Sub genome anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids
Abstract
Like those of many agricultural crops, the cultivated cotton is an allotetraploid and has a large genome (~2.5 gigabase pairs). The two sub genomes, A and D, are highly similar but unequally sized and repeat-rich, which pose significant challenges for accurate genome reconstruction using standard approaches. Here we report the development of BAC libraries, sub genome specific physical maps, and a new-generation sequencing approach that will lead to a reference-grade genome assembly for Upland cotton. Three BAC libraries were constructed, fingerprinted, and integrated with BAC-end sequences (BES) to produce a de novo whole-genome physical map. The BAC map was partitioned by sub genomes through alignment to the diploid progenitor D-genome reference sequence with densely spaced BES anchor points and computational filtering. The physical maps were validated with FISH and genetic mapping of SNP markers derived from BES. Two pairs of homeologous chromosomes, A11/D11 and A12/D12, were used to assess multiplex sequencing approaches for completeness and scalability. The results represent the first sub genome anchored physical maps of Upland cotton, and a new-generation approach to the whole-genome sequencing, which will lead to the reference-grade assembly of allopolyploid cotton and serve as a general strategy for sequencing other polyploid species.
- Authors:
-
[2];
[3];
[4]
- Clemson Univ., SC (United States)
- US Dept. of Agriculture-Agricultural Research Service (USDA-ARS), Stoneville, MS (United States). Genomics and Bioinformatics Research Unit
- Texas A & M Univ., College Station, TX (United States)
- Univ. of Texas, Austin, TX (United States)
- US Dept. of Agriculture-Agricultural Research Service (USDA-ARS), Stoneville, MS (United States). Crop Genetics Research Unit
- HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States)
- Cotton Inc., Cary, NC (United States). Agriculture and Environmental Research
- Mississippi State Univ., Mississippi State, MS (United States)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
- Sponsoring Org.:
- USDOE Office of Science (SC); National Science Foundation (NSF)
- OSTI Identifier:
- 1543775
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Scientific Reports
- Additional Journal Information:
- Journal Volume: 7; Journal Issue: 1; Journal ID: ISSN 2045-2322
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Saski, Christopher A., Scheffler, Brian E., Hulse-Kemp, Amanda M., Liu, Bo, Song, Qingxin, Ando, Atsumi, Stelly, David M., Scheffler, Jodi A., Grimwood, Jane, Jones, Don C., Peterson, Daniel G., Schmutz, Jeremy, and Chen, Z. Jeffery. Sub genome anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids. United States: N. p., 2017.
Web. doi:10.1038/s41598-017-14885-w.
Saski, Christopher A., Scheffler, Brian E., Hulse-Kemp, Amanda M., Liu, Bo, Song, Qingxin, Ando, Atsumi, Stelly, David M., Scheffler, Jodi A., Grimwood, Jane, Jones, Don C., Peterson, Daniel G., Schmutz, Jeremy, & Chen, Z. Jeffery. Sub genome anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids. United States. https://doi.org/10.1038/s41598-017-14885-w
Saski, Christopher A., Scheffler, Brian E., Hulse-Kemp, Amanda M., Liu, Bo, Song, Qingxin, Ando, Atsumi, Stelly, David M., Scheffler, Jodi A., Grimwood, Jane, Jones, Don C., Peterson, Daniel G., Schmutz, Jeremy, and Chen, Z. Jeffery. Fri .
"Sub genome anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids". United States. https://doi.org/10.1038/s41598-017-14885-w. https://www.osti.gov/servlets/purl/1543775.
