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Method: Predicted protein 3D structures provide essential insights into the genetic architecture underlying phenotypic diversity in maize
- Shuai Wang,
- Merritt Khaipho-Burch,
- Lynn C. Johnson,
- Zachary R. Miller,
- Peter J. Bradbury,
- Doug Speed,
- William J. Allen,
- M. Cinta Romay,
- Jiquan Xue,
- Edward S. Buckler,
- Guillaume P. Ramstein,
- and Baoxing Song
Genome Res. January 2026 36: 214-225; Published in Advance October 31, 2025, doi:10.1101/gr.280514.125
...through nested association mapping and near-isogenic line analysis. PLoS Genet 11: e1005045. doi:10.1371/journal.pgen.1005045 ↵Bertolini E, Rice BR, Braud M, Yang J, Hake S, Strable J, Lipka AE, Eveland AL. 2025. Regulatory variation controlling architectural pleiotropy in maize. Nat Commun 16: 2140. doi...
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Research: Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize
- Baoxing Song,
- Edward S. Buckler,
- Hai Wang,
- Yaoyao Wu,
- Evan Rees,
- Elizabeth A. Kellogg,
- Daniel J. Gates,
- Merritt Khaipho-Burch,
- Peter J. Bradbury,
- Jeffrey Ross-Ibarra,
- Matthew B. Hufford,
- and M. Cinta Romay
Genome Res. July 2021 31: 1245-1257; Published in Advance May 27, 2021, doi:10.1101/gr.266528.120
..., structural variation, and transposons. These contribute to the potential of Andropogoneae as a powerful system for studying CNSs and are factors we leverage to understand the function of maize CNSs. We found that 86% of CNSs were comprised of annotated features, including introns, UTRs, putative cis-regulatory...
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Research: The evolution of inflorescence diversity in the nightshades and heterochrony during meristem maturation
- Zachary H. Lemmon,
- Soon Ju Park,
- Ke Jiang,
- Joyce Van Eck,
- Michael C. Schatz,
- and Zachary B. Lippman
Genome Res. December 2016 26: 1676-1686; Published in Advance November 7, 2016, doi:10.1101/gr.207837.116
...controls tillering (Wang et al. 2014). Nevertheless, all these genes share a common function of modulating the process of meristem maturation. Our previous genetic and genomic analyses on tomato mutants and a wild relative with variable inflorescence architectures have suggested that the rate of meristem...
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Research: A high-resolution gene expression atlas links dedicated meristem genes to key architectural traits
- Steffen Knauer,
- Marie Javelle,
- Lin Li,
- Xianran Li,
- Xiaoli Ma,
- Kokulapalan Wimalanathan,
- Sunita Kumari,
- Robyn Johnston,
- Samuel Leiboff,
- Robert Meeley,
- Patrick S. Schnable,
- Doreen Ware,
- Carolyn Lawrence-Dill,
- Jianming Yu,
- Gary J. Muehlbauer,
- Michael J. Scanlon,
- and Marja C.P. Timmermans
Genome Res. December 2019 29: 1962-1973; Published in Advance November 19, 2019, doi:10.1101/gr.250878.119
...circuitries acting in the SAM, with natural variation modulating agronomically important architectural traits enriched specifically near dynamically expressed SAM genes and the TFs that regulate them. Besides unique mechanisms of maize stem cell regulation, our atlas thus identifies key new targets for crop...
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LETTER: Differential methylation of genes and repeats in land plants
- Pablo D. Rabinowicz,
- Robert Citek,
- Muhammad A. Budiman,
- Andrew Nunberg,
- Joseph A. Bedell,
- Nathan Lakey,
- Andrew L. O'Shaughnessy,
- Lidia U. Nascimento,
- W. Richard McCombie,
- and Robert A. Martienssen
Genome Res. October 2005 15: 1431-1440; doi:10.1101/gr.4100405
....e., genic) DNA (Supplemental Fig. 1). In a pilot study, MF applied to the maize yielded a sixfold enrichment for genes relative to a WGS library used as a control ( Rabinowicz et al. 1999 ). Gene-enrichment techniques constitute an effective approach to selectively clone and sequence genes from large plant...
