Wang, S.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 20
A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data
journal, September 2011
- Li, H.
- Bioinformatics, Vol. 27, Issue 21
Sequence-based physical mapping of complex genomes by whole genome profiling
journal, February 2011
- van Oeveren, J.; de Ruiter, M.; Jesse, T.
- Genome Research, Vol. 21, Issue 4
Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ)
journal, October 2013
- Mascher, Martin; Muehlbauer, Gary J.; Rokhsar, Daniel S.
- The Plant Journal, Vol. 76, Issue 4
Whole-genome profiling and shotgun sequencing delivers an anchored, gene-decorated, physical map assembly of bread wheat chromosome 6A
journal, June 2014
- Poursarebani, Naser; Nussbaumer, Thomas; Šimková, Hana
- The Plant Journal, Vol. 79, Issue 2
The Sequence of the Human Genome
journal, February 2001
- Venter, J. Craig; Adams, Mark D.; Myers, Eugene W.
- Science, Vol. 291, Issue 5507
A Physical Map of the 1-Gigabase Bread Wheat Chromosome 3B
journal, October 2008
- Paux, E.; Sourdille, P.; Salse, J.
- Science, Vol. 322, Issue 5898
Structural and functional partitioning of bread wheat chromosome 3B
journal, July 2014
- Choulet, F.; Alberti, A.; Theil, S.
- Science, Vol. 345, Issue 6194
A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome
journal, July 2014
- Mayer, K. F. X.; Rogers, J.; Dole el, J.
- Science, Vol. 345, Issue 6194
Reconstruction of the Synthetic W7984 × Opata M85 wheat reference population
journal, November 2011
- Sorrells, Mark E.; Gustafson, J. Perry; Somers, Daryl
- Genome, Vol. 54, Issue 11
Repbase Update, a database of eukaryotic repetitive elements
journal, January 2005
- Jurka, J.; Kapitonov, V. V.; Pavlicek, A.
- Cytogenetic and Genome Research, Vol. 110, Issue 1-4
e!DAL - a framework to store, share and publish research data
journal, June 2014
- Arend, Daniel; Lange, Matthias; Chen, Jinbo
- BMC Bioinformatics, Vol. 15, Issue 1
Genic regions of a large salamander genome contain long introns and novel genes
journal, January 2009
- Smith, Jeramiah J.; Putta, Srikrishna; Zhu, Wei
- BMC Genomics, Vol. 10, Issue 1
The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences
journal, January 2010
- Kovach, Allen; Wegrzyn, Jill L.; Parra, Genis
- BMC Genomics, Vol. 11, Issue 1
Integration of mate pair sequences to improve shotgun assemblies of flow-sorted chromosome arms of hexaploid wheat
journal, January 2013
- Belova, Tatiana; Zhan, Bujie; Wright, Jonathan
- BMC Genomics, Vol. 14, Issue 1
Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome
journal, January 2011
- Saintenac, Cyrille; Jiang, Dayou; Akhunov, Eduard D.
- Genome Biology, Vol. 12, Issue 9
Mapping-by-sequencing accelerates forward genetics in barley
journal, January 2014
- Mascher, Martin; Jost, Matthias; Kuon, Joel-Elias
- Genome Biology, Vol. 15, Issue 6
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
Meraculous: De Novo Genome Assembly with Short Paired-End Reads
journal, August 2011
- Chapman, Jarrod A.; Ho, Isaac; Sunkara, Sirisha
- PLoS ONE, Vol. 6, Issue 8
Rapid Genome Mapping in Nanochannel Arrays for Highly Complete and Accurate De Novo Sequence Assembly of the Complex Aegilops tauschii Genome
journal, February 2013
- Hastie, Alex R.; Dong, Lingli; Smith, Alexis
- PLoS ONE, Vol. 8, Issue 2
Application of Genotyping-by-Sequencing on Semiconductor Sequencing Platforms: A Comparison of Genetic and Reference-Based Marker Ordering in Barley
journal, October 2013
- Mascher, Martin; Wu, Shuangye; Amand, Paul St.
- PLoS ONE, Vol. 8, Issue 10
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
A High-Density Gene Map of Loblolly Pine ( Pinus taeda L.) Based on Exome Sequence Capture Genotyping
journal, November 2013
- Neves, Leandro Gomide; Davis, John M.; Barbazuk, William B.
- G3: Genes|Genomes|Genetics, Vol. 4, Issue 1
Sequencing, Assembling, and Correcting Draft Genomes Using Recombinant Populations
journal, February 2014
- Hahn, Matthew W.; Zhang, Simo V.; Moyle, Leonie C.
- G3: Genes|Genomes|Genetics, Vol. 4, Issue 4
Sequencing and Assembly of the 22-Gb Loblolly Pine Genome
journal, March 2014
- Zimin, Aleksey; Stevens, Kristian A.; Crepeau, Marc W.