@article{osti_1543775,
title = {Sub genome anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids},
author = {Saski, Christopher A. and Scheffler, Brian E. and Hulse-Kemp, Amanda M. and Liu, Bo and Song, Qingxin and Ando, Atsumi and Stelly, David M. and Scheffler, Jodi A. and Grimwood, Jane and Jones, Don C. and Peterson, Daniel G. and Schmutz, Jeremy and Chen, Z. Jeffery},
abstractNote = {Like those of many agricultural crops, the cultivated cotton is an allotetraploid and has a large genome (~2.5 gigabase pairs). The two sub genomes, A and D, are highly similar but unequally sized and repeat-rich, which pose significant challenges for accurate genome reconstruction using standard approaches. Here we report the development of BAC libraries, sub genome specific physical maps, and a new-generation sequencing approach that will lead to a reference-grade genome assembly for Upland cotton. Three BAC libraries were constructed, fingerprinted, and integrated with BAC-end sequences (BES) to produce a de novo whole-genome physical map. The BAC map was partitioned by sub genomes through alignment to the diploid progenitor D-genome reference sequence with densely spaced BES anchor points and computational filtering. The physical maps were validated with FISH and genetic mapping of SNP markers derived from BES. Two pairs of homeologous chromosomes, A11/D11 and A12/D12, were used to assess multiplex sequencing approaches for completeness and scalability. The results represent the first sub genome anchored physical maps of Upland cotton, and a new-generation approach to the whole-genome sequencing, which will lead to the reference-grade assembly of allopolyploid cotton and serve as a general strategy for sequencing other polyploid species.},
doi = {10.1038/s41598-017-14885-w},
journal = {Scientific Reports},
number = 1,
volume = 7,
place = {United States},
year = {Fri Nov 10 00:00:00 EST 2017},
month = {Fri Nov 10 00:00:00 EST 2017}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 18 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:
A genetically anchored physical framework for Theobroma cacao cv. Matina 1-6
journal, August 2011
- Saski, Christopher A.; Feltus, Frank A.; Staton, Margaret E.
- BMC Genomics, Vol. 12, Issue 1
Microscopy and Bioinformatic Analyses of Lipid Metabolism Implicate a Sporophytic Signaling Network Supporting Pollen Development in Arabidopsis
journal, July 2008
- Wang, Yixing; Wu, Hong; Yang, Ming
- Molecular Plant, Vol. 1, Issue 4
Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome
journal, August 2014
- Chalhoub, B.; Denoeud, F.; Liu, S.
- Science, Vol. 345, Issue 6199
Development of a 63K SNP Array for Cotton and High-Density Mapping of Intraspecific and Interspecific Populations of Gossypium spp.
journal, April 2015
- Hulse-Kemp, A. M.; Lemm, J.; Plieske, J.
- G3: Genes|Genomes|Genetics, Vol. 5, Issue 6
Five-Color-Based High-Information-Content Fingerprinting of Bacterial Artificial Chromosome Clones Using Type IIS Restriction Endonucleases
journal, June 2001
- Ding, Y.; Johnson, M. D.; Chen, W. Q.
- Genomics, Vol. 74, Issue 2
Duplicate gene evolution, homoeologous recombination, and transcriptome characterization in allopolyploid cotton
journal, January 2012
- Flagel, Lex E.; Wendel, Jonathan F.; Udall, Joshua A.
- BMC Genomics, Vol. 13, Issue 1
A comprehensive meta QTL analysis for fiber quality, yield, yield related and morphological traits, drought tolerance, and disease resistance in tetraploid cotton
journal, January 2013
- Said, Joseph I.; Lin, Zhongxu; Zhang, Xianlong
- BMC Genomics, Vol. 14, 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
Trimmomatic: a flexible trimmer for Illumina sequence data
journal, April 2014
- Bolger, Anthony M.; Lohse, Marc; Usadel, Bjoern
- Bioinformatics, Vol. 30, Issue 15
BAC Sequencing Using Pooled Methods
book, September 2014
- Saski, Christopher A.; Feltus, F. Alex; Parida, Laxmi
- Methods in Molecular Biology
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
An Improved Approach for Construction of Bacterial Artificial Chromosome Libraries
journal, August 1998
- Osoegawa, Kazutoyo; Woon, Peng Yeong; Zhao, Baohui
- Genomics, Vol. 52, Issue 1
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
Chromosome structural changes in diploid and tetraploid A genomes of Gossypium
journal, April 2006
- Desai, Aparna; Chee, Peng W.; Rong, Junkang
- Genome, Vol. 49, Issue 4
Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres
journal, December 2012
- Paterson, Andrew H.; Wendel, Jonathan F.; Gundlach, Heidrun
- Nature, Vol. 492, Issue 7429
Estimation of the Nuclear DNA Content of Gossypium Species
journal, February 2005
- Hendrix, B.
