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Resource: The 100-genomes strains, an S. cerevisiae resource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen
- Pooja K. Strope,
- Daniel A. Skelly,
- Stanislav G. Kozmin,
- Gayathri Mahadevan,
- Eric A. Stone,
- Paul M. Magwene,
- Fred S. Dietrich,
- and John H. McCusker
Genome Res. May 2015 25: 762-774; Published in Advance April 3, 2015, doi:10.1101/gr.185538.114
...be used to perform unbiased, -wide searches for quantitative trait loci. Population-phenotype associations in the 100-s strains In contrast to Warringer et al. (2011), we identified relatively few phenotype associations with populations (Table 1), the reasons for which are biological and technical. First...
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Dog Special/Letters: Selective sweep mapping of genes with large phenotypic effects
- John P. Pollinger,
- Carlos D. Bustamante,
- Adi Fledel-Alon,
- Sheila Schmutz,
- Melissa M. Gray,
- and Robert K. Wayne
Genome Res. December 2005 15: 1809-1819; doi:10.1101/gr.4374505
...). Selectively swept regions in the can potentially be identified by a scan, and the low-variation interval surrounding the gene under selection narrowly circumscribed by fine-scale mapping. For example, a marker-based survey of chromosome 1 in rats from warfarin-resistant populations found a 0.5-centimorgan (c...
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Research: Analysis of canine gene constraint identifies new variants for orofacial clefts and stature
- Reuben M. Buckley,
- Nüket Bilgen,
- Alexander C. Harris,
- Peter Savolainen,
- Cafer Tepeli,
- Metin Erdoğan,
- Aitor Serres Armero,
- Dayna L. Dreger,
- Frank G. van Steenbeek,
- Marjo K. Hytönen,
- Heidi G. Parker,
- Jessica Hale,
- Hannes Lohi,
- Bengi Çınar Kul,
- Adam R. Boyko,
- and Elaine A. Ostrander
Genome Res. May 2025 35: 1080-1093; Published in Advance March 24, 2025, doi:10.1101/gr.280092.124
...and sufficiently defined. In this study, we explore how gene constraint can be used to identify variants with potential to impact phenotypes as trait-associated candidates, later determining association by investigating breed traits and characteristics of dogs carrying these alleles. Because variants are first...
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Mini-Review: Toward telomere-to-telomere cat genomes for precision medicine and conservation biology
- William J. Murphy and
- Andrew J. Harris
Genome Res. May 2024 34: 655-664; Published in Advance June 7, 2024, doi:10.1101/gr.278546.123
...into structure and chromosome evolution through comparative genomics and recent success stories using genotype-to-phenotype mapping to clarify the basis for feline traits and species evolution. Lastly, we will explore the potential for discovering and applying genomic evidence to the management and conservation...
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Resource: GenomeMUSter mouse genetic variation service enables multitrait, multipopulation data integration and analysis
- Robyn L. Ball,
- Molly A. Bogue,
- Hongping Liang,
- Anuj Srivastava,
- David G. Ashbrook,
- Anna Lamoureux,
- Matthew W. Gerring,
- Alexander S. Hatoum,
- Matthew J. Kim,
- Hao He,
- Jake Emerson,
- Alexander K. Berger,
- David O. Walton,
- Keith Sheppard,
- Baha El Kassaby,
- Francisco Castellanos,
- Govindarajan Kunde-Ramamoorthy,
- Lu Lu,
- John Bluis,
- Sejal Desai,
- Beth A. Sundberg,
- Gary Peltz,
- Zhuoqing Fang,
- Gary A. Churchill,
- Robert W. Williams,
- Arpana Agrawal,
- Carol J. Bult,
- Vivek M. Philip,
- and Elissa J. Chesler
Genome Res. January 2024 34: 145-159; Published in Advance January 30, 2024, doi:10.1101/gr.278157.123
..., age-related phenotypes, microbiota, response to infections, and other environmental factors, as well as molecularly characterized endpoints, such as transcriptomes, proteomes, and metabolomes across many tissues. Advances in genetics, including transcriptome-wide and phenome-wide association analysis...
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Perspective: Constructing genomic maps of positive selection in humans: Where do we go from here?
- Joshua M. Akey
Genome Res. May 2009 19: 711-722; doi:10.1101/gr.086652.108
...parameters such as population demographic history and local rates of recombination. For each sampled locus, a statistic of interest (denoted here as Ti for the ith locus) is calculated, an empirical distribution is constructed, and outlier loci are identified in the tail of the empirical distribution...
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LETTER: QTL Analysis in a Complex Autopolyploid: Genetic Control of Sugar Content in Sugarcane
- Ray Ming,
- Sin-Chieh Liu,
- Paul H. Moore,
- James E. Irvine,
- and Andrew H. Paterson
Genome Res. December 1, 2001 11: 2075-2084; Published in Advance November 12, 2001, doi:10.1101/gr.198801
...industry; to investigate the molecular basis of phenotypic buffering that may contribute to the success of autopolyploid crops; and to investigate the possibility that candidate genes for QTLs affecting carbohydrate metabolism in biomass crops might be identified based on discrete mutations affecting seed...
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PERSPECTIVE: The canine genome
- Elaine A. Ostrander and
- Robert K. Wayne
Genome Res. December 2005 15: 1706-1716; doi:10.1101/gr.3736605
...that attempts to identify genetically distinct subpopulations based on patterns of allele frequencies ( Pritchard et al. 2000 ). Each genotyped dog is represented by a single vertical line divided into K colors, where K is the number of clusters assumed in each structure analysis. The length of the colored...
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Method: A spectral component approach leveraging identity-by-descent graphs to address recent population structure in genomic analysis
- Ruhollah Shemirani,
- Gillian M. Belbin,
- Sinead Cullina,
- Christa Caggiano,
- Christopher R. Gignoux,
- Noah Zaitlen,
- and Eimear E. Kenny
Genome Res. March 2026 36: 534-546; Published in Advance December 23, 2025, doi:10.1101/gr.280659.125
...affected only by direct genetic effects and random noise. These phenotypes, which we refer to as “polygenic phenotypes,” are modeled through the randomized selection of causal variants with effect sizes assigned based on their allele frequency and the total heritability of the trait. This approach...
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Method: Autoencoders for genomic variation analysis
- Margarita Geleta,
- Daniel Mas Montserrat,
- Xavier Giro-i-Nieto,
- and Alexander G. Ioannidis
Genome Res. February 2026 36: 348-360; Published in Advance January 20, 2026, doi:10.1101/gr.280086.124
..., are powering -wide association studies (GWAS), where many genetic variants (e.g., SNPs) are analyzed across different subjects to find the relationships between genetic and phenotypic traits (Mardis 2011; Wojcik et al. 2019), are used to develop new treatments and drugs (Shah and Gaedigk 2018), and to address...
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