- Genetics, Vol. 196, Issue 3
Joint assembly and genetic mapping of the Atlantic horseshoe crab genome reveals ancient whole genome duplication
text, January 2013
- Nossa, Carlos; Havlak, Paul; Yue, Jia-Xing
- arXiv
An Improved Filtering Algorithm for Big Read Datasets
preprint, January 2016
- Wedemeyer, Axel; Kliemann, Lasse; Srivastav, Anand
- arXiv
Works referencing / citing this record:
Dominant inhibition of awn development by a putative zinc‐finger transcriptional repressor expressed at the B1 locus in wheat
journal, October 2019
- Huang, Daiqing; Zheng, Qian; Melchkart, Tancey
- New Phytologist, Vol. 225, Issue 1
Characterisation of Thinopyrum bessarabicum chromosomes through genome-wide introgressions into wheat
journal, November 2017
- Grewal, Surbhi; Yang, Caiyun; Edwards, Stella Hubbart
- Theoretical and Applied Genetics, Vol. 131, Issue 2
SnpHub: an easy-to-set-up web server framework for exploring large-scale genomic variation data in the post-genomic era with applications in wheat
journal, June 2020
- Wang, Wenxi; Wang, Zihao; Li, Xintong
- GigaScience, Vol. 9, Issue 6
Exploring the tertiary gene pool of bread wheat: sequence assembly and analysis of chromosome 5M g of Aegilops geniculata
journal, November 2015
- Tiwari, Vijay K.; Wang, Shichen; Danilova, Tatiana
- The Plant Journal, Vol. 84, Issue 4
Towards a whole‐genome sequence for rye ( Secale cereale L.)
journal, February 2017
- Bauer, Eva; Schmutzer, Thomas; Barilar, Ivan
- The Plant Journal, Vol. 89, Issue 5
The genetic architecture of genome‐wide recombination rate variation in allopolyploid wheat revealed by nested association mapping
journal, July 2018
- Jordan, Katherine W.; Wang, Shichen; He, Fei
- The Plant Journal, Vol. 95, Issue 6
Mapping causal mutations by exome sequencing in a wheat TILLING population: a tall mutant case study
journal, November 2017
- Mo, Youngjun; Howell, Tyson; Vasquez-Gross, Hans
- Molecular Genetics and Genomics, Vol. 293, Issue 2
BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes
journal, January 2016
- Staňková, Helena; Hastie, Alex R.; Chan, Saki
- Plant Biotechnology Journal, Vol. 14, Issue 7
Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome
journal, July 2018
- Keeble-Gagnere, G.; Rigault, P.; Tibbits, J.
- Genome Biology
TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools
journal, December 2019
- Monat, Cécile; Padmarasu, Sudharsan; Lux, Thomas
- Genome Biology, Vol. 20, Issue 1
Long noncoding miRNA gene represses wheat β-diketone waxes
journal, March 2017
- Huang, Daiqing; Feurtado, J. Allan; Smith, Mark A.
- Proceedings of the National Academy of Sciences, Vol. 114, Issue 15
Genomic Selection in Preliminary Yield Trials in a Winter Wheat Breeding Program
journal, June 2018
- Belamkar, Vikas; Guttieri, Mary J.; Hussain, Waseem
- G3: Genes|Genomes|Genetics, Vol. 8, Issue 8
Nested Association Mapping of Stem Rust Resistance in Wheat Using Genotyping by Sequencing
journal, May 2016
- Bajgain, Prabin; Rouse, Matthew N.; Tsilo, Toi J.
- PLOS ONE, Vol. 11, Issue 5
Rapid de novo assembly of the European eel genome from nanopore sequencing reads
journal, August 2017
- Jansen, Hans J.; Liem, Michael; Jong-Raadsen, Susanne A.
- Scientific Reports, Vol. 7, Issue 1
A highly recombined, high-density, eight-founder wheat MAGIC map reveals extensive segregation distortion and genomic locations of introgression segments
journal, January 2016
- Gardner, Keith A.; Wittern, Lukas M.; Mackay, Ian J.
- Plant Biotechnology Journal, Vol. 14, Issue 6
Strategies for Selecting Crosses Using Genomic Prediction in Two Wheat Breeding Programs
text, January 2017
- Lado, Bettina; Battenfield, Sarah; Guzmán, Carlos
- Unpublished
Insight Into the Prospects for the Improvement of Seed Starch in Legume—A Review
journal, October 2019
- Tayade, Rupesh; Kulkarni, Krishnanand P.; Jo, Hyun
- Frontiers in Plant Science, Vol. 10
A framework for gene mapping in wheat demonstrated using the Yr7 yellow rust resistance gene
journal, April 2020
- Gardiner, Laura-Jayne; Bansept-Basler, Pauline; El-Soda, Mohamed
- PLOS ONE, Vol. 15, Issue 4
Genetic analysis of wheat sensitivity to the ToxB fungal effector from Pyrenophora tritici-repentis, the causal agent of tan spot
journal, January 2020
- Corsi, Beatrice; Percival-Alwyn, Lawrence; Downie, Rowena C.