- Annals of Botany, Vol. 95, Issue 5
The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution
journal, March 2013
- Verde, Ignazio; Abbott, Albert G.; Scalabrin, Simone
- Nature Genetics, Vol. 45, Issue 5
De novo assembly of human genomes with massively parallel short read sequencing
journal, December 2009
- Li, R.; Zhu, H.; Ruan, J.
- Genome Research, Vol. 20, Issue 2
The genome sequence of Sea-Island cotton (Gossypium barbadense) provides insights into the allopolyploidization and development of superior spinnable fibres
journal, December 2015
- Yuan, Daojun; Tang, Zhonghui; Wang, Maojun
- Scientific Reports, Vol. 5, Issue 1
Construction and Identification of Bacterial Artificial Chromosome Library for 0-613-2R in Upland Cotton
journal, February 2006
- Yin, Jian-Mei; Guo, Wang-Zhen; Zhang, Tian-Zhen
- Journal of Integrative Plant Biology, Vol. 48, Issue 2
Development of molecular markers for genetic male sterility in Gossypium hirsutum
journal, June 2015
- Feng, Xuehui; Keim, Don; Wanjugi, Humphrey
- Molecular Breeding, Vol. 35, Issue 6
Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement
journal, April 2015
- Zhang, Tianzhen; Hu, Yan; Jiang, Wenkai
- Nature Biotechnology, Vol. 33, Issue 5
The tobacco genome sequence and its comparison with those of tomato and potato
journal, May 2014
- Sierro, Nicolas; Battey, James N. D.; Ouadi, Sonia
- Nature Communications, Vol. 5, Issue 1
Genome sequence of the cultivated cotton Gossypium arboreum
journal, May 2014
- Li, Fuguang; Fan, Guangyi; Wang, Kunbo
- Nature Genetics, Vol. 46, Issue 6
Genome sequence of the palaeopolyploid soybean
journal, January 2010
- Schmutz, Jeremy; Cannon, Steven B.; Schlueter, Jessica
- Nature, Vol. 463, Issue 7278
Cytochrome b5 Reductase Encoded by CBR1 Is Essential for a Functional Male Gametophyte in Arabidopsis
journal, August 2013
- Wayne, Laura L.; Wallis, James G.; Kumar, Rajesh
- The Plant Cell, Vol. 25, Issue 8
Assembly algorithms for next-generation sequencing data
journal, June 2010
- Miller, Jason R.; Koren, Sergey; Sutton, Granger
- Genomics, Vol. 95, Issue 6
Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution
journal, April 2015
- Li, Fuguang; Fan, Guangyi; Lu, Cairui
- Nature Biotechnology, Vol. 33, Issue 5
Construction of a bacterial artificial chromosome library for Gossypium herbaceum var. africanum
journal, June 2013
- Gao, HaiYan; Wang, XingFen; Liu, Fang
- Chinese Science Bulletin, Vol. 58, Issue 26
Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss
journal, February 2011
- Schnable, J. C.; Springer, N. M.; Freeling, M.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 10
Allele-Specific, Bidirectional Silencing of an Alcohol Dehydrogenase Gene in Different Organs of Interspecific Diploid Cotton Hybrids
journal, September 2005
- Adams, Keith L.; Wendel, Jonathan F.
- Genetics, Vol. 171, Issue 4
Molecular mapping of genic male-sterile genes ms 15 , ms 5 and ms 6 in tetraploid cotton
journal, April 2009
- Chen, D.; Ding, Y.; Guo, W.
