Higgins, Kaitlin Nyabashi, Vital Anderson, Sarah
Published in
G3 (Bethesda, Md.)
Imprinted expression is an essential process for seed viability affecting hundreds of genes in Zea mays endosperm, however most studies have examined just one time point for analysis. The focus on single time points can limit our ability to identify imprinted genes, and our ability to draw conclusions for the role of imprinting in endosperm. In thi...
Dvorak, Etienne Mazet, Isabelle D Couture, Carole Delmotte, François Foulongne-Oriol, Marie
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G3 (Bethesda, Md.)
Plasmopara viticola, the causal agent of grapevine downy mildew, is a biotrophic oomycete engaged in a tight coevolutionary relationship with its host. Rapid adaptation of the pathogen is favored by annual sexual reproduction that generates genotypic diversity. With the aim of studying the recombination landscape across the P. viticola genome, we g...
Hassanpour, Azadeh Geibel, Johannes Simianer, Henner Rohde, Antje Pook, Torsten
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G3 (Bethesda, Md.)
The effective planning and allocation of resources in modern breeding programs is a complex task. Breeding program design and operational management have a major impact on the success of a breeding program and changing parameters such as the number of selected/phenotyped/genotyped individuals in the breeding program will impact genetic gain, geneti...
Long, Evan M Stitzer, Michelle C Monier, Brandon Schulz, Aimee J Romay, M Cinta Robbins, Kelly R Buckler, Edward S
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G3 (Bethesda, Md.)
Centuries of clonal propagation in cassava (Manihot esculenta) have reduced sexual recombination, leading to the accumulation of deleterious mutations. This has resulted in both inbreeding depression affecting yield and a significant decrease in reproductive performance, creating hurdles for contemporary breeding programs. Cassava is a member of th...
Andorf, Carson M Ross-Ibarra, Jeffrey Seetharam, Arun S Hufford, Matthew B Woodhouse, Margaret R
Published in
G3 (Bethesda, Md.)
Efforts to capture and analyze maize nucleotide diversity have ranged widely in scope, but differences in reference genome version and software algorithms used in these efforts inhibit comparison, and these data are generally not available in an easy-to-use visualization platform for quick access and analysis. To address these issues, The Maize Gen...
Kihlman, Ragini Launonen, Ilkka Sillanpää, Mikko J Waldmann, Patrik
Published in
G3 (Bethesda, Md.)
In genomics, use of deep learning (DL) is rapidly growing and DL has successfully demonstrated its ability to uncover complex relationships in large biological and biomedical data sets. With the development of high-throughput sequencing techniques, genomic markers can now be allocated to large sections of a genome. By analyzing allele sharing betwe...
Chen, Anqi Stadulis, Sara E deLeuze, Kayla Gibney, Patrick A
Published in
G3 (Bethesda, Md.)
In the yeast Saccharomyces cerevisiae, 2 types of trehalase activities have been described. Neutral trehalases (Nth1 and Nth2) are considered to be the main proteins that catalyze intracellular trehalose mobilization. In addition to Nth1 and Nth2, studies have shown that acid trehalase Ath1 is required for extracellular trehalose degradation. Altho...
Okamoto, Faith Chitre, Apurva S Missfeldt Sanches, Thiago Chen, Denghui Munro, Daniel Aron, Allegra T Beeson, Angela Bimschleger, Hannah V Eid, Maya Garcia Martinez, Angel G
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G3 (Bethesda, Md.)
Genome-wide association studies typically evaluate the autosomes and sometimes the X Chromosome, but seldom consider the Y or mitochondrial (MT) Chromosomes. We genotyped the Y and MT Chromosomes in heterogeneous stock (HS) rats (Rattus norvegicus), an outbred population created from 8 inbred strains. We identified 8 distinct Y and 4 distinct MT Ch...
Grabowski, Paul P Dang, Phat Jenkins, Jerry J Sreedasyam, Avinash Webber, Jenell Lamb, Marshall Zhang, Qiong Sanz-Saez, Alvaro Feng, Yucheng Bunting, Victoria
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Published in
G3 (Bethesda, Md.)
Peanut (Arachis hypogaea L.) is a globally important oil and food crop frequently grown in arid, semi-arid, or dryland environments. Improving drought tolerance is a key goal for peanut crop improvement efforts. Here, we present the genome assembly and gene model annotation for "Line8," a peanut genotype bred from drought-tolerant cultivars. Our as...
Sakurai, Kengo Hamazaki, Kosuke Inamori, Minoru Kaga, Akito Iwata, Hiroyoshi
Published in
G3 (Bethesda, Md.)
In plant breeding programs, rapid production of novel varieties is highly desirable. Genomic selection allows the selection of superior individuals based on genomic estimated breeding values. However, it is worth noting that superior individuals may not always be superior parents. The choice of the crossing pair significantly influences the genotyp...