Genetic Mapping and Diversity in Plants and Animals

The paper combines GWAS and TWAS to identify 13 candidate causal genes for tocochromanol levels in maize grain, including five previously unassociated genes.

The paper genotypes over 4,000 Sprague Dawley rats to characterize genetic diversity and performs GWAS on Pavlovian conditioned approach behavior, identifying 46 significant loci.

This study identifies 27 significant SNPs associated with resistance to Bipolaris leaf spot in switchgrass through genome-wide association analysis.

This paper presents a chromosome-scale genome assembly for Solanum lycopersicoides and maps introgression lines to support genetic studies of traits in tomato.

This study maps ethanol sensitivity QTLs in Diversity Outbred mice using phenotyping and genotyping data to identify candidate genes for alcohol use disorders.

The paper introduces updated pipelines for MutMap and QTL-seq that are faster, easier to use, and more accessible via bioconda.

This study uses transcriptome-wide association and prediction to identify genes related to carotenoid and tocochromanol levels in sweet corn and shows transcriptomic data improve predictive models.

The paper develops an eggplant MAGIC population to identify genes associated with anthocyanin pigmentation, finding strong associations with MYB113 and COP1 genes.

The paper analyzes genetic diversity and linkage disequilibrium in Brassica napus germplasm to guide breeding strategies and association mapping.

The paper identifies a heterochromatic knob locus on chromosome 9 associated with earlier flowering time in maize through genome size and flowering time measurements and association analysis.

The paper introduces the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel, a vertebrate genetic resource for genotype-to-phenotype studies, enabling controlled experiments on complex traits.

The paper introduces BB-QTL mapping to study complex traits in yeast, revealing polygenic, pleiotropic, and epistatic genetic architectures with increased sample size.

This paper develops a theoretical framework to predict the genomic resolution of bulk segregant analysis (BSA) based on coalescence theory and experimental parameters.

This study compares single-trait and multi-trait GWAS models to dissect the genetic architecture of seedling emergence in wheat, finding that multi-trait models identify more large-effect markers.

This paper introduces an X-QTL mapping strategy using bulked phenotyping and pooled sequencing in Drosophila, demonstrating its power and efficiency for identifying genetic loci associated with traits like caffeine resistance.

This paper presents a chromosome-level genome assembly for longan and identifies genetic factors influencing fruit quality traits through population genomics and GWAS.

The paper presents a high-quality reference genome for tomato, revealing genomic fragments linked to human selection during domestication.

The paper develops a 50K SNP genotyping array for Scots pine to enable genome-wide analyses and improve genetic research and breeding programs.

This paper modifies a BSA-Seq analysis method to identify trait-associated genomic regions without requiring parental genome sequences, demonstrating its effectiveness on a public dataset.

This study uses GWAS to identify candidate genes for drought tolerance in coast redwood and giant sequoia, finding 78 and 6 marker-trait associations respectively.

This study identifies seed storability-related loci in Dongxiang wild rice using BSA-seq and confirms their effects through metabolic and cellular analysis.

The paper introduces a generic hidden Markov model for genotype reconstruction in multi-parent populations and demonstrates its application using R/qtl2 on mouse data.

The paper examines recombination patterns in cassava, finding higher female recombination rates and suppressed recombination in wild introgression segments.

The paper combines data from two independent mouse studies to identify genetic loci for traits, finds poor replication rates, and proposes a method to assess confidence in associations.

The paper maps transcriptome variation in Mimulus guttatus to cis- and trans-acting mutations, finding differing patterns of selection and showing that gene expression modules predict allele frequencies and traits.

This study sequenced 300 Thai rice accessions to identify SNP variants and infer population structure, revealing five subpopulations grouped by location with unique genetic and agronomic traits.

This paper introduces an automated SNP-based method to identify contaminants in polyploid plant progenies using PCA, Mendelian segregation analysis, and clustering, validated on simulated and real data.