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237 results on '"Mandel, Jennifer R"'

2. Impact of the climatic changes in the Pliocene-Pleistocene transition on Irano-Turanian species. The radiation of genus Jurinea (Compositae)

Author

Herrando-Moraira, Sonia, Roquet, Cristina, Calleja, Juan-Antonio, Chen, You-Sheng, Fujikawa, Kazumi, Galbany-Casals, Mercè, Garcia-Jacas, Núria, Liu, Jian-Quan, López-Alvarado, Javier, López-Pujol, Jordi, Mandel, Jennifer R., Mehregan, Iraj, Sáez, Llorenç, Sennikov, Alexander N., Susanna, Alfonso, Vilatersana, Roser, and Xu, Lian-Sheng

Published
2023
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8. Generic boundaries in subtribe Saussureinae (Compositae: Cardueae) : Insights from Hyb-Seq data

Author

The Cardueae Radiations Group, Herrando-Moraira, Sonia, Calleja, Juan-Antonio, Chen, You-Sheng, Fujikawa, Kazumi, Galbany-Casals, Mercè, Garcia-Jacas, Núria, Kim, Seung-Chul, Liu, Jian-Quan, López-Alvarado, Javier, López-Pujol, Jordi, Mandel, Jennifer R., Mehregan, Iraj, Roquet, Cristina, Sennikov, Alexander N., Susanna, Alfonso, Vilatersana, Roser, and Xu, Lian-Sheng

Published
2020

9. Gene Flow in Carrot

Author

Mandel, Jennifer R., Brunet, Johanne, Kole, Chittaranjan, Series Editor, Simon, Philipp, editor, Iorizzo, Massimo, editor, Grzebelus, Dariusz, editor, and Baranski, Rafal, editor

Published
2019
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12. Association mapping in sunflower (Helianthus annuus L.) reveals independent control of apical vs. basal branching

Author

Nambeesan, Savithri U, Mandel, Jennifer R, Bowers, John E, Marek, Laura F, Ebert, Daniel, Corbi, Jonathan, Rieseberg, Loren H, Knapp, Steven J, and Burke, John M

Subjects
Agricultural, Veterinary and Food Sciences, Plant Biology, Biological Sciences, Genetics, Human Genome, Genes, Plant, Helianthus, Polymorphism, Single Nucleotide, Apical dominance, Association mapping, Branching, Helianthus annuus, Linkage disequilibrium, Plant architecture, Sunflower, Microbiology, Crop and Pasture Production, Plant Biology & Botany, Crop and pasture production, Plant biology
Abstract

BackgroundShoot branching is an important determinant of plant architecture and influences various aspects of growth and development. Selection on branching has also played an important role in the domestication of crop plants, including sunflower (Helianthus annuus L.). Here, we describe an investigation of the genetic basis of variation in branching in sunflower via association mapping in a diverse collection of cultivated sunflower lines.ResultsDetailed phenotypic analyses revealed extensive variation in the extent and type of branching within the focal population. After correcting for population structure and kinship, association analyses were performed using a genome-wide collection of SNPs to identify genomic regions that influence a variety of branching-related traits. This work resulted in the identification of multiple previously unidentified genomic regions that contribute to variation in branching. Genomic regions that were associated with apical and mid-apical branching were generally distinct from those associated with basal and mid-basal branching. Homologs of known branching genes from other study systems (i.e., Arabidopsis, rice, pea, and petunia) were also identified from the draft assembly of the sunflower genome and their map positions were compared to those of associations identified herein. Numerous candidate branching genes were found to map in close proximity to significant branching associations.ConclusionsIn sunflower, variation in branching is genetically complex and overall branching patterns (i.e., apical vs. basal) were found to be influenced by distinct genomic regions. Moreover, numerous candidate branching genes mapped in close proximity to significant branching associations. Although the sunflower genome exhibits localized islands of elevated linkage disequilibrium (LD), these non-random associations are known to decay rapidly elsewhere. The subset of candidate genes that co-localized with significant associations in regions of low LD represents the most promising target for future functional analyses.

Published
2015

14. A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae.

Author

Mandel, Jennifer R, Dikow, Rebecca B, Funk, Vicki A, Masalia, Rishi R, Staton, S Evan, Kozik, Alex, Michelmore, Richard W, Rieseberg, Loren H, and Burke, John M

Subjects
base tree, conserved, exon capture, next-generation sequencing, orthologs, phylogenomics, Crop and Pasture Production
Abstract

UnlabelledPremise of the studyThe Compositae (Asteraceae) are a large and diverse family of plants, and the most comprehensive phylogeny to date is a meta-tree based on 10 chloroplast loci that has several major unresolved nodes. We describe the development of an approach that enables the rapid sequencing of large numbers of orthologous nuclear loci to facilitate efficient phylogenomic analyses. •Methods and resultsWe designed a set of sequence capture probes that target conserved orthologous sequences in the Compositae. We also developed a bioinformatic and phylogenetic workflow for processing and analyzing the resulting data. Application of our approach to 15 species from across the Compositae resulted in the production of phylogenetically informative sequence data from 763 loci and the successful reconstruction of known phylogenetic relationships across the family. •ConclusionsThese methods should be of great use to members of the broader Compositae community, and the general approach should also be of use to researchers studying other families.

