Genetic Mapping and Diversity in Plants and Animals

From Phenomics to Genomics: Macro-GWAS of Almond Morphology and Quality

This study integrates high-throughput phenomics and genomics to identify marker-trait associations and candidate genes for almond morphology and quality traits.

Distinct Effects of Domestication and Improvementon Genetic Load and Nitrogen-Response Variation inSorghum

This study examines how domestication and improvement in sorghum have affected genetic load and nitrogen-response variation by integrating genomic and phenotypic data.

Identification of heterotic group-specific haplotypes and impact of residual inbreeding on grain yield of maize elite hybrids

This study identifies heterotic group-specific haplotypes and shows that residual inbreeding from commercial hybrids negatively impacts maize grain yield.

From Kernel to Kitchen: Asparagine Synthetase 3 is Involved in Free Asparagine Accumulation in Maize Kernels

This study identifies a deletion in the ASN3 gene associated with reduced free asparagine in maize kernels, providing a target for breeding and genome-editing to lower acrylamide formation.

Sex chromosome-aware GWAS reveals XY-linked agronomic architecture and breeding targets in cannabis

This study performs a sex chromosome-aware GWAS on cannabis, identifying 16 genome-wide significant markers on ChrX and ChrY that influence agronomic traits.

Development and application of SNP markers to facilitate DUS testing in tomato

The paper develops SNP markers for DUS testing in tomato, identifies marker-trait associations, and evaluates their discriminatory power for variety distinction.

Cis-regulation of gene expression between sexes and life stages in Rumex hastatulus

This study investigates cis-regulation of gene expression between sexes and life stages in Rumex hastatulus using eQTL mapping, finding stronger shared genetic architecture between sexes than between life stages.

Genetic analysis of maize seedling root traits under chilling highlights their importance for early field development

This study identifies QTL for maize seedling root traits under chilling conditions that influence early plant development in the field.

Leveraging genome-wide association studies and genomic prediction for distinctness, uniformity, and stability (DUS) testing in maize

The paper uses GWAS and machine learning to develop molecular markers and a genomic prediction framework for improving maize DUS testing using historical data.

Exploring the genetic architecture underlying dietary fiber content in Colombian Andean blueberry (Vaccinium meridionale Swartz)

The paper uses GWAS to identify genetic loci associated with dietary fiber traits in Colombian Andean blueberry, revealing polygenic control and candidate genes involved in fiber biosynthesis and remodeling.

Orchestrating multi-state QTL analysis with Bioconductor

The paper introduces two Bioconductor packages for multi-state QTL analysis, providing tools for data storage, analysis, and simulation.

Dissecting Agronomically Favorable Genotypes in Temperate Japonica Rice via Haplotype Analysis of a Japan-MAGIC Population

The paper identifies favorable genotype combinations in temperate japonica rice using haplotype analysis of a multi-parent population, showing how specific variants improve yield and lodging tolerance.

Predicting complex phenotypes using multi-omics data in maize

The paper demonstrates that integrating transcriptomic and phenomic data with genotypes improves trait prediction in maize across environments.

The Paraphyletic Origins of Genetic Resistance to Cabbage Stem Flea Beetle in Brassica oleracea

This study identifies a major QTL for resistance to cabbage stem flea beetle in Brassica oleracea using GWAS, showing resistance evolved after domestication and feralization, not from var. botrytis.

Allele-specific expression reveals complex cis- and trans-regulatory divergence underlying fruit phenotypic differences between cultivated and wild tomato species

The Drosophila melanogaster Genetic Reference Panel, Version 3 (DGRP3)

The paper introduces DGRP3, an expanded Drosophila genetic reference panel with 1,233 inbred lines, identifying genetic variants and performing GWAS for traits like inbreeding depression and sensory bristles.

Rice Annotation Project Database (RAP-DB): literature-curated gene annotation and integrated omics resources for rice functional genomics and molecular breeding

RAP-DB curates gene annotations and integrates omics data for rice, supporting functional genomics and molecular breeding through expert curation and community resources.

A panel of near-isogenic lines derived from locally adapted populations of a wild plant: A powerful tool for dissecting additive and non-additive effects on ecologically important traits

The paper introduces a panel of near-isogenic lines from Arabidopsis thaliana to study additive and non-additive genetic effects on ecologically important traits, identifying FLC's role and novel epistatic interactions in flowering time.

Optimizing Strain Selection for Association Studies Under Hard Cost Constraints

The paper evaluates strain selection methods under cost constraints for association studies, finding that cost-based approaches often outperform diversity-focused ones.

Application of Computer Vision Tools to Maize Genomic Data for Trait Prediction and Gene Discovery

This study applies computer vision tools to maize genomic data to predict genotype-phenotype relationships and identify gene regions associated with traits.

A comparative approach for selecting orthologous candidate genes in genome-wide associationstudies across multiple species

The paper develops a method to identify conserved causative genes across species using multi-species GWAS data, finding that conserved genes are more frequently associated with trait variation than expected by chance.

Predicting flowering time using integrated morphophysiological and genomic data with machine learning models

This study uses machine learning to classify flowering time in Cannabis landraces by integrating genomic and morphophysiological data, achieving 96.6% accuracy.

Identification of Freezing Tolerance QTLs in Tripsacum dactyloides Using Open-Pollinated Bulk Segregant Analysis

This study identifies 9 QTLs associated with freezing tolerance in Tripsacum dactyloides using bulk segregant analysis and regression-based allele frequency imputation.

Dissecting the regulatory and genomic drivers of the dichogamy determining G-locus in pecan

The paper identifies the genetic drivers of the G-locus in pecan trees using pangenome-integrated quantitative genomics, revealing a Mendelian super-gene responsible for dichogamy.

Genetic architecture of phenological, morphological, and phytochemical traits in Cannabis landraces

This study identifies 91 genomic regions associated with 40 traits in Cannabis landraces using GWAS, revealing pleiotropic loci and highlighting their potential for genetic improvement.

High-resolution mapping and epistatic QTL of tomato fruit metabolism

This study maps metabolic QTL in tomato using backcross inbred lines, identifies a novel locus affecting sucrose accumulation, and reveals epistatic interactions influencing fruit metabolism.

Highly polygenic control of photosynthetic responses to nighttime temperature in Arabidopsis studied by genomic prediction

This study uses GWAS and genomic prediction to identify SNPs influencing photosynthetic efficiency in Arabidopsis under different nighttime temperatures, showing polygenic control and improved prediction accuracy.

Genetic mapping of Dutch elm disease resistance

The paper constructs a linkage map of the elm genome and identifies genomic regions associated with Dutch elm disease resistance from resistant species.

Genome Assembly of the Iconic Samba Mahsuri Delineates Locus-specific Population Structure within Indica Rice

The paper presents a chromosome-scale genome assembly of Samba Mahsuri rice and shows how structural polymorphisms shape locus-specific population structure within indica rice.

EcoCore; An ecologically diverse panel of Arabidopsis thaliana accessions for studying plant-environment interactions

The paper introduces the EcoCore panel, a curated set of Arabidopsis thaliana accessions, and shows it reveals novel genetic associations with hypocotyl length compared to a larger panel.