Genetic Mapping and Diversity in Plants and Animals

An ultra-dense haploid genetic map for evaluating the highly fragmented genome assembly of Norway spruce (Picea abies)

The paper creates an ultra-dense haploid genetic map for Norway spruce to improve genome assembly and evaluate gene distribution across chromosomes.

Molecular Predicting Drought Tolerance in Maize Inbred Lines by Machine Learning Approaches

The paper uses machine learning to predict drought tolerance in maize inbred lines based on SSR genetic markers data.

Cleaning genotype data from Diversity Outbred mice

The paper describes a process for cleaning SNP genotype data from Diversity Outbred mice, focusing on identifying and handling low-quality samples and markers.

crossword: A data-driven simulation language for the design of genetic-mapping experiments and breeding strategies

The paper introduces crossword, a data-driven simulation language for genetic-mapping experiments and breeding strategies, demonstrating its utility in QTL-seq design and genomic selection.

Construction of a genetic linkage map in Pyropia yezoensis (Bangiales, Rhodophyta) and QTL analysis of several economic traits of blades

The paper constructs a genetic linkage map and identifies QTLs for economic traits in Pyropia yezoensis using a DH population and SRAP markers.

Origins and geographic diversification of African rice (Oryza glaberrima)

This study reanalyzes whole genome sequences of African rice to reassess its domestication origin and geographic diversification, suggesting a non-centric or polycentric origin.

Dynamic plant height QTL revealed in maize through remote sensing phenotyping using a high-throughput unmanned aerial vehicle (UAV)

This study uses UAV-based phenotyping to analyze plant height in maize across four growth stages, identifying 238 QTLs associated with plant height traits.

Genetic Dissection of Haploid Male Fertility in Maize (Zea mays L.)

This study identifies quantitative trait loci (QTL) associated with spontaneous restoration of haploid male fertility in maize, which can aid in haploid breeding.

Development and validation of microsatellite markers from de novo transcriptome assembly of eggplant (Solanum melongena L.) and its putative progenitor S. incanum L. cultivars

The paper develops and validates SSR markers from de novo transcriptome assembly of eggplant and its progenitor to enable QTL mapping and stress response gene identification.

The power of a multivariate approach to genome-wide association studies: an example with Drosophila melanogaster wing shape

This paper demonstrates that multivariate genome-wide association analysis of multiple traits improves power and informativeness compared to univariate analyses, using Drosophila wing shape as an example.

Recombination within the Cepaea nemoralis supergene is confounded by incomplete penetrance and epistasis

The paper investigates recombination within a supergene in Cepaea nemoralis and finds no evidence of recombination, attributing apparent recombinant phenotypes to incomplete penetrance and epistasis.

polyRAD: Genotype calling with uncertainty from sequencing data in polyploids and diploids

polyRAD improves genotype calling in polyploids and diploids by using Bayesian methods with flexible priors, reducing errors from low read depth and improving genotype accuracy.

The genetic basis of cis-regulatory divergence between the subspecies of cultivated rice (Oryza sativa)

This study characterizes transcriptome and cis-regulatory divergence between rice subspecies Indica and Japonica using transcriptome data from 91 accessions, identifying subspecies-specific eQTL and patterns of genetic diversity.

Dissection and validation of minor quantitative trait loci (QTLs) conferring grain size and weight in rice

This study identifies and validates minor QTLs affecting grain size and weight in rice using F2 and BC1F2 populations, revealing their roles in key agronomic traits.

R/qtl2: software for mapping quantitative trait loci with high dimensional data and multi-parent populations

R/qtl2 is a software tool for QTL mapping in multi-parent populations and high-dimensional data, offering features like linear mixed models and SNP imputation.

A Statistical Procedure for Genome-wide Detection of QTL Hotspots Using Public Databases with Application to Rice

The paper introduces a statistical method to detect QTL hotspots using public databases, showing it controls error rates and identifies hotspots in rice data.

BLINK: A Package for Next Level of Genome Wide Association Studies with Both Individuals and Markers in Millions

BLINK improves statistical power and reduces computing time for GWAS by replacing FarmCPU's bin method with Bayesian information criteria and linkage disequilibrium information.

A Draft Genome and High-Density Genetic Mapof European Hazelnut (Corylus avellana L.)

The paper presents the first sequenced genome of European hazelnut and high-density genetic maps to aid breeding efforts.

Bayesian decision theoretic design of two-founder experimental crosses given diallel data

The paper develops a Bayesian decision theoretic framework for designing two-founder experimental crosses using diallel data to optimize QTL mapping experiments.

A Very Oil Yellow1 modifier of the Oil Yellow1-N1989 allele uncovers a cryptic phenotypic impact of cis-regulatory variation in maize

The paper identifies a modifier locus in maize that reveals cis-regulatory variation affecting chlorophyll biosynthesis through a mutant reporter allele.

Heterozygote calling in significantly inbred populations

The paper introduces a method for accurately identifying heterozygotes in large inbred populations using mixture models.

Genome wide association analysis in a mouse advanced intercross line

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

Integrating co-expression networks with GWAS to prioritize causal genes in maize

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: An R package for Mean-Variance QTL Mapping

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

Mean-Variance QTL Mapping Identifies Novel QTL for Circadian Activity and Exploratory Behavior in Mice

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.

QTL Mapping on a Background of Variance Heterogeneity

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.

Combining high-throughput micro-CT-RGB phenotyping and genome-wide association study to dissect the genetic architecture of tiller growth in rice

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

Optimizing the identification of causal variants across varying genetic architectures in crops

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

A multi-parent recombinant inbred line population of Caenorhabditis elegans enhances mapping resolution and identification of novel QTLs for complex life-history traits

This study develops a multi-parent recombinant inbred line population of C. elegans to improve QTL mapping resolution and identify novel QTLs for life-history traits.

An EST-SSR based genetic linkage map and identification of QTLs for anthracnose disease resistance in water yam (Dioscorea alata L.)

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.