When we think of evolution, we often think about physical changes, like a plant developing broader leaves to collect more solar energy. Such evolution actually occurs within the plant’s DNA. I am using computational analysis and modeling to visualize how plant genomes have evolved over time, particularly those of staple crops. We are learning from this work to improve the range and yield of modern plants.
Using multidisciplinary approaches that combine computational analysis, modeling, and prediction with experimental verification, Doreen Ware’s lab seeks a deeper understanding of the evolution of genome sequences in plants and their implications for agricultural improvement. By looking comparatively across the genomes of plants in the same lineage, they seek answers to the following questions: How are genes conserved and lost over time? What are the fates of duplicated genes? What is the impact of structural variation on phenotypic variation? Ware’s team also studies gene regulation in plants, focusing on gene regulatory networks, targeting transcription factors and microRNA genes with the objective of understanding how these parts of the plant genome work together in determining spatial and temporal expression of genes. The lab had an important role in the project to produce a haplotype map reference genome of maize, spearheading the most comprehensive analysis of the crop yet. This has provided important information on the variation of the reference genome, as well as comparative data showing changes in the genome acquired through domestication and breeding. They have devoted special attention to examining diversity within maize, grape, and tomato, aiming to accelerate the development of strategies to introduce new germplasm that is needed to meet demands of increasing population and a changing environment. The lab also has brought fully sequenced genomes into an integrated data framework, to enhance the power of their comparative studies. This past year, Ware was named as its principal investigator for the National Science Foundation-funded Gramene project, a comparative genomics resource for agriculturally important crops and models to support sustainable food and fuel production. Ware, as principal investigator for plants, has also helped lead an effort funded by the Department of Energy to create—out of many separate streams of biological information—a single, integrated cyber-“knowledgebase” for plants and microbial life.
New CSHL website brings together sorghum researchers
May 9, 2022
Plant researchers and breeders are now using a website created by CSHL to get the latest intel on sorghum crop research.
The race to protect sweet corn
April 22, 2022
Breeding a variety that can withstand disease and taste better too
Do you have the dirt on plant research?
March 31, 2022
New research is constantly sprouting. Take this quiz and test your plant knowledge.
The secret history of corn is revealed in its genome
August 5, 2021
For the first time, scientists have assembled in-depth maps of dozens of corn genomes, filling in gaps related to key agricultural traits.
Teachers make genomes more useful… from home
May 21, 2020
Researchers and educators participated in an online annotation jamboree to help researchers understand the corn genome.
CSHL investigators rank among world’s most highly cited
December 11, 2019
Seven researchers affiliated with CSHL are among the scientists producing the top 1 percent of the most highly-cited research in the world.
Researchers double sorghum grain number to improve food supply
October 30, 2019
A set of hormone-controlling genes may be the key to doubling grain number in sorghum plants.
Leading discovery
May 20, 2019
Current discoveries about DNA and human genome position CSHL scientists to make life-changing breakthroughs that will improve the human condition.
An essay from the President: Biology for the planet
May 16, 2019
CSHL plant scientists are looking for solutions to the biggest questions in agriculture as environments are reshaped by climate change.
Profile: Doreen Ware champions the plant genome
May 8, 2019
Molecular biologist Doreen Ware uses computer science to parse out the genetic roadmaps of plants.
All Publications
An improved reference of the grapevine genome reasserts the origin of the PN40024 highly homozygous genotype
2 May 2023 | G3: Genes, Genomes, Genetics | 13(5):jkad067
Velt, Amandine, Frommer, Bianca, Blanc, Sophie, Holtgräwe, Daniela, Duchêne, Éric, Dumas, Vincent, Grimplet, Jérôme, Hugueney, Philippe, Kim, Catherine, Lahaye, Marie, Matus, José, Navarro-Payá, David, Orduña, Luis, Tello-Ruiz, Marcela, Vitulo, Nicola, Ware, Doreen, Rustenholz, Camille, Whiteman, N
Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice.
21 Mar 2023 | Nature Communications | 14(1):1567
Zhou, Yong, Yu, Zhichao, Chebotarov, Dmytro, Chougule, Kapeel, Lu, Zhenyuan, Rivera, Luis, Kathiresan, Nagarajan, Al-Bader, Noor, Mohammed, Nahed, Alsantely, Aseel, Mussurova, Saule, Santos, João, Thimma, Manjula, Troukhan, Maxim, Fornasiero, Alice, Green, Carl, Copetti, Dario, Kudrna, David, Llaca, Victor, Lorieux, Mathias, Zuccolo, Andrea, Ware, Doreen, McNally, Kenneth, Zhang, Jianwei, Wing, Rod
Era of gapless plant genomes: innovations in sequencing and mapping technologies revolutionize genomics and breeding
12 Jan 2023 | Current Opinion in Biotechnology | 79:102886
Gladman, Nicholas, Goodwin, Sara, Chougule, Kapeel, Richard McCombie, William, Ware, Doreen
Ten new high-quality genome assemblies for diverse bioenergy sorghum genotypes
2022 | Frontiers in Plant Science | 13:1040909
Voelker, William, Krishnan, Krittika, Chougule, Kapeel, Alexander, Louie, Lu, Zhenyuan, Olson, Andrew, Ware, Doreen, Songsomboon, Kittikun, Ponce, Cristian, Brenton, Zachary, Boatwright, J, Cooper, Elizabeth
Toward a Data Infrastructure for the Plant Cell Atlas
6 Oct 2022 | Plant Physiology
Fahlgren, Noah, Kapoor, Muskan, Yordanova, Galabina, Papatheodorou, Irene, Waese, Jamie, Cole, Benjamin, Harrison, Peter, Ware, Doreen, Tickle, Timothy, Paten, Benedict, Burdett, Tony, Elsik, Christine, Tuggle, Christopher, Provart, Nicholas
Role of a ZF-HD Transcription Factor in miR157-Mediated Feed-Forward Regulatory Module That Determines Plant Architecture in Arabidopsis
4 Aug 2022 | International Journal of Molecular Sciences | 23(15):8665
Lee, Young, Kumari, Sunita, Olson, Andrew, Hauser, Felix, Ware, Doreen
Sorghum root epigenetic landscape during limiting phosphorus conditions
14 May 2022 | Plant Direct | 6(5):e393
Gladman, Nicholas, Hufnagel, Barbara, Regulski, Michael, Liu, Zhigang, Wang, Xiaofei, Chougule, Kapeel, Kochian, Leon, Magalhães, Jurandir, Ware, Doreen
Transcriptional regulation of primary and specialized metabolism
13 May 2022 | The FASEB Journal | 36(S1)
Brady, Siobhan
Experimental demonstration and pan-structurome prediction of climate-associated riboSNitches in Arabidopsis
19 Apr 2022 | Genome Biology | 23(1):101
Ferrero-Serrano, Ángel, Sylvia, Megan, Forstmeier, Peter, Olson, Andrew, Ware, Doreen, Bevilacqua, Philip, Assmann, Sarah
Author Correction: Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline.
8 Mar 2022 | Genome Biology | 23(1):76
Ou, Shujun, Su, Weijia, Liao, Yi, Chougule, Kapeel, Agda, Jireh, Hellinga, Adam, Lugo, Carlos, Elliott, Tyler, Ware, Doreen, Peterson, Thomas, Jiang, Ning, Hirsch, Candice, Hufford, Matthew