A Saturated Genetic Linkage Map of Autotetraploid Alfalfa (Medicago sativa L.) Developed Using Genotyping-by-Sequencing Is Highly Syntenous with the Medicago truncatula Genome
Abstract
A genetic linkage map is a valuable tool for quantitative trait locus mapping, map-based gene cloning, comparative mapping, and whole-genome assembly. Alfalfa, one of the most important forage crops in the world, is autotetraploid, allogamous, and highly heterozygous, characteristics that have impeded the construction of a high-density linkage map using traditional genetic marker systems. Using genotyping-by-sequencing (GBS), we constructed low-cost, reasonably high-density linkage maps for both maternal and paternal parental genomes of an autotetraploid alfalfa F1 population. The resulting maps contain 3591 single-nucleotide polymorphism markers on 64 linkage groups across both parents, with an average density of one marker per 1.5 and 1.0 cM for the maternal and paternal haplotype maps, respectively. Chromosome assignments were made based on homology of markers to the M. truncatula genome. Four linkage groups representing the four haplotypes of each alfalfa chromosome were assigned to each of the eight Medicago chromosomes in both the maternal and paternal parents. The alfalfa linkage groups were highly syntenous with M. truncatula, and clearly identified the known translocation between Chromosomes 4 and 8. In addition, a small inversion on Chromosome 1 was identified between M. truncatula and M. sativa. GBS enabled us to develop a saturated linkage map formore »
- Authors:
-
- The Samuel Roberts Noble Foundation, Ardmore, OK (United States)
- Chinese Academy of Agricultural Science, Beijing (China)[
- University of California, Davis, CA (United States)
- Publication Date:
- Research Org.:
- Univ. of California, Davis, CA (United States)
- Sponsoring Org.:
- USDOE; USDA; Samuel Roberts Noble Foundation; China Scholarship Council
- OSTI Identifier:
- 1627951
- Grant/Contract Number:
- 2009-65504-05809
- Resource Type:
- Accepted Manuscript
- Journal Name:
- G3
- Additional Journal Information:
- Journal Volume: 4; Journal Issue: 10; Journal ID: ISSN 2160-1836
- Publisher:
- Genetics Society of America
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; genetic linkage map; autotetraploid alfalfa; genotyping-by-sequencing
Citation Formats
Li, Xuehui, Wei, Yanling, Acharya, Ananta, Jiang, Qingzhen, Kang, Junmei, and Brummer, E. Charles. A Saturated Genetic Linkage Map of Autotetraploid Alfalfa (Medicago sativa L.) Developed Using Genotyping-by-Sequencing Is Highly Syntenous with the Medicago truncatula Genome. United States: N. p., 2014.
Web. doi:10.1534/g3.114.012245.
Li, Xuehui, Wei, Yanling, Acharya, Ananta, Jiang, Qingzhen, Kang, Junmei, & Brummer, E. Charles. A Saturated Genetic Linkage Map of Autotetraploid Alfalfa (Medicago sativa L.) Developed Using Genotyping-by-Sequencing Is Highly Syntenous with the Medicago truncatula Genome. United States. https://doi.org/10.1534/g3.114.012245
Li, Xuehui, Wei, Yanling, Acharya, Ananta, Jiang, Qingzhen, Kang, Junmei, and Brummer, E. Charles. Thu .
"A Saturated Genetic Linkage Map of Autotetraploid Alfalfa (Medicago sativa L.) Developed Using Genotyping-by-Sequencing Is Highly Syntenous with the Medicago truncatula Genome". United States. https://doi.org/10.1534/g3.114.012245. https://www.osti.gov/servlets/purl/1627951.