- Plant Breeding, Vol. 128, Issue 2
The draft genome of a diploid cotton Gossypium raimondii
journal, August 2012
- Wang, Kunbo; Wang, Zhiwen; Li, Fuguang
- Nature Genetics, Vol. 44, Issue 10
Functional analysis of Hsp70 superfamily proteins of rice (Oryza sativa)
journal, December 2012
- Sarkar, Neelam K.; Kundnani, Preeti; Grover, Anil
- Cell Stress and Chaperones, Vol. 18, Issue 4
Serine/threonine protein phosphatases: Multi-purpose enzymes in control of defense mechanisms
journal, December 2011
- Bajsa, Joanna; Pan, Zhiqiang; Duke, Stephen O.
- Plant Signaling & Behavior, Vol. 6, Issue 12
Genetic Diversity in Gossypium hirsutum and the Origin of Upland Cotton
journal, November 1992
- Wendel, Jonathan F.; Brubaker, Curt L.; Percival, A. Edward
- American Journal of Botany, Vol. 79, Issue 11
Dissecting the genome of the polyploid crop oilseed rape by transcriptome sequencing
journal, July 2011
- Bancroft, Ian; Morgan, Colin; Fraser, Fiona
- Nature Biotechnology, Vol. 29, Issue 8
Chromosome structural changes in diploid and tetraploid A genomes of Gossypium
journal, April 2006
- Desai, Aparna; Chee, Peng W.; Rong, Junkang
- Genome, Vol. 49, Issue 4
Consed: A Graphical Tool for Sequence Finishing
journal, March 1998
- Gordon, David; Abajian, Chris; Green, Phil
- Genome Research, Vol. 8, Issue 3
Genome sequence of the palaeopolyploid soybean
journal, January 2010
- Schmutz, Jeremy; Cannon, Steven B.; Schlueter, Jessica
- Nature, Vol. 463, Issue 7278
Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss
journal, February 2011
- Schnable, J. C.; Springer, N. M.; Freeling, M.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 10
Plant disease resistance genes: Current status and future directions
journal, April 2012
- Gururani, Mayank Anand; Venkatesh, Jelli; Upadhyaya, Chandrama Prakash
- Physiological and Molecular Plant Pathology, Vol. 78
ABySS: A parallel assembler for short read sequence data
journal, February 2009
- Simpson, J. T.; Wong, K.; Jackman, S. D.
- Genome Research, Vol. 19, Issue 6
Assembly algorithms for next-generation sequencing data
journal, June 2010
- Miller, Jason R.; Koren, Sergey; Sutton, Granger
- Genomics, Vol. 95, Issue 6
The coffee genome provides insight into the convergent evolution of caffeine biosynthesis
journal, September 2014
- Denoeud, F.; Carretero-Paulet, L.; Dereeper, A.
- Science, Vol. 345, Issue 6201
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
journal, December 2000
- Arabidopsis Genome Initiative,
- Nature, Vol. 408, Issue 6814, p. 796-815
The Origin of American Tetraploid Gossypium Species
journal, May 1940
- Beasley, J. O.
- The American Naturalist, Vol. 74, Issue 752
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
Gene Expression Changes and Early Events in Cotton Fibre Development
journal, September 2007
- Lee, J. J.; Woodward, A. W.; Chen, Z. J.
- Annals of Botany, Vol. 100, Issue 7
Construction of a plant-transformation-competent BIBAC library and genome sequence analysis of polyploid Upland cotton (Gossypium hirsutum L.)
journal, January 2013
- Lee, Mi-Kyung; Zhang, Yang; Zhang, Meiping
- BMC Genomics, Vol. 14, Issue 1
A cysteine-rich receptor-like kinase NCRK and a pathogen-induced protein kinase RBK1 are Rop GTPase interactors: Rop GTPases interacting with protein kinases
journal, December 2007
- Molendijk, Arthur J.; Ruperti, Benedetto; Singh, Manoj K.
- The Plant Journal, Vol. 53, Issue 6
A genetically anchored physical framework for Theobroma cacao cv. Matina 1-6
journal, August 2011
- Saski, Christopher A.; Feltus, Frank A.; Staton, Margaret E.