- Theoretical and Applied Genetics, Vol. 133, Issue 3
Phylogenetic analyses and in-seedling expression of ammonium and nitrate transporters in wheat
journal, May 2018
- Bajgain, Prabin; Russell, Blake; Mohammadi, Mohsen
- Scientific Reports, Vol. 8, Issue 1
Ensembl Genomes 2016: more genomes, more complexity
journal, November 2015
- Kersey, Paul Julian; Allen, James E.; Armean, Irina
- Nucleic Acids Research, Vol. 44, Issue D1
Shifting the limits in wheat research and breeding using a fully annotated reference genome
journal, August 2018
- Appels, Rudi; Eversole, Kellye; Stein, Nils
- Science, Vol. 361, Issue 6403
A framework for gene mapping in wheat demonstrated using the Yr7 yellow rust resistance gene
journal, October 2019
- Gardiner, Laura-Jayne; Bansept-Basler, Pauline; El-Soda, Mohamed
- PLOS ONE
Spatiotemporal expression patterns of wheat amino acid transporters reveal their putative roles in nitrogen transport and responses to abiotic stress
journal, July 2017
- Wan, Yongfang; King, Robert; Mitchell, Rowan A. C.
- Scientific Reports, Vol. 7, Issue 1
An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations
journal, April 2017
- Clavijo, Bernardo J.; Venturini, Luca; Schudoma, Christian
- Genome Research, Vol. 27, Issue 5
Multi-Locus Genome Wide Association Mapping for Yield and Its Contributing Traits in Hexaploid Wheat under Different Water Regimes
journal, December 2019
- Gahlaut, Vijay; Jaiswal, Vandana; Singh, Sukhwinder
- Scientific Reports, Vol. 9, Issue 1
Genotype-by-sequencing facilitates genetic mapping of a stem rust resistance locus in Aegilops umbellulata, a wild relative of cultivated wheat
journal, December 2016
- Edae, Erena A.; Olivera, Pablo D.; Jin, Yue
- BMC Genomics, Vol. 17, Issue 1
Association of KASP markers with Hessian fly resistance in wheat of diverse origin
journal, July 2018
- Collins, Damian; Emebiri, Livinus; Tan, Mui-Keng
- Euphytica, Vol. 214, Issue 8
Prediction and analysis of three gene families related to leaf rust (Puccinia triticina) resistance in wheat (Triticum aestivum L.)
journal, June 2017
- Peng, Fred Y.; Yang, Rong-Cai
- BMC Plant Biology, Vol. 17, Issue 1
Hidden variation in polyploid wheat drives local adaptation
journal, December 2017
- Gardiner, Laura-Jayne; Joynson, Ryan; Omony, Jimmy
- Genome Research
Exome sequencing of bulked segregants identified a novel TaMKK3-A allele linked to the wheat ERA8 ABA-hypersensitive germination phenotype
journal, January 2020
- Martinez, Shantel A.; Shorinola, Oluwayesi; Conselman, Samantha
- Theoretical and Applied Genetics, Vol. 133, Issue 3
Genomic and pedigree-based prediction for leaf, stem, and stripe rust resistance in wheat
journal, April 2017
- Juliana, Philomin; Singh, Ravi P.; Singh, Pawan K.
- Theoretical and Applied Genetics, Vol. 130, Issue 7
Genetic modification of spikelet arrangement in wheat increases grain number without significantly affecting grain weight
journal, December 2018
- Wolde, Gizaw M.; Mascher, Martin; Schnurbusch, Thorsten
- Molecular Genetics and Genomics, Vol. 294, Issue 2
A genome-wide survey of DNA methylation in hexaploid wheat
journal, December 2015
- Gardiner, Laura-Jayne; Quinton-Tulloch, Mark; Olohan, Lisa
- Genome Biology, Vol. 16, Issue 1
QTL mapping of pre-harvest sprouting resistance in a white wheat cultivar Danby
journal, June 2018
- Shao, Mingqin; Bai, Guihua; Rife, Trevor W.