Published
2014

15. Compositae‐ParaLoss‐1272: A complementary sunflower‐specific probe set reduces paralogs in phylogenomic analyses of complex systems.

Author

Moore‐Pollard, Erika R., Jones, Daniel S., and Mandel, Jennifer R.

Subjects
SUNFLOWERS, POLYPLOIDY, ASTERACEAE, LOCUS (Genetics), LOCUS (Mathematics)
Abstract

Premise: A family‐specific probe set for sunflowers, Compositae‐1061, enables family‐wide phylogenomic studies and investigations at lower taxonomic levels, but may lack resolution at genus to species levels, especially in groups complicated by polyploidy and hybridization. Methods: We developed a Hyb‐Seq probe set, Compositae‐ParaLoss‐1272, that targets orthologous loci in Asteraceae. We tested its efficiency across the family by simulating target enrichment sequencing in silico. Additionally, we tested its effectiveness at lower taxonomic levels in the historically complex genus Packera. We performed Hyb‐Seq with Compositae‐ParaLoss‐1272 for 19 Packera taxa that were previously studied using Compositae‐1061. The resulting sequences from each probe set, plus a combination of both, were used to generate phylogenies, compare topologies, and assess node support. Results: We report that Compositae‐ParaLoss‐1272 captured loci across all tested Asteraceae members, had less gene tree discordance, and retained longer loci than Compositae‐1061. Most notably, Compositae‐ParaLoss‐1272 recovered substantially fewer paralogous sequences than Compositae‐1061, with only ~5% of the recovered loci reporting as paralogous, compared to ~59% with Compositae‐1061. Discussion: Given the complexity of plant evolutionary histories, assigning orthology for phylogenomic analyses will continue to be challenging. However, we anticipate Compositae‐ParaLoss‐1272 will provide improved resolution and utility for studies of complex groups and lower taxonomic levels in the sunflower family. [ABSTRACT FROM AUTHOR]

Published
2024
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19. Sunflower pan-genome analysis shows that hybridization altered gene content and disease resistance

Author

Hübner, Sariel, Bercovich, Natalia, Todesco, Marco, Mandel, Jennifer R., Odenheimer, Jens, Ziegler, Emanuel, Lee, Joon S., Baute, Gregory J., Owens, Gregory L., Grassa, Christopher J., Ebert, Daniel P., Ostevik, Katherine L., Moyers, Brook T., Yakimowski, Sarah, Masalia, Rishi R., Gao, Lexuan, Ćalić, Irina, Bowers, John E., Kane, Nolan C., Swanevelder, Dirk Z. H., Kubach, Timo, Muños, Stephane, Langlade, Nicolas B., Burke, John M., and Rieseberg, Loren H.

Published
2019
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28. Proceedings of the 16th Annual UT-KBRIN Bioinformatics Summit 2016: bioinformatics: Burns, TN, USA. April 21-23, 2017

Author

Rouchka, Eric C., Chariker, Julia H., Tieri, David A., Park, Juw Won, Rajurkar, Shreedharkumar, Singh, Vikas, Verma, Nishchal K., Cui, Yan, Farman, Mark, Condon, Bradford, Moore, Neil, Jaromczyk, Jerzy, Jaromczyk, Jolanta, Harris, Daniel, Calie, Patrick, Shin, Eun Kyong, Davis, Robert L., Shaban-Nejad, Arash, Mitchell, Joshua M., Flight, Robert M., Wang, Qing Jun, Higashi, Richard M., Fan, Teresa W-M, Lane, Andrew N., Moseley, Hunter N. B., Lu, Liangqun, Daigle, Jr., Bernie J, Chen, Xi, Smelter, Andrey, Moseley, Hunter N. B., Jaromczyk, Jerzy W., Farman, Mark, Chen, Li, Moore, Neil, Phan, Bailey K., Serpico, Nathaniel J., Toney, Ethan G., Melton, Caroline E., Mandel, Jennifer R., Daigle, Jr., Bernie J., Chen, Hao, Zaman, Kazi I., Homayouni, Ramin, Trainor, Patrick J., Carlisle, Samantha M., DeFilippis, Andrew P., and Rai, Shesh N.

