Genetic Mapping and Diversity in Plants and Animals

The paper develops statistical methods to test for pleiotropy or separate QTL in multiparental populations and applies them to find two distinct loci in a genomic region of mice.

This study identifies novel allelic variations in Purpleputtu rice through whole genome sequencing and comparative analysis, revealing genetic diversity linked to coloration and domestication traits.

Rice Galaxy provides an open resource for plant science, enabling researchers to perform advanced genomic analyses using shared datasets and tools.

The paper investigates the genetic architecture of shoot growth variation in Arabidopsis thaliana using QTL mapping and high-throughput phenotyping, revealing complex and dynamic genetic structures.

The paper introduces PCAMP, a method for identifying anthocyanin biosynthesis genes in rice pericarp by analyzing F2 populations and comparing SNP-index between pools.

This paper uses Bayesian confirmatory factor analysis and Bayesian networks to analyze rice phenotypes and identify genetic correlations among traits.

This paper develops GBS-based cytoplasmic markers to study population structural variation in perennial ryegrass, finding that chloroplast and mitochondrial variations differ in their patterns and contributions to population differentiation.

The paper develops a statistical method to detect genomic structural variation using genetic mapping data from Mimulus guttatus crosses, correcting reference genome errors and identifying chromosomal inversions.

The paper constructs a high-density genetic map and develops a molecular sex-typing assay for Mongolian gerbils using GBS data and linkage analysis.

The paper uses metabolome-scale GWAS to identify genetic loci controlling maize specialized metabolites, revealing chemical diversity and gene-metabolite associations.

The paper evaluates QTL mapping power in the Collaborative Cross using real genomes and simulations, providing guidelines for experimental design.

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

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

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

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.

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

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

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

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

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.

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.

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

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.

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

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

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

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