@article{osti_1627951,
title = {A Saturated Genetic Linkage Map of Autotetraploid Alfalfa (Medicago sativa L.) Developed Using Genotyping-by-Sequencing Is Highly Syntenous with the Medicago truncatula Genome},
author = {Li, Xuehui and Wei, Yanling and Acharya, Ananta and Jiang, Qingzhen and Kang, Junmei and Brummer, E. Charles},
abstractNote = {A genetic linkage map is a valuable tool for quantitative trait locus mapping, map-based gene cloning, comparative mapping, and whole-genome assembly. Alfalfa, one of the most important forage crops in the world, is autotetraploid, allogamous, and highly heterozygous, characteristics that have impeded the construction of a high-density linkage map using traditional genetic marker systems. Using genotyping-by-sequencing (GBS), we constructed low-cost, reasonably high-density linkage maps for both maternal and paternal parental genomes of an autotetraploid alfalfa F1 population. The resulting maps contain 3591 single-nucleotide polymorphism markers on 64 linkage groups across both parents, with an average density of one marker per 1.5 and 1.0 cM for the maternal and paternal haplotype maps, respectively. Chromosome assignments were made based on homology of markers to the M. truncatula genome. Four linkage groups representing the four haplotypes of each alfalfa chromosome were assigned to each of the eight Medicago chromosomes in both the maternal and paternal parents. The alfalfa linkage groups were highly syntenous with M. truncatula, and clearly identified the known translocation between Chromosomes 4 and 8. In addition, a small inversion on Chromosome 1 was identified between M. truncatula and M. sativa. GBS enabled us to develop a saturated linkage map for alfalfa that greatly improved genome coverage relative to previous maps and that will facilitate investigation of genome structure. GBS could be used in breeding populations to accelerate molecular breeding in alfalfa.},
doi = {10.1534/g3.114.012245},
journal = {G3},
number = 10,
volume = 4,
place = {United States},
year = {Thu Aug 21 00:00:00 EDT 2014},
month = {Thu Aug 21 00:00:00 EDT 2014}
}
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Works referenced in this record:
A Next-Generation Sequencing Method for Genotyping-by-Sequencing of Highly Heterozygous Autotetraploid Potato
journal, May 2013
- Uitdewilligen, Jan G. A. M. L.; Wolters, Anne-Marie A.; D’hoop, Bjorn B.
- PLoS ONE, Vol. 8, Issue 5
The Sorghum bicolor genome and the diversification of grasses
journal, January 2009
- Paterson, Andrew H.; Bowers, John E.; Bruggmann, Rémy
- Nature, Vol. 457, Issue 7229
Applied Genetics and Genomics in Alfalfa Breeding
journal, March 2012
- Li, Xuehui; Brummer, E. Charles
- Agronomy, Vol. 2, Issue 1
An integrated genetic linkage map for white clover (Trifolium repens L.) with alignment to Medicago
journal, January 2013
- Griffiths, Andrew G.; Barrett, Brent A.; Simon, Deborah
- BMC Genomics, Vol. 14, Issue 1
Bridging the genotyping gap: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations
journal, August 2013
- Spindel, Jennifer; Wright, Mark; Chen, Charles
- Theoretical and Applied Genetics, Vol. 126, Issue 11
Integration of Two Diploid Potato Linkage Maps with the Potato Genome Sequence
journal, April 2012
- Felcher, Kimberly J.; Coombs, Joseph J.; Massa, Alicia N.
- PLoS ONE, Vol. 7, Issue 4
The Medicago truncatula reference accession A17 has an aberrant chromosomal configuration
journal, March 2007
- Kamphuis, Lars G.; Williams, Angela H.; D'Souza, Nola K.
- New Phytologist, Vol. 174, Issue 2
Genome size and base composition in Medicago sativa and M . truncatula species
journal, April 1994
- Blondon, François; Marie, Dominique; Brown, Spencer
- Genome, Vol. 37, Issue 2
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
journal, January 2009
- Langmead, Ben; Trapnell, Cole; Pop, Mihai
- Genome Biology, Vol. 10, Issue 3
Prevalence of segregation distortion in diploid alfalfa and its implications for genetics and breeding applications
journal, May 2011
- Li, Xuehui; Wang, Xiaojuan; Wei, Yanling
- Theoretical and Applied Genetics, Vol. 123, Issue 4
Switchgrass Genomic Diversity, Ploidy, and Evolution: Novel Insights from a Network-Based SNP Discovery Protocol
journal, January 2013
- Lu, Fei; Lipka, Alexander E.; Glaubitz, Jeff
- PLoS Genetics, Vol. 9, Issue 1
Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross: mapping strategy and RAPD markers.
journal, August 1994
- Grattapaglia, D.; Sederoff, R.
- Genetics, Vol. 137, Issue 4
Identification of Aluminum Tolerance Quantitative Trait Loci in Tetraploid Alfalfa
journal, January 2013
- Khu, Dong‐Man; Reyno, Rafael; Han, Yuanhong
- Crop Science, Vol. 53, Issue 1
TetraploidMap for Windows: Linkage Map Construction and QTL Mapping in Autotetraploid Species
journal, September 2007
- Hackett, C. A.; Milne, I.; Bradshaw, J. E.
