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Volume 228, Issue 4, December 2024
Call for Papers
Methods: a call for papers
Review
A review of multimodal deep learning methods for genomic-enabled prediction in plant breeding
Brief Investigation
Gene Expression
Location of polyadenylation sites within 3′ untranslated regions is linked to biological function in yeast
Investigation
Computational Resources, Software, & Databases
Functional analysis of G6PD variants associated with low G6PD activity in the All of Us Research Program
Experimental Technologies and Resources
Automated multimodal imaging of Caenorhabditis elegans behavior in multi-well plates
Behavioral assays in model organisms are widely used in genetic and chemical screens. This study presents an imaging system for longitudinally recording behavior of C. elegans in a 96-well plate. The software automatically measures locomotor activity, behavioral states, egg-laying events, and locomotor frequency. The system is tested by analyzing the roles of serotonin signaling on locomotion and egg-laying behaviors. The results revealed roles of serotonin receptors in regulating these behaviors across different behavioral states. This imaging and analysis pipeline will facilitate screens for genetic or pharmacological modulators of behavior.
Gene Expression
Set2 and H3K36 regulate the Drosophila male X chromosome in a context-specific manner, independent from MSL complex spreading
Higher-order epistasis within Pol II trigger loop haplotypes
Genetics of Complex Traits
Genomic prediction of cereal crop architectural traits using models informed by gene regulatory circuitries from maize
A dominance hypothesis argument for historical genetic gains and the fixation of heterosis in octoploid strawberry
Genome Integrity and Transmission
A maternal germline mutator phenotype in a family affected by heritable colorectal cancer
Drosophila ring chromosomes interact with sisters and homologs to produce anaphase bridges in mitosis
Ring chromosomes in eukaryotes cause problems during cell division and are associated with developmental and intellectual disabilities in humans. Ring chromosome behavior was examined during cell division in the fruit fly, Drosophila melanogaster, and multiple problems were found during division. These result from interactions with the sister chromatid and interactions with the homolog. Surprisingly, the ring can capture its homolog to generate bridges during mitosis. This discovery implicates and explains the role of topoisomerase II in chromosome pairing.
Population and Evolutionary Genetics
Admixture in the fungal pathogen Blastomyces
Genealogical asymmetry under the isolation with migration model and a two-taxon test for gene flow
The distribution of beneficial mutational effects between two sister yeast species poorly explains natural outcomes of vineyard adaptation
Mutation potentiates migration swamping in polygenic local adaptation
Statistical Genetics and Genomics
Bayesian hierarchical hypothesis testing in large-scale genome-wide association analysis
In Genetics, big data revolution-driven technologies, such as pharmacogenomics and precision medicine can be transformative. Although big data-powered innovations are making strides in Genetics, many vital challenges remain. We address the challenges of fine-mapping in the Genome-Wide Association Studies (GWAS) involving millions of variants, many of which may be in high linkage disequilibrium. We devised a Bayesian hierarchical hypothesis testing (BHHT)–a novel multi-resolution testing procedure that offers (1) high power, (2) adequate error control, and (3) fine-mapping resolution.