- Theoretical and Applied Genetics, Vol. 131, Issue 8
Epistatic determinism of durum wheat resistance to the wheat spindle streak mosaic virus
journal, April 2017
- Holtz, Yan; Bonnefoy, Michel; Viader, Véronique
- Theoretical and Applied Genetics, Vol. 130, Issue 7
Hidden variation in polyploid wheat drives local adaptation
journal, August 2018
- Gardiner, Laura-Jayne; Joynson, Ryan; Omony, Jimmy
- Genome Research, Vol. 28, Issue 9
Genotyping-by-sequencing approaches to characterize crop genomes: choosing the right tool for the right application
journal, January 2017
- Scheben, Armin; Batley, Jacqueline; Edwards, David
- Plant Biotechnology Journal, Vol. 15, Issue 2
Strategies for Selecting Crosses Using Genomic Prediction in Two Wheat Breeding Programs
journal, July 2017
- Lado, Bettina; Battenfield, Sarah; Guzmán, Carlos
- The Plant Genome, Vol. 10, Issue 2
Fine mapping of the wheat powdery mildew resistance gene Pm52 using comparative genomics analysis and the Chinese Spring reference genomic sequence
journal, February 2019
- Wu, Peipei; Hu, Jinghuang; Zou, Jingwei
- Theoretical and Applied Genetics, Vol. 132, Issue 5
Chromosome-scale comparative sequence analysis unravels molecular mechanisms of genome dynamics between two wheat cultivars
journal, August 2018
- Thind, Anupriya Kaur; Wicker, Thomas; Müller, Thomas
- Genome Biology, Vol. 19, Issue 1
CerealsDB 3.0: expansion of resources and data integration
journal, June 2016
- Wilkinson, Paul A.; Winfield, Mark O.; Barker, Gary L. A.
- BMC Bioinformatics, Vol. 17, Issue 1
Durum wheat genome highlights past domestication signatures and future improvement targets
journal, April 2019
- Maccaferri, Marco; Harris, Neil S.; Twardziok, Sven O.
- Nature Genetics, Vol. 51, Issue 5
Genetic analysis of wheat sensitivity to the ToxB fungal effector from Pyrenophora tritici-repentis, the causal agent of tan spot
text, January 2020
- Corsi, Beatrice; Percival-Alwyn, Lawrence; Downie, Rowena C.
- Apollo - University of Cambridge Repository
SNP-based pool genotyping and haplotype analysis accelerate fine-mapping of the wheat genomic region containing stripe rust resistance gene Yr26
journal, April 2018
- Wu, Jianhui; Zeng, Qingdong; Wang, Qilin
- Theoretical and Applied Genetics, Vol. 131, Issue 7
Genome-Wide Association Study of Grain Architecture in Wild Wheat Aegilops tauschii
journal, May 2017
- Arora, Sanu; Singh, Narinder; Kaur, Satinder
- Frontiers in Plant Science, Vol. 8
Unraveling Molecular and Genetic Studies of Wheat (Triticum aestivum L.) Resistance against Factors Causing Pre-Harvest Sprouting
journal, March 2019
- Ali, Ahmad; Cao, Jiajia; Jiang, Hao
- Agronomy, Vol. 9, Issue 3
Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.
journal, April 2017
- Beier, Sebastian; Himmelbach, Axel; Colmsee, Christian
- Scientific Data, Vol. 4, Issue 1
A high-resolution reference genetic map positioning 8.8 K genes for the conifer white spruce: structural genomics implications and correspondence with physical distance
journal, March 2017
- Pavy, Nathalie; Lamothe, Manuel; Pelgas, Betty
- The Plant Journal, Vol. 90, Issue 1
Genotyping-by-Sequencing Derived High-Density Linkage Map and its Application to QTL Mapping of Flag Leaf Traits in Bread Wheat
journal, November 2017
- Hussain, Waseem; Baenziger, P. Stephen.; Belamkar, Vikas
- Scientific Reports, Vol. 7, Issue 1
From markers to genome-based breeding in wheat
journal, January 2019
- Rasheed, Awais; Xia, Xianchun
- Theoretical and Applied Genetics, Vol. 132, Issue 3
The improved assembly of 7DL chromosome provides insight into the structure and evolution of bread wheat
journal, September 2019
- Feng, Kewei; Cui, Licao; Wang, Le
- Plant Biotechnology Journal, Vol. 18, Issue 3
Genome-Wide Association Mapping of Grain Micronutrients Concentration in Aegilops tauschii
journal, February 2019
- Arora, Sanu; Cheema, Jitender; Poland, Jesse
- Frontiers in Plant Science, Vol. 10
Broadening the bread wheat D genome
journal, February 2019
- Mirzaghaderi, Ghader; Mason, Annaliese S.
- Theoretical and Applied Genetics, Vol. 132, Issue 5
SnpHub: an easy-to-set-up web server framework for exploring large-scale genomic variation data in the post-genomic era with applications in wheat
journal, February 2020
- Wang, Wenxi; Wang, Zihao; Li, Xintong
- GigaScience
Genome-wide association mapping for resistance to leaf rust, stripe rust and tan spot in wheat reveals potential candidate genes
journal, March 2018
- Juliana, Philomin; Singh, Ravi P.; Singh, Pawan K.