- Journal of Heredity, Vol. 98, Issue 7
Development of a Large SNP Genotyping Array and Generation of High-Density Genetic Maps in Tomato
journal, July 2012
- Sim, Sung-Chur; Durstewitz, Gregor; Plieske, Jörg
- PLoS ONE, Vol. 7, Issue 7
A Sequence-Based Genetic Map of Medicago truncatula and Comparison of Marker Colinearity with M. sativa
journal, March 2004
- Choi, Hong-Kyu; Kim, Dongjin; Uhm, Taesik
- Genetics, Vol. 166, Issue 3
An Improved Genotyping by Sequencing (GBS) Approach Offering Increased Versatility and Efficiency of SNP Discovery and Genotyping
journal, January 2013
- Sonah, Humira; Bastien, Maxime; Iquira, Elmer
- PLoS ONE, Vol. 8, Issue 1
Effects of missing marker and segregation distortion on QTL mapping in F2 populations
journal, June 2010
- Zhang, Luyan; Wang, Shiquan; Li, Huihui
- Theoretical and Applied Genetics, Vol. 121, Issue 6
Multipoint maximum likelihood mapping in a full-sib family of an outbreeding species
journal, August 2011
- Van Ooijen, J. W.
- Genetics Research, Vol. 93, Issue 5
Effects of genotyping errors, missing values and segregation distortion in molecular marker data on the construction of linkage maps
journal, January 2003
- Hackett, C. A.; Broadfoot, L. B.
- Heredity, Vol. 90, Issue 1
Genomic Selection in Wheat Breeding using Genotyping-by-Sequencing
journal, January 2012
- Poland, Jesse; Endelman, Jeffrey; Dawson, Julie
- The Plant Genome Journal, Vol. 5, Issue 3
High-density SNP-based genetic map development and linkage disequilibrium assessment in Brassica napus L
journal, January 2013
- Delourme, Régine; Falentin, Cyril; Fomeju, Berline
- BMC Genomics, Vol. 14, Issue 1
Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems
journal, April 2011
- Yang, S. Samuel; Tu, Zheng Jin; Cheung, Foo
- BMC Genomics, Vol. 12, Issue 1
A molecular marker linkage map of tetraploid alfalfa (Medicago sativa L.)
journal, November 1999
- Brouwer, D. J.; Osborn, T. C.
- Theoretical and Applied Genetics, Vol. 99, Issue 7-8
Genome-wide SNP discovery in tetraploid alfalfa using 454 sequencing and high resolution melting analysis
journal, July 2011
- Han, Yuanhong; Kang, Yun; Torres-Jerez, Ivone
- BMC Genomics, Vol. 12, Issue 1
Genetic Mapping of Biomass Production in Tetraploid Alfalfa
journal, January 2007
- Robins, Joseph G.; Luth, Diane; Campbell, T. Austin
- Crop Science, Vol. 47, Issue 1
Development of a dense SNP-based linkage map of an apple rootstock progeny using the Malus Infinium whole genome genotyping array
journal, January 2012
- Antanaviciute, Laima; Fernández-Fernández, Felicidad; Jansen, Johannes
- BMC Genomics, Vol. 13, Issue 1
Development of an Alfalfa SNP Array and Its Use to Evaluate Patterns of Population Structure and Linkage Disequilibrium
journal, January 2014
- Li, Xuehui; Han, Yuanhong; Wei, Yanling
- PLoS ONE, Vol. 9, Issue 1
Identification of QTL for resistance and susceptibility to Stagonospora meliloti in autotetraploid lucerne
journal, March 2007
- Musial, J. M.; Mackie, J. M.; Armour, D. J.
- Theoretical and Applied Genetics, Vol. 114, Issue 8
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
Construction of two genetic linkage maps in cultivated tetraploid alfalfa (Medicago sativa) using microsatellite and AFLP markers
journal, January 2003
- Julier, Bernadette; Flajoulot, Sandrine; Barre, Philippe
- BMC Plant Biology, Vol. 3, Issue 1, p. 9
RFLP Linkage Map of an Alfalfa Meiotic Mutant Based on an F1 Population
journal, March 1996
- Tavoletti, S.; Veronesi, F.; Osborn, T. C.