Published
2017
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34. Rapid evolution of weedy traits during sunflower de-domestication: the importance of hybridization and standing genetic variation

Author

Hernández, Fernando, Vercellino, Román Boris, Pandolfo, Claudio Ezequiel, Mandel, Jennifer R., and Presotto, Alejandro Daniel

Subjects
purl.org/becyt/ford/1 [https], RAPID EVOLUTION, SUNFLOWER, SEED DORMANCY, purl.org/becyt/ford/1.6 [https], purl.org/becyt/ford/4.5 [https], HYBRIDIZATION, purl.org/becyt/ford/4 [https]
Abstract

Hybridization between crops and their wild relatives may promote the evolution of de-domesticated (feral) weeds. Wild sunflower is typically found in ruderal environments, but crop-wild hybridization may facilitate the evolution of weedy biotypes. Using one crop-specific mitochondrial marker (CMS-PET1) and 14 nuclear SSR markers, we studied the origin and genetic diversity of BRW, a recently discovered weedy biotype. Then, using a resurrection approach, we tested for rapid evolution of weedy traits (seed dormancy, herbicide resistance, and competitive ability) by sampling weedy and wild biotypes 10 years apart (2007 and 2017). All the weedy plants present the CMS-PET1 cytotype, confirming their feral origin. At the nuclear markers, BRW showed higher genetic diversity than the cultivated lines, as high genetic diversity as the most diverse wild biotypes, and low differentiation with one wild biotype, suggesting that wild hybridization increased the genetic diversity of the feral BRW. Regarding weedy trait evolution, we found support for rapid evolution towards higher seed dormancy, but not for higher competitive ability or herbicide resistance. Standing genetic variation probably facilitated the evolution of seed dormancy and limited the evolution of herbicide resistance, as no resistant alleles were found in the ancestral biotype. Our results demonstrate that natural crop-wild hybrids can evolve quickly in farmers? fields, leading to the establishment of weedy biotypes of cultivated origin. Although herbicide resistance did not evolve in BRW, management strategies aimed at preventing the evolution of resistance should be a priority in order to avoid the emergence and spread of herbicide resistant biotypes in Argentina. Fil: Hernández, Fernando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina. Universidad Nacional del Sur. Departamento de Agronomía; Argentina Fil: Vercellino, Román Boris. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina. Universidad Nacional del Sur. Departamento de Agronomía; Argentina Fil: Pandolfo, Claudio Ezequiel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina. Universidad Nacional del Sur. Departamento de Agronomía; Argentina Fil: Mandel, Jennifer R.. University of Memphis; Estados Unidos Fil: Presotto, Alejandro Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina. Universidad Nacional del Sur. Departamento de Agronomía; Argentina

Published
2021

36. MCScanX files

Author

Weaver, Mark A., Mirza, Nahreen, Mandel, Jennifer R., Boyette, C. Douglas, and Brown, Shawn P.

Abstract

MCScanX collinearity file. Statistics for the number and percentage of collinear genes (those with conserved gene order).MCScanX HTML files. Multiple alignments collinear blocks generated by the MCScanX algorithm in HTML format. First and second columns display duplication depth and gene name where tandems are marked in red. Remaining columns show aligned collinear blocks with only the names of anchor genes shown.MCScanX tandem duplicates file. File detailing tandem duplicate genes as identified by the MCScanX algorithm.

Published
2021
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44. The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution

Author

Badouin, Hlne, Gouzy, Jrme, Grassa, Christopher J., Murat, Florent, Staton, S. Evan, Cottret, Ludovic, Lelandais-Brire, Christine, Owens, Gregory L., Carrre, Sbastien, Mayjonade, Baptiste, Legrand, Ludovic, Gill, Navdeep, Kane, Nolan C., Bowers, John E., Hubner, Sariel, Bellec, Arnaud, Brard, Aurlie, Bergs, Hlne, Blanchet, Nicolas, Boniface, Marie-Claude, Brunel, Dominique, Catrice, Olivier, Chaidir, Nadia, Claudel, Clotilde, Donnadieu, Ccile, Faraut, Thomas, Fievet, Ghislain, Helmstetter, Nicolas, King, Matthew, Knapp, Steven J., Lai, Zhao, Le Paslier, Marie-Christine, Lippi, Yannick, Lorenzon, Lolita, Mandel, Jennifer R., Marage, Gwenola, Marchand, Gwenalle, Marquand, Elodie, Bret-Mestries, Emmanuelle, Morien, Evan, Nambeesan, Savithri, Nguyen, Thuy, Pegot-Espagnet, Prune, Pouilly, Nicolas, Raftis, Frances, Sallet, Erika, Schiex, Thomas, Thomas, Justine, Vandecasteele, Cline, Vars, Didier, Vear, Felicity, Vautrin, Sonia, Crespi, Martin, Mangin, Brigitte, Burke, John M., Salse, Jrme, Muos, Stphane, Vincourt, Patrick, Rieseberg, Loren H., and Langlade, Nicolas B.

Subjects
Plant metabolism -- Genetic aspects, Sunflowers -- Genetic aspects, Gene expression -- Observations, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Hlne Badouin [1]; Jrme Gouzy [1]; Christopher J. Grassa [1, 2]; Florent Murat [3]; S. Evan Staton [2]; Ludovic Cottret [1]; Christine Lelandais-Brire [4, 5]; Gregory L. Owens [2]; [...]

Published
2017
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