- Theoretical and Applied Genetics, Vol. 131, Issue 7
Heat in Wheat: Exploit Reverse Genetic Techniques to Discover New Alleles Within the Triticum durum sHsp26 Family
journal, September 2018
- Comastri, Alessia; Janni, Michela; Simmonds, James
- Frontiers in Plant Science, Vol. 9
Dense genotyping-by-sequencing linkage maps of two Synthetic W7984×Opata reference populations provide insights into wheat structural diversity
journal, February 2019
- Gutierrez-Gonzalez, Juan J.; Mascher, Martin; Poland, Jesse
- Scientific Reports, Vol. 9, Issue 1
Mapping and KASP marker development for wheat curl mite resistance in “TAM 112” wheat using linkage and association analysis
journal, September 2018
- Dhakal, Smit; Tan, Chor-Tee; Anderson, Victoria
- Molecular Breeding, Vol. 38, Issue 10
Genetic factors affecting Fusarium head blight resistance improvement from introgression of exotic Sumai 3 alleles (including Fhb1, Fhb2, and Fhb5) in hard red spring wheat
journal, May 2019
- Brar, Gurcharn Singh; Brûlé-Babel, Anita L.; Ruan, Yuefeng
- BMC Plant Biology, Vol. 19, Issue 1
An ancestral NB-LRR with duplicated 3′UTRs confers stripe rust resistance in wheat and barley
journal, September 2019
- Zhang, Chaozhong; Huang, Lin; Zhang, Huifei
- Nature Communications, Vol. 10, Issue 1
Breeding-assisted genomics: Applying meta-GWAS for milling and baking quality in CIMMYT wheat breeding program
journal, November 2018
- Battenfield, Sarah D.; Sheridan, Jaime L.; Silva, Luciano D. C. E.
- PLOS ONE, Vol. 13, Issue 11
Poaceae-specific MS1 encodes a phospholipid-binding protein for male fertility in bread wheat
journal, November 2017
- Wang, Zheng; Li, Jian; Chen, Shaoxia
- Proceedings of the National Academy of Sciences, Vol. 114, Issue 47
Genetic insights into morphometric inflorescence traits of wheat
journal, February 2019
- Wolde, Gizaw M.; Trautewig, Corinna; Mascher, Martin
- Theoretical and Applied Genetics, Vol. 132, Issue 6
High throughput SNP discovery and genotyping in hexaploid wheat
journal, January 2018
- Rimbert, Hélène; Darrier, Benoît; Navarro, Julien
- PLOS ONE, Vol. 13, Issue 1
Unraveling the genetic architecture of grain size in einkorn wheat through linkage and homology mapping, and transcriptomic profiling
journal, July 2018
- Yu, Kang; Liu, Dongcheng; Chen, Yong
- Journal of Experimental Botany
Genetic Mapping of Millions of SNPs in Safflower ( Carthamus tinctorius L.) via Whole-Genome Resequencing
journal, May 2016
- Bowers, John E.; Pearl, Stephanie A.; Burke, John M.
- G3: Genes|Genomes|Genetics, Vol. 6, Issue 7
Genetic diversity and relationship between domesticated rye and its wild relatives as revealed through genotyping‐by‐sequencing
journal, March 2018
- Schreiber, Mona; Himmelbach, Axel; Börner, Andreas
- Evolutionary Applications, Vol. 12, Issue 1
Chromosome-specific sequencing reveals an extensive dispensable genome component in wheat
journal, November 2016
- Liu, Miao; Stiller, Jiri; Holušová, Kateřina
- Scientific Reports, Vol. 6, Issue 1
High-resolution mapping of the pericentromeric region on wheat chromosome arm 5AS harbouring the Fusarium head blight resistance QTL Qfhs.ifa-5A
journal, November 2017
- Buerstmayr, Maria; Steiner, Barbara; Wagner, Christian
- Plant Biotechnology Journal, Vol. 16, Issue 5
Unraveling the genetic architecture of grain size in einkorn wheat through linkage and homology mapping and transcriptomic profiling
journal, June 2019
- Yu, Kang; Liu, Dongcheng; Chen, Yong
- Journal of Experimental Botany, Vol. 70, Issue 18
Assembly of allele-aware, chromosomal-scale autopolyploid genomes based on Hi-C data
journal, August 2019
- Zhang, Xingtan; Zhang, Shengcheng; Zhao, Qian
- Nature Plants, Vol. 5, Issue 8
Chromosome-scale comparative sequence analysis unravels molecular mechanisms of genome dynamics between two wheat cultivars
text, January 2018
- Thind, Anupriya Kaur; Wicker, Thomas; Müller, Thomas
- BioMed Central
Temperature‐sensitive wheat stem rust resistance gene Sr15 is effective against Puccinia graminis f. sp. tritici race TTKSK
journal, August 2018
- Gao, L.; Babiker, E. M.; Nava, I. C.