- BMC Genomics, Vol. 12, Issue 1
Construction and characterization of a bacterial artificial chromosome library for the allotetraploid Gossypium tomentosum
journal, January 2015
- Liu, F.; Wang, Y. H.; Gao, H. Y.
- Genetics and Molecular Research, Vol. 14, Issue 4
Development of a 63K SNP Array for Cotton and High-Density Mapping of Intraspecific and Interspecific Populations of Gossypium spp.
journal, April 2015
- Hulse-Kemp, A. M.; Lemm, J.; Plieske, J.
- G3: Genes|Genomes|Genetics, Vol. 5, Issue 6
Construction of a bacterial artificial chromosome library for Gossypium herbaceum var. africanum
journal, June 2013
- Gao, HaiYan; Wang, XingFen; Liu, Fang
- Chinese Science Bulletin, Vol. 58, Issue 26
Trimmomatic: a flexible trimmer for Illumina sequence data
journal, April 2014
- Bolger, Anthony M.; Lohse, Marc; Usadel, Bjoern
- Bioinformatics, Vol. 30, Issue 15
The wondrous cycles of polyploidy in plants
journal, October 2015
- Wendel, Jonathan F.
- American Journal of Botany, Vol. 102, Issue 11
Genome sequence of the cultivated cotton Gossypium arboreum
journal, May 2014
- Li, Fuguang; Fan, Guangyi; Wang, Kunbo
- Nature Genetics, Vol. 46, Issue 6
Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement
journal, April 2015
- Zhang, Tianzhen; Hu, Yan; Jiang, Wenkai
- Nature Biotechnology, Vol. 33, Issue 5
Duplicate gene evolution, homoeologous recombination, and transcriptome characterization in allopolyploid cotton
journal, January 2012
- Flagel, Lex E.; Wendel, Jonathan F.; Udall, Joshua A.
- BMC Genomics, Vol. 13, Issue 1
De novo assembly of human genomes with massively parallel short read sequencing
journal, December 2009
- Li, R.; Zhu, H.; Ruan, J.
- Genome Research, Vol. 20, Issue 2
Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution
journal, April 2015
- Li, Fuguang; Fan, Guangyi; Lu, Cairui
- Nature Biotechnology, Vol. 33, Issue 5
Cytological studies in cotton: IV. Chromosome conjugation in interspecific hybrids
journal, February 1937
- Skovsted, A.
- Journal of Genetics, Vol. 34, Issue 1
The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution
journal, March 2013
- Verde, Ignazio; Abbott, Albert G.; Scalabrin, Simone
- Nature Genetics, Vol. 45, Issue 5
Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres
journal, December 2012
- Paterson, Andrew H.; Wendel, Jonathan F.; Gundlach, Heidrun
- Nature, Vol. 492, Issue 7429
Microscopy and Bioinformatic Analyses of Lipid Metabolism Implicate a Sporophytic Signaling Network Supporting Pollen Development in Arabidopsis
journal, July 2008
- Wang, Yixing; Wu, Hong; Yang, Ming
- Molecular Plant, Vol. 1, Issue 4
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
Toward Sequencing Cotton ( Gossypium ) Genomes: Figure 1.
journal, December 2007
- Chen, Z. Jeffrey; Scheffler, Brian E.; Dennis, Elizabeth
- Plant Physiology, Vol. 145, Issue 4
Prospecting for Genes involved in transcriptional regulation of plant defenses, a bioinformatics approach
journal, January 2011
- van Verk, Marcel C.; Bol, John F.; Linthorst, Huub JM
- BMC Plant Biology, Vol. 11, Issue 1
Comparative development of fiber in wild and cultivated cotton
journal, January 2001
- Applequist, Wendy L.; Cronn, Richard; Wendel, Jonathan F.
