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1. Gene flow in alfalfa
: biology, mitigation, and potential impact on production
by Van Deynze, Allen Emile and Council for Agricultural Science and Technology
2008, Special publication, ISBN 9781887383301, Volume no. 28., vi, 30
"Although there have been instances in which low-level presence of regulated materials has resulted in market disruptions (e.g., Starlink corn, LL601 and LL604... 
Manipulations génétiques | Biotechnology | Luzerne | Aspect de l'environnement | Environmental aspects | Genetics | Hérédité | Alfalfa | Genetic engineering | Biotechnologie
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2. Full Text Retrospective view of North American potato (Solanum tuberosum L.) breeding in the 20th and 21st centuries
by Hirsch, Candice N and Hirsch, Cory D and Felcher, Kimberly and Coombs, Joseph and Zarka, Dan and Van Deynze, Allen and De Jong, Walter and Veilleux, Richard E and Jansky, Shelley and Bethke, Paul and Douches, David S and Buell, C. Robin
G3: Genes, Genomes, Genetics, ISSN 2160-1836, 2013, Volume 3, Issue 6, pp. 1003 - 1013
Cultivated potato (Solanum tuberosum L.), a vegetatively propagated autotetraploid, has been bred for distinct market classes, including fresh market,... 
Phenotypic diversity | Genotypic diversity | Solanum tuberosum | Genomics | VARIETY | CYCLASE | STORAGE | QUALITY | CAROTENOIDS | POLYMORPHISM | genotypic diversity | SOLIDS | GENETICS & HEREDITY | genomics | phenotypic diversity | ACCUMULATION | GERMPLASM | HYBRIDS | Geography | Solanum tuberosum - history | Gene Frequency - genetics | Solanum tuberosum - growth & development | History, 21st Century | Seeds - genetics | History, 20th Century | Selection, Genetic | Solanum tuberosum - economics | North America | Marketing | Phenotype | Biosynthetic Pathways - genetics | Carotenoids - metabolism | Polymorphism, Single Nucleotide - genetics | Heterozygote | Agriculture | Breeding - history | Solanum tuberosum - genetics
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3. Full Text Genetic structure and domestication of carrot (Daucus carota subsp. sativus) (Apiaceae) 1
by Iorizzo, Massimo and Senalik, Douglas A and Ellison, Shelby L and Grzebelus, Dariusz and Cavagnaro, Pablo F and Allender, Charlotte and Brunet, Johanne and Spooner, David M and Van Deynze, Allen and Simon, Philipp W
American Journal of Botany, ISSN 0002-9122, 05/2013, Volume 100, Issue 5, pp. 930 - 938
Domestication | Genetic diversity | Daucus carota | Apiaceae | Single nucleotide polymorphism (snp)
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4. Full Text Andromonoecy in Gynandropsis gynandra (L.) Briq. (Cleomaceae) and effects on fruit and seed production
by Zohoungbogbo, Herbaud P. F and Houdegbe, Carlos A and Sogbohossou, Dêêdi E. O and Tossou, Monique G and Maundu, Patrick and Schranz, Eric M and Van Deynze, Allen and Zoundjihekpon, Jeanne and Achigan-Dako, Enoch G
Genetic Resources and Crop Evolution, ISSN 0925-9864, 12/2018, Volume 65, Issue 8, pp. 2231 - 2239
Spider plant (Gynandropsis gynandra) is a traditional leafy vegetable widespread in sub-Saharan Africa and tropical Asia that is also valued for its medicinal... 
