Genetic Mapping and Diversity in Plants and Animals

The paper uses a mouse advanced intercross line to identify genetic associations and eQTLs for traits related to human health and disease.

The paper develops Camoco, a method integrating GWAS loci with co-expression networks to prioritize causal genes in maize, showing improved performance with tissue-specific expression data.

vqtl is an R package for mean-variance QTL mapping that corrects for variance heterogeneity and integrates with existing tools for genetic analysis.

This paper introduces mean-variance QTL mapping to identify novel QTL for circadian activity and exploratory behavior in mice, showing its superiority over traditional interval mapping in detecting both mean- and variance-controlling QTL.

This paper develops a method to detect mean-variance QTLs while accounting for background variance heterogeneity, identifying a new mean QTL for bodyweight in mice.

The paper combines high-throughput micro-CT-RGB phenotyping with GWAS to identify genetic loci associated with rice tiller growth traits and yield.

This study evaluates statistical methods for GWAS in crops with varying genetic architectures, finding that different approaches are optimal for different trait complexities.

The paper constructs an EST-SSR-based genetic linkage map and identifies a QTL for anthracnose resistance in water yam, aiding in marker-assisted breeding.

The paper maps a QTL for early maturity in tetraploid potato using a segregation population and identifies a 471kb interval containing 34 genes, including PUB14, potentially related to maturity.

ShinyAIM provides an interactive tool for visualizing longitudinal GWAS results through Manhattan plots and dynamic data exploration.

This study evaluates how different phenotyping methods affect GWAS results by simulating traits with varying heritability and causative loci, finding that lower heritability and more loci reduce AUCs.

This study identifies selection signatures in maize genes associated with reduced tassel size during hybrid breeding.

The paper identifies genetic loci controlling metabolite levels in C. elegans using recombinant inbred lines and QTL mapping.

This paper introduces AlphaPlantImpute, a heuristic method for phasing and imputing SNP data in bi-parental plant populations, showing better accuracy and efficiency than existing software.

The paper identifies FLC alleles as a major determinant of flowering time variation in Arabidopsis thaliana using population-scale data and shows their effect is mediated through gene expression.

The paper evaluates the prevalence of high-order linkage disequilibrium as an explanation for statistical epistasis in genome-wide association studies using A. thaliana data.

QTLseqr is an R package for NGS-BSA that identifies QTL using QTL-seq and G methods, providing tools for SNP analysis and visualization.

This study uses genotyping by sequencing to improve QTL detection sensitivity and resolution in a sorghum RIL population, identifying new syntenic regions and separating QTLs for plant height and flowering time.

This study refines the rat genetic map to sub-centimorgan resolution using 95,769 markers and 870 meioses, revealing sex-specific recombination patterns and improving QTL localization.

This study fine maps a mouse QTL for lean body mass (Burly1) to a 0.8-Mb region on chromosome 2, showing the B6 allele increases lean body mass without affecting food intake or activity.

polymapR is an R package for genetic linkage analysis and map construction in polyploid crops, handling triploid, tetraploid, and hexaploid data with preferential pairing correction.

This paper introduces a Squared-LMM model to correct confounding factors in genomic association mapping, showing improved accuracy in predicting trait-locus associations using synthetic and real data.

This paper introduces FarmCPUpp, an efficient implementation of the FarmCPU method for GWAS that improves speed and memory management using C++ and parallel computing.

The paper maps loci with nonlinear responses to combined drought and nitrogen stress in maize using three-dimensional dose-response surfaces.

The paper identifies genetic loci associated with body color and spotting patterns in redheaded pine sawfly larvae using QTL mapping and genome anchoring.

The paper introduces GUSMap, a method to construct accurate genetic maps from low coverage sequencing data by accounting for sequencing and genotyping errors in biparental outcrossed populations.

The paper introduces lme4qtl, an R package extending lme4 to enable flexible covariance structures and parameter constraints for QTL mapping in genetic studies of related individuals.

The paper identifies and develops SSR markers for Passiflora edulis using bioinformatics, finding high polymorphism and specificity in selected markers.