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Research: Major impacts of widespread structural variation on sorghum
- Zhihai Zhang,
- Joao Paulo Gomes Viana,
- Bosen Zhang,
- Kimberly K.O. Walden,
- Hans Müller Paul,
- Stephen P. Moose,
- Geoffrey P. Morris,
- Chris Daum,
- Kerrie W. Barry,
- Nadia Shakoor,
- and Matthew E. Hudson
Genome Res. February 2024 34: 286-299; Published in Advance March 13, 2024, doi:10.1101/gr.278396.123
...Department of Soil and Crop Science, Colorado State University, Fort Collins, Colorado 80523, USA; 5United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; 6Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA...
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Review: The structure, function, and evolution of plant centromeres
- Matthew Naish and
- Ian R. Henderson
Genome Res. February 2024 34: 161-178; Published in Advance March 14, 2024, doi:10.1101/gr.278409.123
...microtubule attachment (Fig. 1A; Musacchio and Desai 2017; Yatskevich et al. 2023). Knowledge of centromere identity and function is fundamentally important for understanding cell biology and architecture across eukaryotes and has applied relevance in the design of stably inherited synthetic chromosomes...
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Research: Dynamic effects of interacting genes underlying rice flowering-time phenotypic plasticity and global adaptation
- Tingting Guo,
- Qi Mu,
- Jinyu Wang,
- Adam E. Vanous,
- Akio Onogi,
- Hiroyoshi Iwata,
- Xianran Li,
- and Jianming Yu
Genome Res. May 2020 30: 673-683; Published in Advance April 16, 2020, doi:10.1101/gr.255703.119
...to temperature. By integrating knowledge from genomics, gene cloning and functional characterization, and environment quantification, we propose a conceptual model with multiple levels of reaction norms to help bridge the gaps among individual gene discovery, field-level phenotypic plasticity, and genomic...
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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
...Baoxing Song1, Edward S. Buckler1,2,3, Hai Wang1,4, Yaoyao Wu1,5, Evan Rees2, Elizabeth A. Kellogg6, Daniel J. Gates7, Merritt Khaipho-Burch2, Peter J. Bradbury3, Jeffrey Ross-Ibarra7,8, Matthew B. Hufford9 and M. Cinta Romay1 1Institute for Genomic Diversity, Cornell University, Ithaca, New York...
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Research: Genome-wide A-to-I RNA editing in fungi independent of ADAR enzymes
- Huiquan Liu,
- Qinhu Wang,
- Yi He,
- Lingfeng Chen,
- Chaofeng Hao,
- Cong Jiang,
- Yang Li,
- Yafeng Dai,
- Zhensheng Kang,
- and Jin-Rong Xu
Genome Res. April 2016 26: 499-509; Published in Advance March 2, 2016, doi:10.1101/gr.199877.115
...Genome-wide A-to-I RNA editing in fungi independent of ADAR enzymes Huiquan Liu 1 , Qinhu Wang 1 , Yi He 2 , Lingfeng Chen 1 , Chaofeng Hao 1 , Cong Jiang 1 , Yang Li 3 , Yafeng Dai 1 , Zhensheng Kang 1...
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Research: Regulatory modules controlling maize inflorescence architecture
- Andrea L. Eveland,
- Alexander Goldshmidt,
- Michael Pautler,
- Kengo Morohashi,
- Christophe Liseron-Monfils,
- Michael W. Lewis,
- Sunita Kumari,
- Susumu Hiraga,
- Fang Yang,
- Erica Unger-Wallace,
- Andrew Olson,
- Sarah Hake,
- Erik Vollbrecht,
- Erich Grotewold,
- Doreen Ware,
- and David Jackson
Genome Res. March 2014 24: 431-443; Published in Advance December 4, 2013, doi:10.1101/gr.166397.113
.... Louis, MO 63167, USA Abstract Genetic control of branching is a primary determinant of yield, regulating seed number and harvesting ability, yet little is known about the molecular networks that shape grain-bearing inflorescences of cereal crops. Here, we used the maize ( Zea mays...