Life Sciences | Plant Systematics/Taxonomy/Biogeography | Pollination systems | Plant Genetics and Genomics | Gynandropsis gynandra | Hermaphroditism | Plant Physiology | Agriculture | Andromonoecy | Anthesis | Plant Sciences | PHYLOGENY | AGRONOMY | REPRODUCTIVE ECOLOGY | CAPPARACEAE | PLANT SCIENCES | EVOLUTION | CLEOME-GYNANDRA | PLANTS | SYSTEMS | POLLINATION | DIVERSITY | SELF-FERTILIZATION | Seeds | Seed industry | Flowers | Plant reproduction | Fruit set | Breeding | Hand | Pollination | Fruits | Hermaphrodites | Reproduction | Seed set | Randomization | Morphology | Breeding success | Cross-pollination | Cultivars
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5. Full Text Texture diversity in melon (Cucumis melo L.): Sensory and physical assessments
by Farcuh, Macarena and Copes, Bill and Le-Navenec, Gaelle and Marroquin, Juan and Jaunet, Thierry and Chi-Ham, Cecilia and Cantu, Dario and Bradford, Kent J and Van Deynze, Allen
Postharvest Biology and Technology, ISSN 0925-5214, 01/2020, Volume 159, p. 111024
Melon ( L.) is a commercially important horticultural crop worldwide that exhibits extensive phenotypic and genetic variation. Texture is one of the key... 
Cucumis melo L | Postharvest storage | Sensory attributes | Texture | Instrumental parameters | Fruit quality
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6. Genetic Analysis of Resistance to Multiple Isolates of Phytophthora capsici and Linkage to Horticultural Traits in Bell Pepper
by Chunthawodtiporn, J and Hill, T and Stoffel, K and Van Deynze, A
HORTSCIENCE, ISSN 0018-5345, 07/2019, Volume 54, Issue 7, pp. 1143 - 1143
Phytophthora capsici is one of the major pathogens found in pepper production, especially in bell pepper. Due to the high level of genetic diversity of the... 
MANAGEMENT | plant breeding | FOLIAR-BLIGHT | IDENTIFICATION | C. annuum | PLANT-RESISTANCE | HORTICULTURE | disease resistance | ANNUUM | QTL analysis | P. capsici | BROAD-SPECTRUM RESISTANCE | RACE-SPECIFIC RESISTANCE | ROOT-ROT | INHERITANCE
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7. Full Text The zinc‐finger transcription factor Cc LOL 1 controls chloroplast development and immature pepper fruit color in Capsicum chinense and its function is conserved in tomato
by Borovsky, Yelena and Monsonego, Noam and Mohan, Vijee and Shabtai, Sara and Kamara, Itzhak and Faigenboim, Adi and Hill, Theresa and Chen, Shiyu and Stoffel, Kevin and Van Deynze, Allen and Paran, Ilan
The Plant Journal, ISSN 0960-7412, 07/2019, Volume 99, Issue 1, pp. 41 - 55
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8. Full Text The draft genomes of five agriculturally important African orphan crops
by Chang, Yue and Liu, Huan and Liu, Min and Liao, Xuezhu and Sahu, Sunil Kumar and Fu, Yuan and Song, Bo and Cheng, Shifeng and Kariba, Robert and Muthemba, Samuel and Hendre, Prasad S and Mayes, Sean and Ho, Wai Kuan and Yssel, Anna E J and Kendabie, Presidor and Wang, Sibo and Li, Linzhou and Muchugi, Alice and Jamnadass, Ramni and Lu, Haorong and Peng, Shufeng and Van Deynze, Allen and Simons, Anthony and Yana-Shapiro, Howard and de Peer, Yves Van and Xu, Xun and Yang, Huanming and Wang, Jian and Liu, Xin
GigaScience, ISSN 2047-217X, 03/2019, Volume 8, Issue 3
Background: The expanding world population is expected to double the worldwide demand for food by 2050. Eighty-eight percent of countries currently face a... 
transcription factor | orphan crops | root nodule symbiosis | transcriptome | whole-genome sequencing | food security | SUPPLEMENT | PROTEIN | MULTIDISCIPLINARY SCIENCES | CLASSIFICATION | IDENTIFICATION | NITROGEN-FIXATION | ORIGIN | ALIGNMENT | RESISTANT STARCH | ANNOTATION | DIVERSITY
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9. Full Text Selection and validation of reference genes for gene expression analysis in switchgrass (Panicum virgatum) using quantitative real-time RT-PCR
by Gimeno, Jacinta and Eattock, Nicholas and Van Deynze, Allen and Blumwald, Eduardo
PLoS ONE, ISSN 1932-6203, 03/2014, Volume 9, Issue 3, p. e91474
Switchgrass (Panicum virgatum) has received a lot of attention as a forage and bioenergy crop during the past few years. Gene expression studies are in... 
