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Research: Identification of the male-specific region on the guppy Y Chromosome from a haplotype-resolved assembly
- Kang Du,
- Oliver Deusch,
- Ilja Bezrukov,
- Christa Lanz,
- Yann Guiguen,
- Margarete Hoffmann,
- Anette Habring,
- Detlef Weigel,
- Manfred Schartl,
- and Christine Dreyer
Genome Res. March 2025 35: 489-498; Published in Advance March 5, 2025, doi:10.1101/gr.279582.124
...possible fidelity of more individuals from different populations and different guppy species to distinguish private SNPs and sequence variation from those that are conserved across all individuals that share the same SD gene and genes encoding sex-linked traits. One possible strategy could be amplicon...
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Research: Long-read sequencing of 111 rice genomes reveals significantly larger pan-genomes
- Fan Zhang,
- Hongzhang Xue,
- Xiaorui Dong,
- Min Li,
- Xiaoming Zheng,
- Zhikang Li,
- Jianlong Xu,
- Wensheng Wang,
- and Chaochun Wei
Genome Res. May 2022 32: 853-863; Published in Advance April 8, 2022, doi:10.1101/gr.276015.121
..., and private members in gene families. (E) The PCA analysis of 111 rice accessions using gene family PAVs. (F) The clustering of 111 rice accessions using gene family PAVs.Different populations/subpopulations varied in terms of pan- sizes and the proportions of their core and distributed gene families/genes...
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Research: Limited allele-specific gene expression in highly polyploid sugarcane
- Gabriel Rodrigues Alves Margarido,
- Fernando Henrique Correr,
- Agnelo Furtado,
- Frederik C. Botha,
- and Robert James Henry
Genome Res. February 2022 32: 297-308; Published in Advance December 23, 2021, doi:10.1101/gr.275904.121
...from 56.0 million to 85.1 million raw reads per library, of which 50.6% to 84.7% remained after preprocessing to remove low-quality reads and contaminant ribosomal RNA, with a median yield of 81.8% (Supplemental Table S2). Hierarchical clustering was used to assess the variation between biological...
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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
...to contribute quantitative variation rather than major, qualitative defects. This may result in high levels of structural variation in crop plant s that contributes to important quantitative variation. Indeed, there are recent examples of rice quantitative trait loci (QTL) that are caused by deletion of genes...
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Review: Population genetic inference from genomic sequence variation
- John E. Pool,
- Ines Hellmann,
- Jeffrey D. Jensen,
- and Rasmus Nielsen
Genome Res. March 2010 20: 291-300; Published in Advance January 12, 2010, doi:10.1101/gr.079509.108
...) used linked clusters ofmutations to detect signals of archaic structure in human populations. Thus, while Pool et al. 294 Genome Research www..org long-range haplotype patterns carry unique information about the history of recent migration, short-range haplotype patterns can be strong signals of more...
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Research: Extensive recombination rate variation in the house mouse species complex inferred from genetic linkage maps
- Beth L. Dumont,
- Michael A. White,
- Brian Steffy,
- Tim Wiltshire,
- and Bret A. Payseur
Genome Res. January 2011 21: 114-125; Published in Advance October 26, 2010, doi:10.1101/gr.111252.110
...and underscore the continued importance of genetic linkage maps in the post- era. [Supplemental material is available online at http://www..org.] The rate of recombination—defined as the number of crossovers per unit DNA—is a quantitative genetic trait that displays marked variationwithin populations (Broman et...
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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
...(Li et al. 2021).Phenotypic plasticity occurs when a genotype produces different phenotype values in response to differing environments (Via et al. 1995). This plasticity is ubiquitous, present in staple crops including maize, wheat, and rice, and affecting traits ranging from yield to plant height...
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REVIEW: Allelic variation and heterosis in maize: How do two halves make more than a whole?
- Nathan M. Springer and
- Robert M. Stupar
Genome Res. March 2007 17: 264-275; Published in Advance January 25, 2007, doi:10.1101/gr.5347007
...that are relatively well-characterized in terms of genetic mapping, gene expression, and organization. The relative measurements for several traits of the B73 and Mo17 parental inbred lines and the hybrid are listed in Table 1 ( Zanoni and Dudley 1989 ; Auger et al. 2005b ). Note that the quantitative measurements...
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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
...abundance (Mergner et al. 2020). Protein 3D structure, as determinant of protein function, also influences various important biological activities. An improved understanding of protein 3D structural variation might provide critical insights into the molecular mechanisms underlying complex traits...
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Research: Genetic analysis of isoform usage in the human anti-viral response reveals influenza-specific regulation of ERAP2 transcripts under balancing selection
- Chun Jimmie Ye,
- Jenny Chen,
- Alexandra-Chloé Villani,
- Rachel E. Gate,
- Meena Subramaniam,
- Tushar Bhangale,
- Mark N. Lee,
- Towfique Raj,
- Raktima Raychowdhury,
- Weibo Li,
- Noga Rogel,
- Sean Simmons,
- Selina H. Imboywa,
- Portia I. Chipendo,
- Cristin McCabe,
- Michelle H. Lee,
- Irene Y. Frohlich,
- Barbara E. Stranger,
- Philip L. De Jager,
- Aviv Regev,
- Tim Behrens,
- and Nir Hacohen
Genome Res. December 2018 28: 1812-1825; Published in Advance November 16, 2018, doi:10.1101/gr.240390.118
...haplotype (top) and box-whisker plots (bottom three panels) between ERAP2 transcript quantitative traits (y-axis: log2(normalized gene abundance), log2(normalized isoform abundance), or isoform usage percentage)) and genotype (x-axis). (C) Correlation between ERAP2/Iso1 (orange), ERAP2/Iso3 (light blue...
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