- Plant Pathology, Vol. 68, Issue 1
Genotyping by Sequencing Using Specific Allelic Capture to Build a High-Density Genetic Map of Durum Wheat
journal, May 2016
- Holtz, Yan; Ardisson, Morgane; Ranwez, Vincent
- PLOS ONE, Vol. 11, Issue 5
Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum
journal, June 2016
- Zhang, Jisen; Sharma, Anupma; Yu, Qingyi
- BMC Genomics, Vol. 17, Issue 1
Genome-wide characterization of microsatellites in Triticeae species: abundance, distribution and evolution
journal, August 2016
- Deng, Pingchuan; Wang, Meng; Feng, Kewei
- Scientific Reports, Vol. 6, Issue 1
Genomics as the key to unlocking the polyploid potential of wheat
journal, June 2015
- Borrill, Philippa; Adamski, Nikolai; Uauy, Cristobal
- New Phytologist, Vol. 208, Issue 4
Unravelling the Complex Genetics of Karnal Bunt ( Tilletia indica ) Resistance in Common Wheat ( Triticum aestivum ) by Genetic Linkage and Genome-Wide Association Analyses
journal, March 2019
- Emebiri, Livinus; Singh, Sukhwinder; Tan, Mui-Keng
- G3: Genes|Genomes|Genetics, Vol. 9, Issue 5
A High-Density Consensus Map of Common Wheat Integrating Four Mapping Populations Scanned by the 90K SNP Array
journal, August 2017
- Wen, Weie; He, Zhonghu; Gao, Fengmei
- Frontiers in Plant Science, Vol. 8
Wheat ms5 male‐sterility is induced by recessive homoeologous A and D genome non‐specific lipid transfer proteins
journal, June 2019
- Pallotta, Margaret A.; Warner, Patricia; Kouidri, Allan
- The Plant Journal, Vol. 99, Issue 4
De novo hybrid assembly of the rubber tree genome reveals evidence of paleotetraploidy in Hevea species
journal, February 2017
- Pootakham, Wirulda; Sonthirod, Chutima; Naktang, Chaiwat
- Scientific Reports, Vol. 7, Issue 1
Genome‐Wide Association and Prediction of Grain and Semolina Quality Traits in Durum Wheat Breeding Populations
journal, November 2017
- Fiedler, Jason D.; Salsman, Evan; Liu, Yuan
- The Plant Genome, Vol. 10, Issue 3
Forward genetics using radiation hybrids (deletion mutants) in plants
journal, November 2018
- Kumar, Ajay; Jain, Shalu
- Indian Journal of Plant Physiology, Vol. 23, Issue 4
Genomic Selection for Processing and End-Use Quality Traits in the CIMMYT Spring Bread Wheat Breeding Program
journal, July 2016
- Battenfield, Sarah D.; Guzmán, Carlos; Gaynor, R. Chris
- The Plant Genome, Vol. 9, Issue 2
The high-quality genome of Brassica napus cultivar ‘ZS11’ reveals the introgression history in semi-winter morphotype
journal, October 2017
- Sun, Fengming; Fan, Guangyi; Hu, Qiong
- The Plant Journal, Vol. 92, Issue 3
Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome
journal, August 2018
- Keeble-Gagnère, Gabriel; Rigault, Philippe; Tibbits, Josquin
- Genome Biology, Vol. 19, Issue 1
Genomic approaches for studying crop evolution
journal, September 2018
- Schreiber, Mona; Stein, Nils; Mascher, Martin
- Genome Biology, Vol. 19, Issue 1
Multi-Locus Genome Wide Association Mapping for Yield and Its Contributing Traits in Hexaploid Wheat under Different Water Regimes
text, January 2019
- Gahlaut, Vijay; Jaiswal, Vandana; Singh, Sukhwinder
- Unpublished
The complex genetic architecture of recombination and structural variation in wheat uncovered using a large 8-founder MAGIC population
posted_content, March 2019
- Shah, Rohan; Huang, B. Emma; Whan, Alex
- BioRxiv
Imputation accuracy of wheat genotyping-by-sequencing (GBS) data using barley and wheat genome references
journal, January 2019
- Alipour, Hadi; Bai, Guihua; Zhang, Guorong
- PLOS ONE, Vol. 14, Issue 1
Features of the organization of bread wheat chromosome 5BS based on physical mapping
journal, February 2018
- Salina, Elena A.; Nesterov, Mikhail A.; Frenkel, Zeev
- BMC Genomics, Vol. 19, Issue S3
A modified sequence capture approach allowing standard and methylation analyses of the same enriched genomic DNA sample
journal, April 2018
- Olohan, Lisa; Gardiner, Laura-Jayne; Lucaci, Anita
- BMC Genomics, Vol. 19, Issue 1
Selection and evaluation of reference genes for qRT-PCR analysis in Euscaphis konishii Hayata based on transcriptome data
journal, June 2018
- Liang, Wenxian; Zou, Xiaoxing; Carballar-Lejarazú, Rebeca
- Plant Methods, Vol. 14, Issue 1
Genetic insights into morphometric inflorescence traits of wheat
journal, February 2019
- Wolde, Gizaw M.; Trautewig, Corinna; Mascher, Martin
- Theoretical and Applied Genetics, Vol. 132, Issue 6
Mapping causal mutations by exome sequencing in a wheat TILLING population: a tall mutant case study
journal, November 2017
- Mo, Youngjun; Howell, Tyson; Vasquez-Gross, Hans
- Molecular Genetics and Genomics, Vol. 293, Issue 2
Developing integrated crop knowledge networks to advance candidate gene discovery
journal, December 2016
- Hassani-Pak, Keywan; Castellote, Martin; Esch, Maria
- Applied & Translational Genomics, Vol. 11
An ancestral NB-LRR with duplicated 3′UTRs confers stripe rust resistance in wheat and barley
journal, September 2019
- Zhang, Chaozhong; Huang, Lin; Zhang, Huifei
- Nature Communications, Vol. 10, Issue 1
Spatiotemporal expression patterns of wheat amino acid transporters reveal their putative roles in nitrogen transport and responses to abiotic stress
journal, July 2017
- Wan, Yongfang; King, Robert; Mitchell, Rowan A. C.
