5 Works

Data from: Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection

Jorge Duitama, Alexander Silva, Yamid Sanabria, Daniel Felipe Cruz, Constanza Quintero, Carolina Ballen, Mathias Lorieux, Brian Scheffler, Andrew Farmer, Edgar Torres, James Oard & Joe Tohme
Current advances in sequencing technologies and bioinformatics revealed the genomic background of rice, a staple food for the poor people, and provided the basis to develop large genomic variation databases for thousands of cultivars. Proper analysis of this massive resource is expected to give novel insights into the structure, function, and evolution of the rice genome, and to aid the development of rice varieties through marker assisted selection or genomic selection. In this work we...

Data from: Genome-wide association genetics of an adaptive trait in lodgepole pine

Thomas L. Parchman, Zachariah Gompert, Craig W. Benkman, Faye D. Schilkey, Joann Mudge & C. Alex Buerkle
Pine cones that remain closed and retain seeds until fire causes the cones to open (cone serotiny) represent a key adaptive trait in a variety of pine species. In lodgepole pine, there is substantial geographic variation in serotiny across the Rocky Mountain region. This variation in serotiny has evolved as a result of geographically divergent selection, with consequences that extend to forest communities and ecosystems. An understanding of the genetic architecture of this trait is...

Data from: De novo assembly of a tadpole shrimp (Triops newberryi) transcriptome and preliminary differential gene expression analysis

Rebekah L. Horn, Thiruvarangan Ramaraj, Nicholas P. Devitt, Faye D. Schilkey & David E. Cowley
Next-generation sequencing techniques, such as RNA sequencing, have provided a wealth of genomic information for nonmodel species. Transcriptomic information can be used to quantify the patterns of gene expression, which can identify how environmental differences invoke organismal stress responses and provide a gauge in predicting species adaptability. In our study, we used RNA sequencing to characterize the first transcriptome from a naupliar tadpole shrimp (Triops newberryi) to identify the genes expressed during the early life...

Data from: Differential hippocampal gene expression is associated with climate-related natural variation in memory and the hippocampus in food-caching chickadees

Vladimir V. Pravosudov, , Matthew L. Forister, Lara D. LaDage, Robin Kramer, Faye Schilkey, Alexander M. Van Der Linden & T. C. Roth
There is significant and often heritable variation in cognition and its underlying neural mechanisms, yet specific genetic contributions to such variation are not well characterized. Black-capped chickadees present a good model to investigate the genetic basis of cognition because they exhibit tremendous climate-related variation in memory, hippocampal morphology and neurogenesis rates throughout the North American continent, and these cognitive traits appear to have a heritable basis. We examined the hippocampal transcriptome profiles of laboratory-reared chickadees...

Data from: Candidate genes and genetic architecture of symbiotic and agronomic traits revealed by whole-genome, sequence-based association genetics in Medicago truncatula

John Stanton-Geddes, Timothy Paape, Brendan Epstein, Roman Briskine, Jeremy Yoder, Joann Mudge, Arvind K. Bharti, Andrew D. Farmer, Peng Zhou, Roxanne Denny, Gregory D. May, Stephanie Erlandson, Mohammed Yakub, Masayuki Sugawara, Michael J. Sadowsky, Nevin D. Young & Peter Tiffin
Genome-wide association study (GWAS) has revolutionized the search for the genetic basis of complex traits. To date, GWAS have generally relied on relatively sparse sampling of nucleotide diversity, which is likely to bias results by preferentially sampling high-frequency SNPs not in complete linkage disequilibrium (LD) with causative SNPs. To avoid these limitations we conducted GWAS with >6 million SNPs identified by sequencing the genomes of 226 accessions of the model legume Medicago truncatula. We used...

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