YIELDS | RECALCITRANCE | FORAGE | MULTIDISCIPLINARY SCIENCES | NITROGEN | MARKERS | ETHANOL | CELLULOSE SYNTHASE GENES | NORMALIZATION | BIOMASS PRODUCTION | HARVEST | Real-Time Polymerase Chain Reaction - standards | Reference Standards | DNA Primers - genetics | Gene Expression Profiling - standards | Genes, Plant - genetics | Panicum - genetics | Gene expression | Biomass energy | Genes | Statistical analysis | Transcription | Abundance | Statistical methods | Stability analysis | Biomass | Real time | Biofuels | Polymerase chain reaction | Algorithms | Plant tissues | Glyceraldehyde-3-phosphate dehydrogenase | Cultivars
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10. Full Text Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres
by Paterson, Andrew H and Wendel, Jonathan F and Gundlach, Heidrun and Guo, Hui and Jenkins, Jerry and Jin, Dianchuan and Llewellyn, Danny and Showmaker, Kurtis C and Shu, Shengqiang and Udall, Joshua and Yoo, Mi-Jeong and Byers, Robert and Chen, Wei and Doron-Faigenboim, Adi and Duke, Mary V and Gong, Lei and Grimwood, Jane and Grover, Corrinne and Grupp, Kara and Hu, Guanjing and Lee, Tae-Ho and Li, Jingping and Lin, Lifeng and Liu, Tao and Marler, Barry S and Page, Justin T and Roberts, Alison W and Romanel, Elisson and Sanders, William S and Szadkowski, Emmanuel and Tan, Xu and Tang, Haibao and Xu, Chunming and Wang, Jinpeng and Wang, Zining and Zhang, Dong and Zhang, Lan and Ashrafi, Hamid and Bedon, Frank and Bowers, John E and Brubaker, Curt L and Chee, Peng W and Das, Sayan and Gingle, Alan R and Haigler, Candace H and Harker, David and Hoffmann, Lucia V and Hovav, Ran and Jones, Donald C and Lemke, Cornelia and Mansoor, Shahid and Rahman, Mehboob Ur and Rainville, Lisa N and Rambani, Aditi and Reddy, Umesh K and Rong, Jun-Kang and Saranga, Yehoshua and Scheffler, Brian E and Scheffler, Jodi A and Stelly, David M and Triplett, Barbara A and Van Deynze, Allen and Vaslin, Maite F. S and Waghmare, Vijay N and Walford, Sally A and Wright, Robert J and Zaki, Essam A and Zhang, Tianzhen and Dennis, Elizabeth S and Mayer, Klaus F. X and Peterson, Daniel G and Rokhsar, Daniel S and Wang, Xiyin and Schmutz, Jeremy and Joint Genome Institute (JGI)
Nature, ISSN 0028-0836, 12/2012, Volume 492, Issue 7429, pp. 423 - 427
Polyploidy often confers emergent properties, such as the higher fibre productivity and quality of tetraploid cottons than diploid cottons bred for the same... 