- Scientific Reports, Vol. 7, Issue 1
Genotyping-by-Sequencing Derived High-Density Linkage Map and its Application to QTL Mapping of Flag Leaf Traits in Bread Wheat
journal, November 2017
- Hussain, Waseem; Baenziger, P. Stephen.; Belamkar, Vikas
- Scientific Reports, Vol. 7, Issue 1
Phylogenetic analyses and in-seedling expression of ammonium and nitrate transporters in wheat
journal, May 2018
- Bajgain, Prabin; Russell, Blake; Mohammadi, Mohsen
- Scientific Reports, Vol. 8, Issue 1
Dense genotyping-by-sequencing linkage maps of two Synthetic W7984×Opata reference populations provide insights into wheat structural diversity
journal, February 2019
- Gutierrez-Gonzalez, Juan J.; Mascher, Martin; Poland, Jesse
- Scientific Reports, Vol. 9, Issue 1
RNAseq analysis reveals drought-responsive molecular pathways with candidate genes and putative molecular markers in root tissue of wheat
journal, September 2019
- Iquebal, Mir Asif; Sharma, Pradeep; Jasrotia, Rahul Singh
- Scientific Reports, Vol. 9, Issue 1
De novo hybrid assembly of the rubber tree genome reveals evidence of paleotetraploidy in Hevea species
journal, February 2017
- Pootakham, Wirulda; Sonthirod, Chutima; Naktang, Chaiwat
- Scientific Reports, Vol. 7, Issue 1
Gramene 2016: comparative plant genomics and pathway resources
journal, November 2015
- Tello-Ruiz, Marcela K.; Stein, Joshua; Wei, Sharon
- Nucleic Acids Research, Vol. 44, Issue D1
pBACode: a random-barcode-based high-throughput approach for BAC paired-end sequencing and physical clone mapping
journal, December 2016
- Wei, Xiaolin; Xu, Zhichao; Wang, Guixing
- Nucleic Acids Research
A modified sequence capture approach allowing standard and methylation analyses of the same enriched genomic DNA sample
journal, November 2017
- Olohan, Lisa; Gardiner, Laura-Jayne; Lucaci, Anita
- BMC Genomics
Unraveling the genetic architecture of grain size in einkorn wheat through linkage and homology mapping, and transcriptomic profiling
journal, July 2018
- Yu, Kang; Liu, Dongcheng; Chen, Yong
- Journal of Experimental Botany
Genetic diversity and relationship between domesticated rye and its wild relatives as revealed through genotyping‐by‐sequencing
journal, March 2018
- Schreiber, Mona; Himmelbach, Axel; Börner, Andreas
- Evolutionary Applications, Vol. 12, Issue 1
Dominant inhibition of awn development by a putative zinc‐finger transcriptional repressor expressed at the B1 locus in wheat
journal, October 2019
- Huang, Daiqing; Zheng, Qian; Melchkart, Tancey
- New Phytologist, Vol. 225, Issue 1
A highly recombined, high-density, eight-founder wheat MAGIC map reveals extensive segregation distortion and genomic locations of introgression segments
journal, January 2016
- Gardner, Keith A.; Wittern, Lukas M.; Mackay, Ian J.
- Plant Biotechnology Journal, Vol. 14, Issue 6
Multiplex sequencing of bacterial artificial chromosomes for assembling complex plant genomes
journal, January 2016
- Beier, Sebastian; Himmelbach, Axel; Schmutzer, Thomas
- Plant Biotechnology Journal, Vol. 14, Issue 7
BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes
journal, January 2016
- Staňková, Helena; Hastie, Alex R.; Chan, Saki
- Plant Biotechnology Journal, Vol. 14, Issue 7
Thein silicoidentification and characterization of a bread wheat/Triticum militinaeintrogression line
journal, September 2016
- Abrouk, Michael; Balcárková, Barbora; Šimková, Hana
- Plant Biotechnology Journal, Vol. 15, Issue 2
The improved assembly of 7DL chromosome provides insight into the structure and evolution of bread wheat
journal, September 2019
- Feng, Kewei; Cui, Licao; Wang, Le
- Plant Biotechnology Journal, Vol. 18, Issue 3
The genetic architecture of genome‐wide recombination rate variation in allopolyploid wheat revealed by nested association mapping
journal, July 2018
- Jordan, Katherine W.; Wang, Shichen; He, Fei
- The Plant Journal, Vol. 95, Issue 6
CerealsDB 3.0: expansion of resources and data integration
journal, June 2016
- Wilkinson, Paul A.; Winfield, Mark O.; Barker, Gary L. A.