- Journal of Heredity, Vol. 87, Issue 2
Prevalence of single nucleotide polymorphism among 27 diverse alfalfa genotypes as assessed by transcriptome sequencing
journal, January 2012
- Li, Xuehui; Acharya, Ananta; Farmer, Andrew D.
- BMC Genomics, Vol. 13, Issue 1
R/qtl: high-throughput multiple QTL mapping: Fig. 1.
journal, October 2010
- Arends, Danny; Prins, Pjotr; Jansen, Ritsert C.
- Bioinformatics, Vol. 26, Issue 23
High-density linkage mapping in a pine tree reveals a genomic region associated with inbreeding depression and provides clues to the extent and distribution of meiotic recombination
journal, January 2013
- Chancerel, Emilie; Lamy, Jean-Baptiste; Lesur, Isabelle
- BMC Biology, Vol. 11, Issue 1
MapChart: Software for the Graphical Presentation of Linkage Maps and QTLs
journal, January 2002
- Voorrips, R. E.
- Journal of Heredity, Vol. 93, 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
An expressed sequence tag SSR map of tetraploid alfalfa (Medicago sativa L.)
journal, August 2005
- Sledge, M. K.; Ray, I. M.; Jiang, G.
- Theoretical and Applied Genetics, Vol. 111, Issue 5
An economic method for the fluorescent labeling of PCR fragments
journal, February 2000
- Schuelke, Markus
- Nature Biotechnology, Vol. 18, Issue 2
An expressed sequence tag SSR map of tetraploid alfalfa (Medicago sativa L.)
journal, August 2005
- Sledge, M. K.; Ray, I. M.; Jiang, G.
- Theoretical and Applied Genetics, Vol. 111, Issue 5
Identification of QTL for resistance and susceptibility to Stagonospora meliloti in autotetraploid lucerne
journal, March 2007
- Musial, J. M.; Mackie, J. M.; Armour, D. J.
- Theoretical and Applied Genetics, Vol. 114, Issue 8
Prevalence of segregation distortion in diploid alfalfa and its implications for genetics and breeding applications
journal, May 2011
- Li, Xuehui; Wang, Xiaojuan; Wei, Yanling
- Theoretical and Applied Genetics, Vol. 123, Issue 4
Bridging the genotyping gap: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations
journal, August 2013
- Spindel, Jennifer; Wright, Mark; Chen, Charles
- Theoretical and Applied Genetics, Vol. 126, Issue 11
Effects of genotyping errors, missing values and segregation distortion in molecular marker data on the construction of linkage maps
journal, January 2003
- Hackett, C. A.; Broadfoot, L. B.
- Heredity, Vol. 90, Issue 1
R/qtl: high-throughput multiple QTL mapping: Fig. 1.
journal, October 2010
- Arends, Danny; Prins, Pjotr; Jansen, Ritsert C.
- Bioinformatics, Vol. 26, Issue 23
MapChart: Software for the Graphical Presentation of Linkage Maps and QTLs
journal, January 2002
- Voorrips, R. E.
- Journal of Heredity, Vol. 93, Issue 1
RFLP Linkage Map of an Alfalfa Meiotic Mutant Based on an F1 Population
journal, March 1996
- Tavoletti, S.; Veronesi, F.; Osborn, T. C.
- Journal of Heredity, Vol. 87, Issue 2
Genome size and base composition in Medicago sativa and M . truncatula species
journal, April 1994
- Blondon, François; Marie, Dominique; Brown, Spencer
- Genome, Vol. 37, Issue 2
Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems
journal, April 2011
- Yang, S. Samuel; Tu, Zheng Jin; Cheung, Foo
- BMC Genomics, Vol. 12, Issue 1
Development of a dense SNP-based linkage map of an apple rootstock progeny using the Malus Infinium whole genome genotyping array
journal, January 2012
- Antanaviciute, Laima; Fernández-Fernández, Felicidad; Jansen, Johannes
- BMC Genomics, Vol. 13, Issue 1
Prevalence of single nucleotide polymorphism among 27 diverse alfalfa genotypes as assessed by transcriptome sequencing
journal, January 2012
- Li, Xuehui; Acharya, Ananta; Farmer, Andrew D.
