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Research: Genic and nongenic contributions to natural variation of quantitative traits in maize
- Xianran Li,
- Chengsong Zhu,
- Cheng-Ting Yeh,
- Wei Wu,
- Elizabeth M. Takacs,
- Katherine A. Petsch,
- Feng Tian,
- Guihua Bai,
- Edward S. Buckler,
- Gary J. Muehlbauer,
- Marja C.P. Timmermans,
- Michael J. Scanlon,
- Patrick S. Schnable,
- and Jianming Yu
Genome Res. December 2012 22: 2436-2444; Published in Advance June 14, 2012, doi:10.1101/gr.140277.112
...is to identify what part of a complex can be prioritized. Intuitively, this is known from mutational dissection of ‘‘qualitative phenotypes,’’ but a global assessment for ‘‘quantitative traits’’ is lacking and the relative importance of genic and nongenic portions of the has significant bearings on further...
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Resource: A high-resolution association mapping panel for the dissection of complex traits in mice
- Brian J. Bennett,
- Charles R. Farber,
- Luz Orozco,
- Hyun Min Kang,
- Anatole Ghazalpour,
- Nathan Siemers,
- Michael Neubauer,
- Isaac Neuhaus,
- Roumyana Yordanova,
- Bo Guan,
- Amy Truong,
- Wen-pin Yang,
- Aiqing He,
- Paul Kayne,
- Peter Gargalovic,
- Todd Kirchgessner,
- Calvin Pan,
- Lawrence W. Castellani,
- Emrah Kostem,
- Nicholas Furlotte,
- Thomas A. Drake,
- Eleazar Eskin,
- and Aldons J. Lusis
Genome Res. February 2010 20: 281-290; Published in Advance January 6, 2010, doi:10.1101/gr.099234.109
...A high-resolution association mapping panel for the dissection of complex traits in mice Brian J. Bennett 1 , 10 , Charles R. Farber 2 , 10 , Luz Orozco 1 , 10 , Hyun Min Kang 3 , 10 , Anatole Ghazalpour 1 , Nathan Siemers 4...
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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
...University, Ithaca, New York 14853, USA; 4Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA; 5Agricultural Research Service, United States Department of Agriculture, Ithaca, New York 14853, USA; 6Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus 8000...
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Resource: Comprehensive identification of genomic and environmental determinants of phenotypic plasticity in maize
- Laura E. Tibbs-Cortes,
- Tingting Guo,
- Carson M. Andorf,
- Xianran Li,
- and Jianming Yu
Genome Res. August 2024 34: 1253-1263; Published in Advance September 13, 2024, doi:10.1101/gr.279027.124
...on day length, temperature, moisture, and combinations of these are biologically meaningful. Next, we leveraged a total of more than 20 million SNP and SV markers derived from recent de novo sequencing of the NAM founders for trait prediction and dissection. When combined with identified environmental...
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Research: Genetic analysis of complex traits in the emerging Collaborative Cross
- David L. Aylor,
- William Valdar,
- Wendy Foulds-Mathes,
- Ryan J. Buus,
- Ricardo A. Verdugo,
- Ralph S. Baric,
- Martin T. Ferris,
- Jeff A. Frelinger,
- Mark Heise,
- Matt B. Frieman,
- Lisa E. Gralinski,
- Timothy A. Bell,
- John D. Didion,
- Kunjie Hua,
- Derrick L. Nehrenberg,
- Christine L. Powell,
- Jill Steigerwalt,
- Yuying Xie,
- Samir N.P. Kelada,
- Francis S. Collins,
- Ivana V. Yang,
- David A. Schwartz,
- Lisa A. Branstetter,
- Elissa J. Chesler,
- Darla R. Miller,
- Jason Spence,
- Eric Yi Liu,
- Leonard McMillan,
- Abhishek Sarkar,
- Jeremy Wang,
- Wei Wang,
- Qi Zhang,
- Karl W. Broman,
- Ron Korstanje,
- Caroline Durrant,
- Richard Mott,
- Fuad A. Iraqi,
- Daniel Pomp,
- David Threadgill,
- Fernando Pardo-Manuel de Villena,
- and Gary A. Churchill
Genome Res. August 2011 21: 1213-1222; Published in Advance March 15, 2011, doi:10.1101/gr.111310.110
...-wide analysis of the incipient strains reveals high genetic diversity, balanced allele frequencies, and dense, evenly distributed recombination sites—all ideal qualities for a systems genetics resource. We map discrete, complex, and biomolecular traits and contrast two quantitative trait locus (QTL) mapping...