ORGANIZATION | PATHWAYS | RECOMBINATION | PROTEIN | DNA | MULTIDISCIPLINARY SCIENCES | SEQUENCE | PLANTS | BARBADENSE | ANCIENT | ARABIDOPSIS | Polyploidy | Genome, Plant - genetics | Molecular Sequence Annotation | Phylogeny | Cacao - genetics | Biological Evolution | Cotton Fiber | Gossypium - classification | Diploidy | Genes, Plant - genetics | Gossypium - genetics | Alleles | Gene Duplication - genetics | Chromosomes, Plant - genetics | Vitis - genetics | Physiological aspects | Genetic research | Genetic aspects | Research | Cotton | Genomics | Genetics | Genomes | RNA polymerase | Gene expression | Chromosomes | Binding sites | Life Sciences | Vegetal Biology
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11. Full Text A survey of mixed Begomovirus infection in solanaceae and fabaceae at different altitudes in East Java, Indonesia
by Lukman, Rudy and Afifuddin, Ahmad and Van Deynze, Allen and Hill, Theresa and Jimenez, Randi
Archives of Phytopathology and Plant Protection, ISSN 0323-5408, 02/2019, Volume 52, Issue 3-4, pp. 385 - 406
A multiplex primer set was developed to detect four Begomoviruses in East Java, Indonesia, i.e. Tomato leaf curl New Delhi virus (ToLCNDV), Tomato yellow leaf... 
begomovirus | mixed infection | virus diversity at different altitudes | multiplex PCR (mPCR) | Surveys | Leaf-curl | Beans | Mixed infection | Low altitude | Crops | Yellow leaf | Viruses | Infections | Tomatoes | Altitude
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12. Full Text Development of a large snp genotyping array and generation of high-density genetic maps in tomato
by Sim, Sung-Chur and Durstewitz, Gregor and Plieske, Jörg and Wieseke, Ralf and Ganal, Martin W and van Deynze, Allen and Hamilton, John P and Buell, C. Robin and Causse, Mathilde and Wijeratne, Saranga and Francis, David M
PLoS ONE, ISSN 1932-6203, 07/2012, Volume 7, Issue 7, p. e40563
The concurrent development of high-throughput genotyping platforms and next generation sequencing (NGS) has increased the number and density of genetic... 
MULTIDISCIPLINARY SCIENCES | GENOMIC SELECTION | IN-SITU HYBRIDIZATION | MARKERS | LYCOPERSICON-PENNELLII | LOCI | POLYMORPHISM | DISEASE RESISTANCE | CULTIVATED TOMATO | DISCOVERY | LINKAGE MAPS | Chromosome Mapping - methods | Genotype | Lycopersicon esculentum - genetics | Polymorphism, Single Nucleotide | Genome, Plant | DNA, Plant - genetics | Genetic Linkage | Genetic markers | Genomics | Quality control | Genetic research | Genetic aspects | Genomes | Single nucleotide polymorphisms | Chromosomes | Recombination | Horticulture | Genes | Plant biology | Interspecific | Single-nucleotide polymorphism | Density | Gene sequencing | Accuracy | Germplasm | Maps | Euchromatin | Population | Tomatoes | Crop science | Nucleotide sequence | Research & development--R&D | Markers | Inversions | Corn | Gene expression | Bins | Genotyping | Gene mapping | Polymorphism | Research & development | R&D
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13. Full Text A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution
by Iorizzo, Massimo and Ellison, Shelby and Senalik, Douglas and Zeng, Peng and Satapoomin, Pimchanok and Huang, Jiaying and Bowman, Megan and Iovene, Marina and Sanseverino, Walter and Cavagnaro, Pablo and Yildiz, Mehtap and Macko-Podgórni, Alicja and Moranska, Emilia and Grzebelus, Ewa and Grzebelus, Dariusz and Ashrafi, Hamid and Zheng, Zhijun and Cheng, Shifeng and Spooner, David and Van Deynze, Allen and Simon, Philipp
Nature Genetics, ISSN 1061-4036, 06/2016, Volume 48, Issue 6, pp. 657 - 666
We report a high-quality chromosome-scale assembly and analysis of the carrot (Daucus carota) genome, the first sequenced genome to include a comparative... 