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Research: Improved redox homeostasis owing to the up-regulation of one-carbon metabolism and related pathways is crucial for yeast heterosis at high temperature
- Liang Song,
- Jun-Yan Shi,
- Shou-Fu Duan,
- Da-Yong Han,
- Kuan Li,
- Ri-Peng Zhang,
- Peng-Yu He,
- Pei-Jie Han,
- Qi-Ming Wang,
- and Feng-Yan Bai
Genome Res. April 2021 31: 622-634; Published in Advance March 15, 2021, doi:10.1101/gr.262055.120
...-regulated in the heterotic F1 hybrids. Furthermore, genes associated with protein quality control systems were also generally down-regulated in the heterotic F1 hybrids, suggesting a lower level of protein turnover and thus higher energy use efficiency in these strains. In contrast, the depressed F1 hybrids, which were...
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Research: Genome-wide redistribution of 24-nt siRNAs in rice gametes
- Chenxin Li,
- Hengping Xu,
- Fang-Fang Fu,
- Scott D. Russell,
- Venkatesan Sundaresan,
- and Jonathan I. Gent
Genome Res. February 2020 30: 173-184; Published in Advance January 2, 2020, doi:10.1101/gr.253674.119
...that the small RNA transcriptome undergoes large-scale redistribution in both male and female gametes, which is not correlated with recruitment of DNA methyltransferases in gametes and suggestive of unexplored regulatory activities of gamete small RNAs.During sexual reproduction in angiosperms, cells undergo...
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PERSPECTIVE: The Arabidopsis genome: A foundation for plant research
- Michael Bevan and
- Sean Walsh
Genome Res. December 2005 15: 1632-1642; doi:10.1101/gr.3723405
...( Prusinkiewicz 2004 ), and for describing physiological responses ( Allen et al. 2005 ). This approach describes plants as a set of modules, each of which has a single mathematical description. Variables such as growth rate, genetic regulatory networks, and so on can be incorporated into these modules...
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LETTER: Evolution of Arabidopsis microRNA families through duplication events
- Christopher Maher,
- Lincoln Stein,
- and Doreen Ware
Genome Res. April 2006 16: 510-519; Published in Advance March 6, 2006, doi:10.1101/gr.4680506
...of conserved genes flanking a miRNA. In addition, using the best match selects for paralogs that are more likely to be recently duplicated from one another over less conserved genes from the same family. As a control, we generated a simulated data set in which we selected random genomic locations and aligned...
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RESOURCE: Analysis and Functional Annotation of an Expressed Sequence Tag Collection for Tropical Crop Sugarcane
- André L. Vettore,
- Felipe R. da Silva,
- Edson L. Kemper,
- Glaucia M. Souza,
- Aline M. da Silva,
- Maria Inês T. Ferro,
- Flavio Henrique-Silva,
- Éder A. Giglioti,
- Manoel V.F. Lemos,
- Luiz L. Coutinho,
- Marina P. Nobrega,
- Helaine Carrer,
- Suzelei C. França,
- Maurício Bacci, Jr.,
- Maria Helena S. Goldman,
- Suely L. Gomes,
- Luiz R. Nunes,
- Luis E.A. Camargo,
- Walter J. Siqueira,
- Marie-Anne Van Sluys,
- Otavio H. Thiemann,
- Eiko E. Kuramae,
- Roberto V. Santelli,
- Celso L. Marino,
- Maria L.P.N. Targon,
- Jesus A. Ferro,
- Henrique C.S. Silveira,
- Danyelle C. Marini,
- Eliana G.M. Lemos,
- Claudia B. Monteiro-Vitorello,
- José H.M. Tambor,
- Dirce M. Carraro,
- Patrícia G. Roberto,
- Vanderlei G. Martins,
- Gustavo H. Goldman,
- Regina C. de Oliveira,
- Daniela Truffi,
- Carlos A. Colombo,
- Magdalena Rossi,
- Paula G. de Araujo,
- Susana A. Sculaccio,
- Aline Angella,
- Marleide M.A. Lima,
- Vicente E. de Rosa, Jr,
- Fábio Siviero,
- Virginia E. Coscrato,
- Marcos A. Machado,
- Laurent Grivet,
- Sonia M.Z. Di Mauro,
- Francisco G. Nobrega,
- Carlos F.M. Menck,
- Marilia D.V. Braga,
- Guilherme P. Telles,
- Frank A.A. Cara,
- Guilherme Pedrosa,
- João Meidanis,
- and Paulo Arruda
Genome Res. December 2003 13: 2725-2735; Published in Advance January 1, 2003, doi:10.1101/gr.1532103
...belongs to the grass family (Poaceae), an economically important seed plant family that includes cereals such as maize, wheat, rice, and sorghum as well as many forage crops. The main product of sugarcane is sucrose, which accumulates in the stalk internodes. Sucrose, extracted and purified in specialized...

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