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LETTER: Comparative DNA Sequence Analysis of Wheat and Rice Genomes
- Mark E. Sorrells,
- Mauricio La Rota,
- Catherine E. Bermudez-Kandianis,
- Robert A. Greene,
- Ramesh Kantety,
- Jesse D. Munkvold,
- Miftahudin,
- Ahmed Mahmoud,
- Xuefeng Ma,
- Perry J. Gustafson,
- Lili L. Qi,
- Benjamin Echalier,
- Bikram S. Gill,
- David E. Matthews,
- Gerard R. Lazo,
- Shiaoman Chao,
- Olin D. Anderson,
- Hugh Edwards,
- Anna M. Linkiewicz,
- Jorge Dubcovsky,
- Eduard D. Akhunov,
- Jan Dvorak,
- Deshui Zhang,
- Henry T. Nguyen,
- Junhua Peng,
- Nora L.V. Lapitan,
- Jose L. Gonzalez-Hernandez,
- James A. Anderson,
- Khwaja Hossain,
- Venu Kalavacharla,
- Shahryar F. Kianian,
- Dong-Woog Choi,
- Timothy J. Close,
- Muharrem Dilbirligi,
- Kulvinder S. Gill,
- Camille Steber,
- Mary K. Walker-Simmons,
- Patrick E. McGuire,
- and Calvin O. Qualset
Genome Res. August 2003 13: 1818-1827; doi:10.1101/gr.1113003
...numerous chromosomal rearrangements that will significantly complicate the use of rice as a model for cross-species transfer of information in nonconserved regions. Footnotes [Supplemental material is available online at www.genome.org and also at the GrainGenes Web site: http...
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Research: Complementation contributes to transcriptome complexity in maize (Zea mays L.) hybrids relative to their inbred parents
- Anja Paschold,
- Yi Jia,
- Caroline Marcon,
- Steve Lund,
- Nick B. Larson,
- Cheng-Ting Yeh,
- Stephan Ossowski,
- Christa Lanz,
- Dan Nettleton,
- Patrick S. Schnable,
- and Frank Hochholdinger
Genome Res. December 2012 22: 2445-2454; Published in Advance October 19, 2012, doi:10.1101/gr.138461.112
...-Ting Yeh 2 , Stephan Ossowski 5 , 8 , Christa Lanz 5 , Dan Nettleton 4 , Patrick S. Schnable 2 , 3 , 9 and Frank Hochholdinger 1 , 9 1 Institute of Crop Science and Resource Conservation, Division of Crop Functional Genomics...
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PERSPECTIVE: Genome-wide analyses of alternative splicing in plants: Opportunities and challenges
- W. Brad Barbazuk,
- Yan Fu,
- and Karen M. McGinnis
Genome Res. September 2008 18: 1381-1392; Published in Advance July 30, 2008, doi:10.1101/gr.053678.106
...), and mRNA processing ( Golovkin and Reddy 1996 ; Kalyna et al. 2006 ), and AS impacts many important plant process such as photosynthesis, defense response, flowering, and cereal grain quality (for review, see Reddy 2007 ). Conservation of alternatively spliced genes between evolutionarily distant plant...
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Letter: Alternative splicing of anciently exonized 5S rRNA regulates plant transcription factor TFIIIA
- Yan Fu,
- Oliver Bannach,
- Hao Chen,
- Jan-Hendrik Teune,
- Axel Schmitz,
- Gerhard Steger,
- Liming Xiong,
- and W. Brad Barbazuk
Genome Res. May 2009 19: 913-921; Published in Advance February 10, 2009, doi:10.1101/gr.086876.108
...known and predicted plant AS events has yet to be determined; however, the results of a few functional analyses conducted demonstrate roles for AS in important plant processes such as photosynthesis, defense response, flowering, and cereal grain quality (Reddy 2007), as well as somemetabolic pathways...

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