- Evolution and Development, Vol. 3, Issue 1
An Improved Approach for Construction of Bacterial Artificial Chromosome Libraries
journal, August 1998
- Osoegawa, Kazutoyo; Woon, Peng Yeong; Zhao, Baohui
- Genomics, Vol. 52, Issue 1
Plant disease resistance genes: Current status and future directions
journal, April 2012
- Gururani, Mayank Anand; Venkatesh, Jelli; Upadhyaya, Chandrama Prakash
- Physiological and Molecular Plant Pathology, Vol. 78
BAC Sequencing Using Pooled Methods
book, September 2014
- Saski, Christopher A.; Feltus, F. Alex; Parida, Laxmi
- Methods in Molecular Biology
A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. japonica)
journal, April 2002
- Goff, S. A.
- Science, Vol. 296, Issue 5565
Roles for mannitol and mannitol dehydrogenase in active oxygen-mediated plant defense
journal, December 1998
- Jennings, D. B.; Ehrenshaft, M.; Pharr, D. M.
- Proceedings of the National Academy of Sciences, Vol. 95, Issue 25
Gene Expression Changes and Early Events in Cotton Fibre Development
journal, September 2007
- Lee, J. J.; Woodward, A. W.; Chen, Z. J.
- Annals of Botany, Vol. 100, Issue 7
The coffee genome provides insight into the convergent evolution of caffeine biosynthesis
journal, September 2014
- Denoeud, F.; Carretero-Paulet, L.; Dereeper, A.
- Science, Vol. 345, Issue 6201
Serine/threonine protein phosphatases: Multi-purpose enzymes in control of defense mechanisms
journal, December 2011
- Bajsa, Joanna; Pan, Zhiqiang; Duke, Stephen O.
- Plant Signaling & Behavior, Vol. 6, Issue 12
Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome
journal, August 2014
- Chalhoub, B.; Denoeud, F.; Liu, S.
- Science, Vol. 345, Issue 6199
A comprehensive meta QTL analysis for fiber quality, yield, yield related and morphological traits, drought tolerance, and disease resistance in tetraploid cotton
journal, January 2013
- Said, Joseph I.; Lin, Zhongxu; Zhang, Xianlong
- BMC Genomics, Vol. 14, Issue 1
Allele-Specific, Bidirectional Silencing of an Alcohol Dehydrogenase Gene in Different Organs of Interspecific Diploid Cotton Hybrids
journal, September 2005
- Adams, Keith L.; Wendel, Jonathan F.
- Genetics, Vol. 171, Issue 4
Contigs Built with Fingerprints, Markers, and FPC V4.7
journal, November 2000
- Soderlund, C.
- Genome Research, Vol. 10, Issue 11
Functional analysis of Hsp70 superfamily proteins of rice (Oryza sativa)
journal, December 2012
- Sarkar, Neelam K.; Kundnani, Preeti; Grover, Anil
- Cell Stress and Chaperones, Vol. 18, Issue 4
Molecular mapping of genic male-sterile genes ms 15 , ms 5 and ms 6 in tetraploid cotton
journal, April 2009
- Chen, D.; Ding, Y.; Guo, W.
- Plant Breeding, Vol. 128, Issue 2
The draft genome of a diploid cotton Gossypium raimondii
journal, August 2012
- Wang, Kunbo; Wang, Zhiwen; Li, Fuguang
- Nature Genetics, Vol. 44, Issue 10
BAC-End Sequence-Based SNP Mining in Allotetraploid Cotton (Gossypium) Utilizing Resequencing Data, Phylogenetic Inferences, and Perspectives for Genetic Mapping
journal, April 2015
- Hulse-Kemp, A. M.; Ashrafi, H.; Stoffel, K.
- G3: Genes|Genomes|Genetics, Vol. 5, Issue 6
Construction of a plant-transformation-competent BIBAC library and genome sequence analysis of polyploid Upland cotton (Gossypium hirsutum L.)
journal, January 2013
- Lee, Mi-Kyung; Zhang, Yang; Zhang, Meiping
- BMC Genomics, Vol. 14, Issue 1
The Origin of American Tetraploid Gossypium Species
journal, May 1940
- Beasley, J. O.