MAXIMUM-LIKELIHOOD | GENE | GENETICS & HEREDITY | TRANSPOSABLE ELEMENTS | POPULATION-STRUCTURE | ANALYSIS TOOLKIT | SEQUENCING DATA | FLOWERING TIME | TRANSCRIPTION FACTOR | 1-DEOXY-D-XYLULOSE 5-PHOSPHATE SYNTHASE | DAUCUS-CAROTA | Biological Evolution | Plant Roots - metabolism | Carotenoids - metabolism | Genes, Regulator | Daucus carota - metabolism | Daucus carota - classification | Genetic Markers | Genome, Plant | Phylogeny | Daucus carota - genetics | Genetic Linkage | Genomes | Carrots | Analysis | Evolution | Carotenoids | Genes | Quality
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14. Full Text De novo assembly of the pepper transcriptome (Capsicum annuum): A benchmark for in silico discovery of SNPs, SSRs and candidate genes
by Ashrafi, Hamid and Hill, Theresa and Stoffel, Kevin and Kozik, Alexander and Yao, JiQiang and Chin-Wo, Sebastian R and Van Deynze, Allen
BMC Genomics, ISSN 1471-2164, 10/2012, Volume 13, Issue 1, pp. 571 - 571
Background: Molecular breeding of pepper (Capsicum spp.) can be accelerated by developing DNA markers associated with transcriptomes in breeding germplasm.... 
SPP | SSR | SNP | Pepper | Capsicum spp | EST | Transcriptome | Molecular Markers | RNAseq | Annotation | LINKAGE MAP | ALIGNMENT | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | GENETICS & HEREDITY | DIVERSITY | TOOL | Capsicum - metabolism | Molecular Sequence Annotation | Databases, Genetic | Genetic Association Studies - methods | Polymorphism, Single Nucleotide - genetics | Genotype | Transcriptome - genetics | Proteomics - methods | DNA Shuffling - methods | Capsicum - genetics | Expressed Sequence Tags | Microsatellite Repeats - genetics | Usage | Genetic aspects | Peppers | Research | Nucleotide sequencing | Single nucleotide polymorphisms | DNA sequencing | RNA sequencing | Genetic markers | Analysis | Genes | Genomics | DNA probes | Nucleotide sequence | software | Breeding | Crops | Data processing | Genomes | Single-nucleotide polymorphism | Gene expression | Computer programs | Simple sequence repeats | Quantitative trait loci | Germplasm | DNA microarrays | Databases | Plant breeding | Primers | expressed sequence tags | Genotypes
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15. Full Text De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversity
by Iorizzo, Massimo and Senalik, Douglas A and Grzebelus, Dariusz and Bowman, Megan and Cavagnaro, Pablo F and Matvienko, Marta and Ashrafi, Hamid and Van Deynze, Allen and Simon, Philipp W
BMC Genomics, ISSN 1471-2164, 08/2011, Volume 12, Issue 1, pp. 389 - 389
Background: Among next generation sequence technologies, platforms such as Illumina and SOLiD produce short reads but with higher coverage and lower cost per... 
SNP DISCOVERY | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | ANNOTATION | DAUCUS-CAROTA L | SEQUENCE | EST | GENETICS & HEREDITY | TRANSPOSABLE ELEMENTS | SSR-MARKERS | SUPERFAMILY | INVERTED-REPEAT ELEMENTS | FAMILY | Genes, Plant | Introns | Molecular Sequence Annotation | Transcriptome | Gene Expression Profiling - methods | Genotype | Genetic Markers | Genetic Variation | Contig Mapping | Polymorphism, Single Nucleotide | Sequence Analysis, DNA - methods | DNA, Plant - genetics | Daucus carota - genetics | Expressed Sequence Tags | Genetic aspects | Carrots | Research | Single nucleotide polymorphisms | Health aspects | Biological diversity | Seeds | Genes | Genomics | Colleges & universities | Technological change | Genomes | Libraries | Manuscripts
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