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RESOURCE: A Deep-Coverage Tomato BAC Library and Prospects Toward Development of an STC Framework for Genome Sequencing
- Muhammad A. Budiman,
- Long Mao,
- Todd C. Wood,
- and Rod A. Wing
Genome Res. January 1, 2000 10: 129-136; doi:10.1101/gr.10.1.129
...maps ( Tanksley et al. 1992 ), comparative molecular genetic maps between closely related species (e.g., potato, pepper, and tobacco; Bonierbale et al. 1988 ; Tanksley et al. 1988 ), plant transformation ( McCormick et al. 1986 ), the molecular dissection of quantitative inheritance ( Paterson et al...
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Mini-Review: Large-scale genomic analysis of the domestic dog informs biological discovery
- Reuben M. Buckley and
- Elaine A. Ostrander
Genome Res. June 2024 34: 811-821; Published in Advance July 2, 2024, doi:10.1101/gr.278569.123
...and Eichler 2023).Studies that link genetic variation to gene function and expression should also be prioritized, as canines offer unique opportunities to identify new functions for recognized DNA sequence motifs. To accomplish this, the development of expression quantitative trait loci data sets...
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LETTER: Using Advanced Intercross Lines for High-Resolution Mapping of HDL Cholesterol Quantitative Trait Loci
- Xiaosong Wang,
- Isabelle Le Roy,
- Edwige Nicodeme,
- Renhua Li,
- Richard Wagner,
- Christina Petros,
- Gary A. Churchill,
- Stephen Harris,
- Ariel Darvasi,
- Jorge Kirilovsky,
- Pierre L. Roubertoux,
- and Beverly Paigen
Genome Res. July 2003 13: 1654-1664; Published in Advance June 12, 2003, doi:10.1101/gr.1185803
...Using Advanced Intercross Lines for High-Resolution Mapping of HDL Cholesterol Quantitative Trait Loci Xiaosong Wang 1 , Isabelle Le Roy 2 , Edwige Nicodeme 3 , Renhua Li 1 , Richard Wagner 1 , Christina Petros 1 , Gary A...
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Method: High-throughput and genome-scale targeted mutagenesis using CRISPR in a nonmodel multicellular organism, Bombyx mori
- Sanyuan Ma,
- Tong Zhang,
- Ruolin Wang,
- Pan Wang,
- Yue Liu,
- Jiasong Chang,
- Aoming Wang,
- Xinhui Lan,
- Le Sun,
- Hao Sun,
- Run Shi,
- Wei Lu,
- Dan Liu,
- Na Zhang,
- Wenbo Hu,
- Xiaogang Wang,
- Weiqing Xing,
- Ling Jia,
- and Qingyou Xia
Genome Res. January 2024 34: 134-144; Published in Advance January 8, 2024, doi:10.1101/gr.278297.123
.... The cocoon shape was measured for length and breadth using ImageJ software (https://imagej.nih.gov/ij/index.html), and 10 female and 10 male cocoons were randomly measured.Quantitative real-time PCRThe larvae were dissected to obtain different tissues, and the total RNA from BmE cells or different tissues...
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Review: Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics
- Natan Belchikov,
- Justine Hsu,
- Xiang Jennie Li,
- Julien Jarroux,
- Wen Hu,
- Anoushka Joglekar,
- and Hagen U. Tilgner
Genome Res. November 2024 34: 1735-1746; doi:10.1101/gr.279640.124
...at each location. In this way, the expression of several hundred to 1000 genes can be measured simultaneously and quantitatively (Chen et al. 2015). MERFISH and related nonsequencing-based methods provide a high degree of spatial resolution but lack the capability to detect the expression of genes beyond...
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