- The American Naturalist, Vol. 74, Issue 752
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
The genome sequence of Sea-Island cotton (Gossypium barbadense) provides insights into the allopolyploidization and development of superior spinnable fibres
journal, December 2015
- Yuan, Daojun; Tang, Zhonghui; Wang, Maojun
- Scientific Reports, Vol. 5, Issue 1
Estimation of the Nuclear DNA Content of Gossypium Species
journal, February 2005
- Hendrix, B.
- Annals of Botany, Vol. 95, Issue 5
Cytochrome b5 Reductase Encoded by CBR1 Is Essential for a Functional Male Gametophyte in Arabidopsis
journal, August 2013
- Wayne, Laura L.; Wallis, James G.; Kumar, Rajesh
- The Plant Cell, Vol. 25, Issue 8
Consed: A Graphical Tool for Sequence Finishing
journal, March 1998
- Gordon, David; Abajian, Chris; Green, Phil
- Genome Research, Vol. 8, Issue 3
Roles for mannitol and mannitol dehydrogenase in active oxygen-mediated plant defense
journal, December 1998
- Jennings, D. B.; Ehrenshaft, M.; Pharr, D. M.
- Proceedings of the National Academy of Sciences, Vol. 95, Issue 25
Cotton: Origin, History, Technology, and Production
journal, October 2000
- Brown, D. Clayton
- Agricultural History, Vol. 74, Issue 4
Five-Color-Based High-Information-Content Fingerprinting of Bacterial Artificial Chromosome Clones Using Type IIS Restriction Endonucleases
journal, June 2001
- Ding, Y.; Johnson, M. D.; Chen, W. Q.
- Genomics, Vol. 74, Issue 2
Works referencing / citing this record:
Cotton CENTRORADIALIS/TERMINAL FLOWER 1/SELF-PRUNING genes functionally diverged to differentially impact plant architecture
journal, September 2018
- Prewitt, Sarah F.; Ayre, Brian G.; McGarry, Roisin C.
- Journal of Experimental Botany
Impact of Chromosomal Rearrangements on the Interpretation of Lupin Karyotype Evolution
journal, April 2019
- Susek, Karolina; Bielski, Wojciech; Czyż, Katarzyna B.
- Genes, Vol. 10, Issue 4
Unraveling cis and trans regulatory evolution during cotton domestication
journal, November 2019
- Bao, Ying; Hu, Guanjing; Grover, Corrinne E.
- Nature Communications, Vol. 10, Issue 1
Functional divergence of cellulose synthase orthologs in between wild Gossypium raimondii and domesticated G. arboreum diploid cotton species
journal, September 2019
- Kim, Hee Jin; Thyssen, Gregory N.; Song, Xianliang
- Cellulose, Vol. 26, Issue 18
Genetic Analysis of the Transition from Wild to Domesticated Cotton ( Gossypium hirsutum L.)
journal, February 2020
- Grover, Corrinne E.; Yoo, Mi-Jeong; Lin, Meng
- G3 Genes|Genomes|Genetics, Vol. 10, Issue 2
Unraveling cis and trans regulatory evolution during cotton domestication
journal, November 2019
- Bao, Ying; Hu, Guanjing; Grover, Corrinne E.
- Nature Communications, Vol. 10, Issue 1
Impact of Chromosomal Rearrangements on the Interpretation of Lupin Karyotype Evolution
journal, April 2019
- Susek, Karolina; Bielski, Wojciech; Czyż, Katarzyna B.
- Genes, Vol. 10, Issue 4
Genetic Analysis of the Transition from Wild to Domesticated Cotton ( Gossypium hirsutum L.)
journal, February 2020
- Grover, Corrinne E.; Yoo, Mi-Jeong; Lin, Meng
- G3 Genes|Genomes|Genetics, Vol. 10, Issue 2
Identification of cotton MOTHER OF FT AND TFL1 homologs, GhMFT1 and GhMFT2, involved in seed germination
journal, April 2019
- Yu, Xiuli; Liu, Hui; Sang, Na
- PLOS ONE, Vol. 14, Issue 4