Volume 14, Issue 12, December 2024

Large, complex data sets can be difficult to model in a single comprehensive genome-wide association study (GWAS). The best practice for two-stage analyses is to consider lines as fixed effects in the first stage statistical model. Best linear unbiased estimates of lines can then be used as input phenotypes to the second stage analysis. In the second stage, lines can be modeled as random effects with genomic relationships to adjust for population structure when estimating individual SNP effects in GWAS.

Mutant tRNA genes can cause mistranslation, the misincorporation of amino acids into protein, and are associated with human disease. This study investigated tRNA variants that caused threonine-to-serine (T→S) or valine-to-serine (V→S) substitutions. Both variants caused developmental delays, lethality, and females to present with more deformities. Surprisingly, mistranslation increased female lifespan and mistranslating males and females showed improved locomotion. These results suggest that mistranslation has positive and negative effects that depend on the tRNA variant and sex of the fly.

Soybean cyst nematode (SCN) infestation devastates soybean crops, impacting the US economy. The Rhg1 gene, the most crucial for SCN resistance, exhibits varying copy number in soybeans. This study discovers significant changes in defense gene expression even with slight copy number variation. Chaiprom et al. also identified intricate regulatory pathways affected by Rhg1 copy number. Additionally, during SCN infection, genes related to defense mechanisms, such as phytoalexin biosynthesis and NBS-LRR, showed heightened activity in resistant plants, offering insights into enhancing SCN resistance.

This study explored genetic variation in winter wheat for disease resistance and the biocontrol efficacy of a beneficial fungus, Clonostachys rosea, in controlling Fusarium graminearum causing fusarium foot rot. Testing 190 wheat genotypes, significant variation in disease resistance and biocontrol efficacy was found. Further genome-wide analysis revealed independent inheritance of disease resistance and biocontrol efficacy, suggesting a possibility for simultaneous breeding for these traits. It can contribute to sustainable agriculture practices by reducing chemical pesticide use and enhancing biocontrol effectiveness.

Romero et al. present a new high-quality genome assembly and annotation for the Florida Scrub-Jay (Aphelocoma coerulescens), a Federally Threatened bird species. In comparison to other genome assemblies of this species, the authors’ assembly is the first one generated using long-read sequencing technology and from a female individual. They also constructed the first linkage map for this species. The authors’ genome assembly is highly contiguous and is of similar quality to other bird genome assemblies.