Genetic Mapping and Diversity in Plants and Animals

Mapping and Analysis of QTL for Early Maturity Trait in Tetraploid Potato (Solanum tuberosum L.)

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: Shiny-based Application of Interactive Manhattan Plots for Longitudinal Genome-Wide Association Studies

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

Comparing genome-wide association study results from different measurements of an underlying phenotype

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.

Selection signatures underlying dramatic male inflorescence transformation during modern hybrid maize breeding

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

Natural genetic variation in C. elegans reveals genomic loci controlling metabolite levels

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

Assessment of population differentiation and linkage disequilibrium in Solanum pimpinellifolium using genome-wide high-density SNP markers

The paper assesses population differentiation and linkage disequilibrium in Solanum pimpinellifolium using high-density SNP markers to improve genome-wide association studies for tomato breeding.

Common genomic regions underlie natural variation in diverse toxin responses

The paper identifies QTL underlying toxin response variation in C. elegans and validates their contributions through experimental assays.

A heuristic method for fast and accurate phasing and imputation of single nucleotide polymorphism data in bi-parental plant populations

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 genetic architecture of the network underlying flowering time variation in Arabidopsis thaliana

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.

On the relationship between high-order linkage disequilibrium and epistasis

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.

Detection of epistatic interactions with Random Forest

This paper develops three methods to detect epistasis using Random Forest, outperforming existing approaches in simulated and real yeast datasets.

A fast mrMLM algorithm for multi-locus genome-wide association studies

FASTmrMLM swaps mrMLM's numerical gradients and Hessians for analytic ones, cutting runtime by more than 50% while matching or slightly beating its simulated power and accuracy.

QTLseqr: An R package for bulk segregant analysis with next-generation sequencing

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

Explorations of the polygenic genetic architecture of flowering time in the worldwide Arabidopsis thaliana population

This study investigates how 48 flowering time loci contribute to genetic differences among Arabidopsis thaliana subpopulations across ecological habitats, revealing polygenic adaptation and gene-by-temperature interactions.

Genotyping by sequencing of 393 Sorghum bicolor BTx623 x IS3620C recombinant inbred lines improves sensitivity and resolution of QTL detection

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.

A High-Resolution Genetic Map for the Laboratory Rat

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.

Identification of candidate genes for gelatinization temperature, gel consistency and pericarp color by GWAS in rice based on SLAF-sequencing

Burly1 is a mouse QTL for lean body mass that maps to a 0.8-Mb region on chromosome 2

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: linkage analysis and genetic map construction from F1 populations of outcrossing polyploids

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.

Multiplex Confounding Factor Correction for Genomic Association Mapping with Squared Sparse Linear Mixed Model

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.

FarmCPUpp: Efficient Large-Scale GWAS

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

Dose-response surface fits to drought and nitrogen limitation applied together allow mapping of loci that exhibit nonlinear responses

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

Genetic basis of body color and spotting pattern in redheaded pine sawfly larvae (Neodiprion lecontei)

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

Accounting for Errors in Low Coverage High-Throughput Sequencing Data when Constructing Genetic Maps using Biparental Outcrossed Populations

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.

lme4qtl: linear mixed models with flexible covariance structure for genetic studies of related individuals

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.

Is this a fake QTL? A short note on analysis of multiple QTL peaks on the same chromosome

The paper proposes a method to identify spurious QTLs by comparing expected test statistic values at putative QTL positions with observed values.

Genetic basis of transgressive segregation in rice heading phenotypes

The paper identifies five new QTLs associated with transgressive segregation in rice heading time by analyzing F2 progeny from two japonica rice cultivars.

A multi-locus association analysis method integrating phenotype and expression data reveals multiple novel associations to flowering time variation in wild-collected Arabidopsis thaliana

High-throughput identification and marker development of perfect SSR for cultivated genus of passion fruit (Passiflora edulis)

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

Adiposity QTL Adip20 decomposes into at least four loci when dissected using congenic strains

The paper fine-maps a QTL for gonadal adipose depot weight in mice using congenic strains, revealing at least four distinct loci within the original QTL region.