- BMC Genomics, Vol. 13, Issue 1
High-density SNP-based genetic map development and linkage disequilibrium assessment in Brassica napus L
journal, January 2013
- Delourme, Régine; Falentin, Cyril; Fomeju, Berline
- BMC Genomics, Vol. 14, Issue 1
An integrated genetic linkage map for white clover (Trifolium repens L.) with alignment to Medicago
journal, January 2013
- Griffiths, Andrew G.; Barrett, Brent A.; Simon, Deborah
- BMC Genomics, Vol. 14, Issue 1
High-density linkage mapping in a pine tree reveals a genomic region associated with inbreeding depression and provides clues to the extent and distribution of meiotic recombination
journal, January 2013
- Chancerel, Emilie; Lamy, Jean-Baptiste; Lesur, Isabelle
- BMC Biology, Vol. 11, 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
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
Integration of Two Diploid Potato Linkage Maps with the Potato Genome Sequence
journal, April 2012
- Felcher, Kimberly J.; Coombs, Joseph J.; Massa, Alicia N.
- PLoS ONE, Vol. 7, Issue 4
Development of a Large SNP Genotyping Array and Generation of High-Density Genetic Maps in Tomato
journal, July 2012
- Sim, Sung-Chur; Durstewitz, Gregor; Plieske, Jörg
- PLoS ONE, Vol. 7, Issue 7
An Improved Genotyping by Sequencing (GBS) Approach Offering Increased Versatility and Efficiency of SNP Discovery and Genotyping
journal, January 2013
- Sonah, Humira; Bastien, Maxime; Iquira, Elmer
- PLoS ONE, Vol. 8, Issue 1
A Next-Generation Sequencing Method for Genotyping-by-Sequencing of Highly Heterozygous Autotetraploid Potato
journal, May 2013
- Uitdewilligen, Jan G. A. M. L.; Wolters, Anne-Marie A.; D’hoop, Bjorn B.
- PLoS ONE, Vol. 8, Issue 5
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
A Sequence-Based Genetic Map of Medicago truncatula and Comparison of Marker Colinearity with M. sativa
journal, March 2004
- Choi, Hong-Kyu; Kim, Dongjin; Uhm, Taesik
- Genetics, Vol. 166, Issue 3
Works referencing / citing this record:
A Parthenogenesis Gene Candidate and Evidence for Segmental Allopolyploidy in Apomictic Brachiaria decumbens
journal, July 2016
- Worthington, Margaret; Heffelfinger, Christopher; Bernal, Diana
- Genetics, Vol. 203, Issue 3
A fully automated pipeline for quantitative genotype calling from next generation sequencing data in autopolyploids
journal, November 2018
- Pereira, Guilherme S.; Garcia, Antonio Augusto F.; Margarido, Gabriel R. A.
- BMC Bioinformatics, Vol. 19, Issue 1
Genome-Wide Association Mapping and Genomic Selection for Alfalfa (Medicago sativa) Forage Quality Traits
journal, January 2017
- Biazzi, Elisa; Nazzicari, Nelson; Pecetti, Luciano
- PLOS ONE, Vol. 12, Issue 1
Mining sequence variations in representative polyploid sugarcane germplasm accessions
journal, August 2017
- Yang, Xiping; Song, Jian; You, Qian
- BMC Genomics, Vol. 18, Issue 1
A High-Density Linkage Map of the Forage Grass Eragrostis curvula and Localization of the Diplospory Locus
journal, July 2019
- Zappacosta, Diego; Gallardo, Jimena; Carballo, José
- Frontiers in Plant Science, Vol. 10
Translocation of a parthenogenesis gene candidate to an alternate carrier chromosome in apomictic Brachiaria humidicola
journal, January 2019
- Worthington, Margaret; Ebina, Masumi; Yamanaka, Naoki
- BMC Genomics, Vol. 20, Issue 1
Identification of Single-Nucleotide Polymorphic Loci Associated with Biomass Yield under Water Deficit in Alfalfa (Medicago sativa L.) Using Genome-Wide Sequencing and Association Mapping
journal, June 2017
- Yu, Long-Xi
- Frontiers in Plant Science, Vol. 8
Expected Genotype Quality and Diploidized Marker Data from Genotyping-by-Sequencing of Urochloa spp. Tetraploids
posted_content, January 2019
- Matias, Filipe Inácio; Meireles, Karem Guimarães Xavier; Nagamatsu, Sheila Tiemi
- bioRxiv
Expected Genotype Quality and Diploidized Marker Data from Genotyping‐by‐Sequencing of Urochloa spp. Tetraploids
