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Research: miRNA-like secondary structures in maize (Zea mays) genes and transposable elements correlate with small RNAs, methylation, and expression
- Galen T. Martin,
- Edwin Solares,
- Jeanelle Guadardo-Mendez,
- Aline Muyle,
- Alexandros Bousios,
- and Brandon S. Gaut
Genome Res. November 2023 33: 1932-1946; Published in Advance November 2, 2023, doi:10.1101/gr.277459.122
..., and this variability positively correlates with the number of mapping smRNAs. We conclude that local miRNA-like structures are a nearly ubiquitous feature of expressed regions of the maize , that they correlate with higher smRNA mapping and methylation, and that they may represent a trade-off between functional...
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Research: Large haplotypes highlight a complex age structure within the maize pan-genome
- Jianing Liu and
- R. Kelly Dawe
Genome Res. March 2023 33: 359-370; Published in Advance February 28, 2023, doi:10.1101/gr.276705.122
...of this ancient diversity.The origins of maize can be traced to stands of teosinte, a tall grass with many small ears that is native to Mexico (Doebley 2004). Teosintes are divided into four species, one of which is Zea mays, which is divided into three subspecies: Zea mays mays (cultivated maize), Zea mays...
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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
...-wide duplications, numerous rearrangements, and gene loss (Fig. 1; Schnable et al. 2011). Andropogoneae s (see below) were aligned to the maize B73 v4 assembly (Jiao et al. 2017), which was used as a reference. First, we lifted over maize protein-coding genes to each query (Fig. 1, step 1) by mapping...
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Research: Differential retention and divergent resolution of duplicate genes following whole-genome duplication
- Casey L. McGrath,
- Jean-Francois Gout,
- Parul Johri,
- Thomas G. Doak,
- and Michael Lynch
Genome Res. October 2014 24: 1665-1675; Published in Advance August 1, 2014, doi:10.1101/gr.173740.114
...observed in Arabidopsis (Thomas et al. 2006), maize (Woodhouse et al. 2010), and rice (Wu et al. 2008). On the other hand, in the case of autopolyploidy, paralogous chromosomes are initially identical and are expected to be unbiased in their pattern of gene loss. We investigated whether duplicate loss...
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Research: Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor
- Ruth A. Swanson-Wagner,
- Steven R. Eichten,
- Sunita Kumari,
- Peter Tiffin,
- Joshua C. Stein,
- Doreen Ware,
- and Nathan M. Springer
Genome Res. December 2010 20: 1689-1699; Published in Advance October 29, 2010, doi:10.1101/gr.109165.110
...structural variants near the end of the chromosomes than within the central centromeric regions of the maize chromosomes, but this generally mirrors the genic density. Chromosomal regions were classified as high, moderate, or low recombination rates based upon a comparisonof the genetic and physical map (Liu...
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LETTER: Uneven chromosome contraction and expansion in the maize genome
- Rémy Bruggmann,
- Arvind K. Bharti,
- Heidrun Gundlach,
- Jinsheng Lai,
- Sarah Young,
- Ana C. Pontaroli,
- Fusheng Wei,
- Georg Haberer,
- Galina Fuks,
- Chunguang Du,
- Christina Raymond,
- Matt C. Estep,
- Renyi Liu,
- Jeffrey L. Bennetzen,
- Agnes P. Chan,
- Pablo D. Rabinowicz,
- John Quackenbush,
- W. Brad Barbazuk,
- Rod A. Wing,
- Bruce Birren,
- Chad Nusbaum,
- Steve Rounsley,
- Klaus F.X. Mayer,
- and Joachim Messing
Genome Res. October 2006 16: 1241-1251; Published in Advance August 10, 2006, doi:10.1101/gr.5338906
...synteny between grass s ( Gale and Devos 1998 ), sequence analysis of orthologous chromosomal regions shows extensive gene movement during speciation. A study comparing the duplicated regions of maize with orthologous regions in rice and sorghum has shown that ∼15% of all genes in any pairwise comparison...
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LETTER: Gene Loss and Movement in the Maize Genome
- Jinsheng Lai,
- Jianxin Ma,
- Zuzana Swigoňová,
- Wusirika Ramakrishna,
- Eric Linton,
- Victor Llaca,
- Bahattin Tanyolac,
- Yong-Jin Park,
- O-Young Jeong,
- Jeffrey L. Bennetzen,
- and Joachim Messing
Genome Res. October 2004 14: 1924-1931; doi:10.1101/gr.2701104
...years. Science 282 : 656 -659. ↵ Gaut, B.S. 2001 . Patterns of chromosomal duplication in maize and their implications for comparative maps of the grasses. Genome Res. 11 : 55 -66. ↵ Goodman, M.M., Stuber, C.W., Newton, K., and Weissinger, H.H. 1980 . Linkage relationships of 19 enzyme loci in maize...
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LETTER: Uneven distribution of expressed sequence tag loci on maize pachytene chromosomes
- Lorinda K. Anderson,
- Ann Lai,
- Stephen M. Stack,
- Carene Rizzon,
- and Brandon S. Gaut
Genome Res. January 2006 16: 115-122; Published in Advance December 7, 2005, doi:10.1101/gr.4249906
...difficult because only a few markers connect genetic linkage maps with physical maps. Here, we have positioned 1195 genetically mapped expressed sequence tag (EST) markers onto the 10 pachytene chromosomes of maize by using a newly developed resource, the RN-cM map. The RN-cM map charts the distribution...
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METHODS: LineUp: Statistical Detection of Chromosomal Homology With Application to Plant Comparative Genomics
- Steve Hampson,
- Aoife McLysaght,
- Brandon Gaut,
- and Pierre Baldi
Genome Res. May 1, 2003 13: 999-1010; Published in Advance April 14, 2003, doi:10.1101/gr.814403
...that the maize genome contains extensive regions of genomic duplication and multiplication. Nonetheless, maps differ substantially in the location of homologous regions, probably reflecting the incomplete nature of genetic map data. The variation among maps has important implications for evolutionary inference...
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LETTER: Sequence, Regulation, and Evolution of the Maize 22-kD α Zein Gene Family
- Rentao Song,
- Victor Llaca,
- Eric Linton,
- and Joachim Messing
Genome Res. November 1, 2001 11: 1817-1825; Published in Advance October 15, 2001, doi:10.1101/gr.197301
...to determine the expression and regulation patterns of gene family members. The results of this research provide insight into chromosome structure, the regulation of multicopy genes, gene density in maize, and the evolution of multigene families in plants. RESULTS Construction of Zea mays BSSS53-Specific...

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