- BMC Bioinformatics, Vol. 17, Issue 1
Genotype-by-sequencing facilitates genetic mapping of a stem rust resistance locus in Aegilops umbellulata, a wild relative of cultivated wheat
journal, December 2016
- Edae, Erena A.; Olivera, Pablo D.; Jin, Yue
- BMC Genomics, Vol. 17, Issue 1
Prediction and analysis of three gene families related to leaf rust (Puccinia triticina) resistance in wheat (Triticum aestivum L.)
journal, June 2017
- Peng, Fred Y.; Yang, Rong-Cai
- BMC Plant Biology, Vol. 17, Issue 1
Selection and evaluation of reference genes for qRT-PCR analysis in Euscaphis konishii Hayata based on transcriptome data
journal, June 2018
- Liang, Wenxian; Zou, Xiaoxing; Carballar-Lejarazú, Rebeca
- Plant Methods, Vol. 14, Issue 1
Genotyping by Sequencing Using Specific Allelic Capture to Build a High-Density Genetic Map of Durum Wheat
journal, May 2016
- Holtz, Yan; Ardisson, Morgane; Ranwez, Vincent
- PLOS ONE, Vol. 11, Issue 5
Nested Association Mapping of Stem Rust Resistance in Wheat Using Genotyping by Sequencing
journal, May 2016
- Bajgain, Prabin; Rouse, Matthew N.; Tsilo, Toi J.
- PLOS ONE, Vol. 11, Issue 5
Breeding-assisted genomics: Applying meta-GWAS for milling and baking quality in CIMMYT wheat breeding program
journal, November 2018
- Battenfield, Sarah D.; Sheridan, Jaime L.; Silva, Luciano D. C. E.
- PLOS ONE, Vol. 13, Issue 11
Genetic Mapping of Millions of SNPs in Safflower ( Carthamus tinctorius L.) via Whole-Genome Resequencing
journal, May 2016
- Bowers, John E.; Pearl, Stephanie A.; Burke, John M.
- G3: Genes|Genomes|Genetics, Vol. 6, Issue 7
Genomic Selection in Preliminary Yield Trials in a Winter Wheat Breeding Program
journal, June 2018
- Belamkar, Vikas; Guttieri, Mary J.; Hussain, Waseem
- G3: Genes|Genomes|Genetics, Vol. 8, Issue 8
Using linkage maps to correct and scaffold de novo genome assemblies: methods, challenges, and computational tools
journal, June 2015
- Fierst, Janna L.
- Frontiers in Genetics, Vol. 6
A High Resolution Radiation Hybrid Map of Wheat Chromosome 4A
journal, January 2017
- Balcárková, Barbora; Frenkel, Zeev; Škopová, Monika
- Frontiers in Plant Science, Vol. 7
Genome-Wide Association Study of Grain Architecture in Wild Wheat Aegilops tauschii
journal, May 2017
- Arora, Sanu; Singh, Narinder; Kaur, Satinder
- Frontiers in Plant Science, Vol. 8
Genotyping-by-Sequencing (GBS) Revealed Molecular Genetic Diversity of Iranian Wheat Landraces and Cultivars
journal, August 2017
- Alipour, Hadi; Bihamta, Mohammad R.; Mohammadi, Valiollah
- Frontiers in Plant Science, Vol. 8
A High-Density Consensus Map of Common Wheat Integrating Four Mapping Populations Scanned by the 90K SNP Array
journal, August 2017
- Wen, Weie; He, Zhonghu; Gao, Fengmei
- Frontiers in Plant Science, Vol. 8
Genome-Wide Association Mapping of Grain Micronutrients Concentration in Aegilops tauschii
journal, February 2019
- Arora, Sanu; Cheema, Jitender; Poland, Jesse
- Frontiers in Plant Science, Vol. 10
Uncovering Genomic Regions Associated With 36 Agro-Morphological Traits in Indian Spring Wheat Using GWAS
journal, April 2019
- Sheoran, Sonia; Jaiswal, Sarika; Kumar, Deepender
- Frontiers in Plant Science, Vol. 10
Insight Into the Prospects for the Improvement of Seed Starch in Legume—A Review
journal, October 2019
- Tayade, Rupesh; Kulkarni, Krishnanand P.; Jo, Hyun
- Frontiers in Plant Science, Vol. 10
Next-Generation Sequencing — An Overview of the History, Tools, and “Omic” Applications
book, January 2016
- Kulski, Jerzy K.
- Next Generation Sequencing - Advances, Applications and Challenges