Genetic Mapping and Diversity in Plants and Animals

Comparison of GWAS models to identify non-additive genetic control of flowering time in sunflower hybrids

This study compares additive and non-additive GWAS models to identify genomic regions controlling flowering time in sunflower hybrids, finding non-additive models better detect trait-associated loci.

Genome-Wide Mining, Characterization and Development of miRNA-SSRs in Arabidopsis thaliana

The paper identifies and characterizes miRNA-SSRs in Arabidopsis thaliana pre-miRNA sequences, finding they are abundant in non-coding regions and could serve as new markers for breeding.

Mapfuser: an integrative toolbox for consensus map construction and Marey maps

Mapfuser integrates genetic map visualization, consensus map construction, and Marey map analysis into a standardized toolbox with interactive features and reproducibility tools.

Widespread Inter-Chromosomal Epistasis Regulates Glucose Homeostasis And Gene Expression

The paper shows that inter-chromosomal epistasis significantly influences glucose homeostasis and gene expression in mice, often overriding additive genetic effects.

The Potential Role of Genetic Assimilation during Maize Domestication

The paper examines gene expression changes in maize and teosinte under past and present environmental conditions to explore the role of genetic assimilation in maize domestication.

High-Resolution Maps of Mouse Reference Populations

The paper generates high-resolution genetic maps of mouse inbred strains and identifies genetic variations and gene conversions.

Ras/MAPK modifier loci revealed by eQTL in C. elegans

The paper identifies eQTLs in C. elegans that modulate Ras/MAPK signaling, revealing genetic modifiers that are not detectable in single genetic backgrounds.

A set of Columbia-0-specific single nucleotide polymorphism markers for the genetic analysis of natural variation in Arabidopsis thaliana

The paper develops 140 SNP markers for distinguishing Columbia-0 from other Arabidopsis thaliana accessions and validates their utility for genetic analysis.

Epistatic networks jointly influence phenotypes related to metabolic disease and gene expression in Diversity Outbred mice

The paper models epistatic networks in Diversity Outbred mice linking genetic variation, gene expression, and phenotypes related to metabolic disease and diet.

Crosslink: A Fast, Scriptable Genetic Mapper For Outcrossing Species

Crosslink is a genetic mapping tool for outcrossing species that is faster than existing programs while maintaining similar accuracy.

The genomic architecture of flowering time varies across space and time in Mimulus guttatus

This study maps flowering time loci in Mimulus guttatus across space and time, finding significant genetic variation and genotype-by-environment interactions.

Gene co-expression network connectivity is an important determinant of selective constraint

The paper investigates the genetic architecture of gene expression variation in Populus tremula, finding that eQTLs are more common in regulatory regions and that network connectivity correlates with selective constraint.

Genomic inferences of domestication events are corroborated by written records in Brassica rapa

The paper uses genomic data and written records to validate domestication events in Brassica rapa, finding support for specific genetic groups and domestication timelines.

Constructing high-density linkage maps with MapDisto 2.0

MapDisto 2.0 constructs genetic linkage maps with features for handling large datasets, VCF import, linkage detection, data imputation, and QTL analysis.

Construction of a high-density American cranberry (Vaccinium macrocarpon Ait.) composite map using genotyping-by-sequencing for multi-pedigree linkage mapping

The paper constructs a high-density cranberry composite map using GBS and SSRs to enable molecular-assisted breeding and genomic studies.

Efficiency of genome-wide association study in random cross populations

The paper evaluates GWAS efficiency in different plant populations, finding that inbred lines panels offer the best QTL detection power and precision, especially for low and intermediate heritability traits.

Comparison of one-stage and two-stage genome-wide association studies

This study compares one-stage and two-stage GWAS methods, finding that a weighted two-stage approach reduces bias and improves power, especially in unbalanced data.

Regulatory architecture of gene expression variation in the threespine stickleback, Gasterosteus aculeatus.

The paper identifies eQTL and trans regulatory hotspots in threespine stickleback liver tissue, showing complex transcription factor interactions and some links to salinity tolerance.

rAmpSeq: Using repetitive sequences for robust genotyping

Primers anchored in conserved repeat sequence amplify thousands of maize middle-repetitive loci at once, with markers called from the low-copy sequence between copies for under $5 per sample.

Diversity patterns across 1,800 chloroplast genomes of wild (Oryza rufipogon Griff.) and cultivated rice (O. sativa L.)

The paper analyzes chloroplast genome diversity in 1,800 wild and cultivated rice accessions, revealing distinct domestication histories for aus and aromatic rice groups.

Identifying the diamond in the rough: a study of allelic diversity underlying flowering time adaptation in maize landraces

This study identifies genes underlying flowering time adaptation in maize landraces by integrating genomic mapping and association analysis across multiple environments.

DMAP - Graphical representation of physical and genetic map correlation

DMAP visualizes and optimizes the correlation between physical and genetic maps, reducing data redundancy and highlighting anomalies in contig orientation.

A large scale joint analysis of flowering time reveals independent temperate adaptations in maize

This study identifies independent temperate adaptations in maize flowering time across different populations using GWAS and machine learning.