journal, November 2019
- Matias, Filipe Inácio; Xavier Meireles, Karem Guimarães; Nagamatsu, Sheila Tiemi
- The Plant Genome, Vol. 12, Issue 3
Genome-Wide Association Study Identifies Loci for Salt Tolerance during Germination in Autotetraploid Alfalfa (Medicago sativa L.) Using Genotyping-by-Sequencing
journal, June 2016
- Yu, Long-Xi; Liu, Xinchun; Boge, William
- Frontiers in Plant Science, Vol. 7
SNP Discovery by GBS in Olive and the Construction of a High-Density Genetic Linkage Map
journal, February 2016
- İpek, Ahmet; Yılmaz, Kübra; Sıkıcı, Pelin
- Biochemical Genetics, Vol. 54, Issue 3
Genotyping Polyploids from Messy Sequencing Data
journal, September 2018
- Gerard, David; Ferrão, Luis Felipe Ventorim; Garcia, Antonio Augusto Franco
- Genetics, Vol. 210, Issue 3
Polyploidy: Pitfalls and paths to a paradigm
journal, May 2016
- Soltis, Douglas E.; Visger, Clayton J.; Marchant, D. Blaine
- American Journal of Botany, Vol. 103, Issue 7
Insights Into the Genetic Basis of Blueberry Fruit-Related Traits Using Diploid and Polyploid Models in a GWAS Context
journal, July 2018
- Ferrão, Luís Felipe V.; Benevenuto, Juliana; Oliveira, Ivone de Bem
- Frontiers in Ecology and Evolution, Vol. 6
Development and Applications of a High Throughput Genotyping Tool for Polyploid Crops: Single Nucleotide Polymorphism (SNP) Array
journal, February 2018
- You, Qian; Yang, Xiping; Peng, Ze
- Frontiers in Plant Science, Vol. 9
Genotyping Polyploids from Messy Sequencing Data
posted_content, August 2018
- Gerard, David; Ferrão, Luis Felipe Ventorim; Garcia, Antonio Augusto Franco
Automated tetraploid genotype calling by hierarchical clustering
journal, January 2017
- Schmitz Carley, Cari A.; Coombs, Joseph J.; Douches, David S.
- Theoretical and Applied Genetics, Vol. 130, Issue 4
A high-density SNP genetic map consisting of a complete set of homologous groups in autohexaploid sweetpotato (Ipomoea batatas)
journal, March 2017
- Shirasawa, Kenta; Tanaka, Masaru; Takahata, Yasuhiro
- Scientific Reports, Vol. 7, Issue 1
QTL mapping of flowering time and biomass yield in tetraploid alfalfa (Medicago sativa L.)
journal, August 2019
- Adhikari, Laxman; Makaju, Shiva Om; Missaoui, Ali M.
- BMC Plant Biology, Vol. 19, Issue 1
Genomic Prediction of Biomass Yield in Two Selection Cycles of a Tetraploid Alfalfa Breeding Population
journal, July 2015
- Li, Xuehui; Wei, Yanling; Acharya, Ananta
- The Plant Genome, Vol. 8, Issue 2
The Medicago sativa gene index 1.2: a web-accessible gene expression atlas for investigating expression differences between Medicago sativa subspecies
journal, July 2015
- O’Rourke, Jamie A.; Fu, Fengli; Bucciarelli, Bruna
- BMC Genomics, Vol. 16, Issue 1
Restriction site-associated DNA sequencing for SNP discovery and high-density genetic map construction in southern catfish ( Silurus meridionalis )
journal, May 2018
- Xie, Mimi; Ming, Yao; Shao, Feng
- Royal Society Open Science, Vol. 5, Issue 5
The Chromosome-Level Genome Sequence of the Autotetraploid Alfalfa and Resequencing of Core Germplasms Provide Genomic Resources for Alfalfa Research
journal, September 2020
- Shen, Chen; Du, Huilong; Chen, Zhuo
- Molecular Plant, Vol. 13, Issue 9
Ultra-high density intra-specific genetic linkage maps accelerate identification of functionally relevant molecular tags governing important agronomic traits in chickpea
journal, May 2015
- Kujur, Alice; Upadhyaya, Hari D.; Shree, Tanima
- Scientific Reports, Vol. 5, Issue 1
A high-density SNP genetic map consisting of a complete set of homologous groups in autohexaploid sweetpotato (Ipomoea batatas)
journal, March 2017
- Shirasawa, Kenta; Tanaka, Masaru; Takahata, Yasuhiro
- Scientific Reports, Vol. 7, Issue 1
Mapping Loci that Control Tuber and Foliar Symptoms Caused by PVY in Autotetraploid Potato (Solanum tuberosum L.)
journal, June 2017
- da Silva, Washington; Ingram, Jason; Hackett, Christine A.
