Genetic Mapping and Diversity in Plants and Animals

Efficient Permutation-based Genome-wide Association Studies for Normal and Skewed Phenotypic Distributions

The paper introduces permGWAS, a permutation-based GWAS method that improves significance thresholds for skewed phenotypes and reduces false discovery rates compared to Bonferroni correction.

rTASSEL: an R interface to TASSEL for association mapping of complex traits

rTASSEL provides an R interface to TASSEL for association mapping, offering faster performance than other R packages for genomic analyses.

Genome scan of landrace populations of the self-fertilizing crop species rice, collected across time, revealed climate changes' selective footprints in the genes network regulating flowering time.

The paper analyzes genetic adaptation to climate change in rice landraces over time, identifying selection footprints in flowering time regulatory genes.

Comparative transcriptomic analysis of maize ear heterosis during the inflorescence meristem differentiation stage

The paper identifies nonadditive gene expression and allele-specific expression in maize hybrids, linking them to heterosis in ear development.

Genetic mapping of some key plant architecture traits in Brassica juncea using a cross between two distinct lines - vegetable type Tumida and oleiferous Varuna

The paper identifies environmentally stable QTL and candidate genes for plant architectural traits in Brassica juncea using a cross between vegetable and oleiferous lines.

Genome-wide association study in the pseudocereal quinoa reveals selection pattern typical for crops with a short breeding history

This paper conducts a genome-wide association study on quinoa to identify genetic markers linked to agronomic traits and reveals selection patterns in an underutilized crop.

The genetic architectures of vine and skin maturity in tetraploid potato

The paper investigates the genetic architectures of vine and skin maturity in tetraploid potato using genome-wide association and linkage mapping, identifying key QTL and confirming their biological basis through haplotype analysis.

Refining Bulk Segregant Analyses: Ontology-Mediated Discovery of Flowering Time Genes in Brassica oleracea

The paper improves bulk segregant analysis by using Gene Ontology to filter flowering time genes in Brassica oleracea, identifying relevant pathways and candidate genes.

Mapping-by-sequencing reveals genomic regions associated with seed quality parameters in Brassica napus

This study identifies genomic regions associated with seed quality traits in Brassica napus using mapping-by-sequencing, revealing new intervals and potential causal genes for seed glucosinolate, protein, and oil content.

QTLViewer: An interactive webtool for genetic analysis in the Collaborative Cross and Diversity Outbred mouse populations

QTLViewer provides an interactive webtool for QTL mapping and exploration in CC and DO mouse populations, enhancing accessibility to genetic analysis resources.

Combining GWAS and TWAS to identify candidate causal genes for tocochromanol levels in maize grain

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

Portrait of a genus: genome sequencing reveals evidence of adaptive variation in Zea

The paper characterizes genomic variation across 744 Zea genomes, identifies adaptive variants, and highlights their potential for breeding applications.

Genetic characterization of outbred Sprague Dawley rats and utility for genome-wide association studies

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.

Genome-wide identification of microsatellite markers and their application in genetic studies of wolfberry (Lycium barbarum)

The paper identifies 397,558 microsatellite markers in wolfberry genome sequences and evaluates their utility for genetic diversity analysis and breeding applications.

Genome-Wide Associations with Resistance to Bipolaris Leaf Spot (Bipolaris oryzae (Breda de Haan) Shoemaker) in a Northern Switchgrass Population (Panicum virgatum)

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

Genetic architectures of floral pigment and patterning in hybrid monkeyflowers

This study identifies genetic factors influencing floral pigment intensity and spatial patterning in hybrid monkeyflowers through QTL analysis and gene candidate hypotheses.

Detecting epistatic interactions in genomic data using Random Forests

This paper introduces a computationally efficient Random Forests method to detect epistatic interactions in genomic data and validates it on simulated and real datasets.

Linkage mapping reveals loci that underlie differences in C. elegans growth

This study identifies three QTL associated with body size variation in C. elegans using linkage mapping between two strains.

Genome-wide Association Study Reveals that PvGUX1_1 is Associated with Pod Stringlessness in Snap Bean (Phaseolus vulgaris L.)

The broad shell colour variation in common cockle (Cerastoderma edule) from Northeast Atlantic relies on a major QTL revealed by GWAS using a new high-density genetic map

This study identifies a major QTL for shell colour variation in common cockles using GWAS and a high-density genetic map, linking it to candidate genes involved in shell architecture and local adaptation.

A Solanum lycopersicoides reference genome facilitates biological discovery in tomato

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

Genome-wide association mapping of ethanol sensitivity in the Diversity Outbred mouse population

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

High-density mapping of QTL controlling agronomically important traits in quinoa (Chenopodium quinoa Willd.)

This study constructs a high-density genetic map of quinoa using Skim-seq and identifies fifteen QTL for ten agronomically important traits, including pleiotropic loci for flowering time and plant height.

High-performance pipeline for MutMap and QTL-seq

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

QTLs analysis for cold tolerance in rice (Oryza sp.) at the seedling stage using F2 population developed from cross between the genotypes NERICA L-19 and Diamante

This study identifies QTLs associated with cold tolerance in rice seedlings using an F2 population from NERICA L-19 and Diamante, aiming to improve cold tolerance in African rice varieties.

Transcriptome-wide association and prediction for carotenoids and tocochromanols in fresh sweet corn kernels

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.

Newly developed MAGIC population allows identification of strong associations and candidate genes for anthocyanin pigmentation in eggplant

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

Pervasive Under-Dominance in Gene Expression Underlying Emergent Growth Trajectories in Arabidopsis thaliana Hybrids

The paper investigates gene expression patterns in Arabidopsis thaliana hybrids, finding that non-additive gene expression is common and correlates with F1 rosette size, highlighting under-dominance as a key factor in growth trajectories.

Linkage disequilibrium and population structure in a core collection of Brassica napus (L.)

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

A heterochromatic knob reducing the flowering time in maize

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.