- bioRxiv
A fully automated pipeline for quantitative genotype calling from next generation sequencing data in autopolyploids
journal, November 2018
- Pereira, Guilherme S.; Garcia, Antonio Augusto F.; Margarido, Gabriel R. A.
- BMC Bioinformatics, Vol. 19, Issue 1
The Medicago sativa gene index 1.2: a web-accessible gene expression atlas for investigating expression differences between Medicago sativa subspecies
journal, July 2015
- O’Rourke, Jamie A.; Fu, Fengli; Bucciarelli, Bruna
- BMC Genomics, Vol. 16, Issue 1
QTL mapping of flowering time and biomass yield in tetraploid alfalfa (Medicago sativa L.)
journal, August 2019
- Adhikari, Laxman; Makaju, Shiva Om; Missaoui, Ali M.
- BMC Plant Biology, Vol. 19, Issue 1
Construction of High Density Sweet Cherry (Prunus avium L.) Linkage Maps Using Microsatellite Markers and SNPs Detected by Genotyping-by-Sequencing (GBS)
journal, May 2015
- Guajardo, Verónica; Solís, Simón; Sagredo, Boris
- PLOS ONE, Vol. 10, Issue 5
Validation of Genotyping-By-Sequencing Analysis in Populations of Tetraploid Alfalfa by 454 Sequencing
journal, June 2015
- Rocher, Solen; Jean, Martine; Castonguay, Yves
- PLOS ONE, Vol. 10, Issue 6
Genetic Linkage Mapping of Economically Important Traits in Cultivated Tetraploid Potato (Solanum tuberosum L.)
journal, November 2015
- Massa, Alicia N.; Manrique-Carpintero, Norma C.; Coombs, Joseph J.
- G3 Genes|Genomes|Genetics, Vol. 5, Issue 11
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journal, February 2018
- Munjal, Gitanshu; Hao, Jingjie; Teuber, Larry R.
- G3 Genes|Genomes|Genetics, Vol. 8, Issue 2
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journal, May 2018
- Ates, Duygu; Aldemir, Secil; Yagmur, Bulent
- G3 Genes|Genomes|Genetics, Vol. 8, Issue 5
A Parthenogenesis Gene Candidate and Evidence for Segmental Allopolyploidy in Apomictic Brachiaria decumbens
journal, July 2016
- Worthington, Margaret; Heffelfinger, Christopher; Bernal, Diana
- Genetics, Vol. 203, Issue 3
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journal, June 2016
- Yu, Long-Xi; Liu, Xinchun; Boge, William
- Frontiers in Plant Science, Vol. 7
The Impact of Genotyping-by-Sequencing Pipelines on SNP Discovery and Identification of Markers Associated with Verticillium Wilt Resistance in Autotetraploid Alfalfa (Medicago sativa L.)
journal, February 2017
- Yu, Long-Xi; Zheng, Ping; Bhamidimarri, Suresh
- Frontiers in Plant Science, Vol. 8
Identification of Single-Nucleotide Polymorphic Loci Associated with Biomass Yield under Water Deficit in Alfalfa (Medicago sativa L.) Using Genome-Wide Sequencing and Association Mapping
journal, June 2017
- Yu, Long-Xi
- Frontiers in Plant Science, Vol. 8
Development and Applications of a High Throughput Genotyping Tool for Polyploid Crops: Single Nucleotide Polymorphism (SNP) Array
journal, February 2018
- You, Qian; Yang, Xiping; Peng, Ze
- Frontiers in Plant Science, Vol. 9
Genomic Prediction for 25 Agronomic and Quality Traits in Alfalfa (Medicago sativa)
journal, August 2018
- Jia, Congjun; Zhao, Fuping; Wang, Xuemin
- Frontiers in Plant Science, Vol. 9
Transcriptome Analysis of Fusarium Root-Rot-Resistant and -Susceptible Alfalfa (Medicago sativa L.) Plants during Plant–Pathogen Interactions
journal, April 2022
- Zhang, Wenyu; Wang, Zicheng; Dan, Zhencuo
- Genes, Vol. 13, Issue 5