Genetic Mapping and Diversity in Plants and Animals

Single-Plant Genome-Wide Association Study Identifies Loci Controlling Multiple Vegetative Architecture Traits in Cultivated Northern Wild Rice (Zizania palustris L.)

This study uses single-plant GWAS to identify genetic loci controlling vegetative traits in Northern Wild Rice, finding polygenic control and shared loci across multiple traits.

Non-uniform chromosomal SNP density biases sites of meiotic crossovers in Drosophila melanogaster

The paper identifies how uneven SNP distribution on the X-chromosome of Drosophila affects meiotic crossover sites, reducing mapping resolution for genetic traits.

Conditional genome-wide associations reveal novel genes

This paper introduces two new methods for gene discovery using conditional genome-wide associations and validates three novel genes affecting flowering time in Arabidopsis.

A Bayesian multidimensional approach to decipher the genetic basis of dynamic phenotypes in multiple species

This paper introduces a Bayesian Varying Coefficient Model to analyze time-related phenotypic plasticity across species, revealing dynamic QTLs and improving phenotypic variance explanation.

Integration of QTL Mapping, Transcriptomics, and Genome Resequencing Identifies Yield-Associated Genes for Salt Stress in Rice

Time series analysis in a maize landrace reveals rapid fixation of beneficial alleles

The paper analyzes a maize landrace selection experiment to identify loci under selection and track genetic changes over time.

A GWAS-machine learning framework reveals protein-synthesis pathway signals for yield in Theobroma cacao after population-structure correction

This study uses a GWAS and machine learning framework to identify genetic signals related to protein-synthesis pathways that influence cacao yield after correcting for population structure.

Deciphering the Genetic Architecture of Sorghum Grain Oil Content via Lipidome-Integrated Genome-Wide Association Analysis

This study integrates lipidomics with GWAS in sorghum to identify genetic loci associated with grain oil content and composition, revealing new insights into lipid metabolism and its genetic regulation.

Genetic architecture and functional consequences of lateral root length in maize (Zea mays L.)

The paper identifies QTL for lateral root length in maize across developmental stages and examines their correlation with biomass under different nutrient conditions.

Quantitative Trait Loci Controlling Oil Sorption in Kenaf: Mapping and Implications

This paper identifies QTL associated with oil sorption capacity in kenaf using linkage and QTL analyses to aid in marker-assisted selection for oil spill cleanup.

Natural variation in rice mitogen-activated protein kinase 4 contributes to increased photosynthetic rate under field conditions

This study identifies OsMPK4 as a genetic factor enhancing photosynthetic rate in rice under field conditions through increased stomatal conductance.

A major chromosome 4 region modulates early vigor under chilling through brassinosteroid signaling associated genes in maize

A Global Genomic Resource for Outcrossing Arabidopsis lyrata and Arabidopsis arenosa

The paper presents a genomic resource with 1018 A. lyrata and 736 A. arenosa genomes, enabling studies of adaptation and genetic diversity through a searchable database and GWAS analysis of latitudinal clines.

Shotgun sequencing data and SSR mining data of aibika (Abelmoschus manihot, Malvaceae)

The paper develops 21 SSR markers for A. manihot using NGS data to aid in genetic diversity analysis and breeding programs.

Sex-specific Genetic Regulatory Effects in Chickens

The paper identifies sex-specific genetic regulatory effects in chickens using whole-genome sequencing and transcriptomes, revealing sex-dependent gene regulation and structural variants.

Genetic correlation-guided mega-analysis of DO mice provides mechanistic insight and candidate genes for age-related pathologies

The paper uses genetic correlation analysis in DO mice to identify QTL and candidate genes linked to age-related pathologies.

Haplotype-resolved genome assembly advances genetic understanding of trait diversity in Phalaenopsis orchids

This study presents a haplotype-resolved genome for Phalaenopsis orchids, revealing genetic factors underlying trait diversity such as lip morphology and color patterns.

Spatial analysis of cell patterning to aid genetic and phenotypic understanding of grass stomatal density: a case study in maize

This study uses a new spatial analysis approach to decompose stomatal density into component traits, revealing specific QTL for lateral and longitudinal patterning in maize.

Development and evaluation of a cost-effective, mid-density SNP array as a sorghum community genotyping resource

The paper develops and validates a mid-density SNP array for sorghum using NGS, showing it performs as well as high-density GBS for trait prediction and breeding applications.

Life, the universe, and everything for $42: ultra-low pass sequencing of maize for genotyping, mapping, and pedigree analysis

The paper presents an economical ultra-low pass sequencing method for genotyping, mapping, and pedigree analysis in maize using skim sequencing.

Simplifying Systems Genetics with QTLretrievR: An R Package for Molecular QTL Identification

QTLretrievR simplifies molecular QTL identification in genetically diverse populations by integrating existing tools with parallelization, reducing computational time and improving accessibility.

Development of a Flex-Seq SNP panel for raspberry (Rubus idaeus L.) and validation through linkage map construction and identification of QTL for several traits of agronomic importance to raspberry breeding

The paper develops a Flex-Seq SNP panel for red raspberry and validates it through linkage maps and QTL identification for agronomic traits.

T2T Genome and Population Resequencing Reveal OfCCD4 Alleles Orchestrate Petal Color and Scent in Osmanthus fragrans

The paper identifies OfCCD4 alleles that regulate petal color and scent in Osmanthus fragrans using a T2T genome and population resequencing, revealing a color-scent trade-off and developing a molecular marker for breeding.

From Diversity to Discovery: Genome-Wide Insights into the Genetic Landscape of Tropical Maize DH Lines

The paper analyzes genetic diversity and population structure in 2,555 tropical maize DH lines using SNP markers, revealing two major genetic clusters and high within-group diversity for genomic studies.

A cryptic hybrid zone reveals the genomic basis of flower colour variation in a plant with a large and complex genome

The paper identifies candidate loci for flower color variation in Pedicularis comosa using a multi-omic approach, revealing the involvement of anthocyanin pathway genes.

Additive and partially dominant effects from genomic variation contribute to rice heterosis

This study identifies heterosis-associated genes and metabolites in rice, showing additive and partially dominant genetic effects contribute to 17 agronomic traits and yield heterosis across species.

Prime-InDel version 1: A web tool providing InDel markers for targeted regions narrowing

Prime-InDel provides PCR-based InDel markers for fine-mapping in rice, narrowing QTL intervals effectively.

Leveraging whole-genome re-sequencing for diversity, population structure, and a public mid-density genotyping enrichment panel in crimson clover (Trifolium incarnatum L.) for breeding purposes

This paper uses whole-genome resequencing to analyze diversity and structure in crimson clover and develops a mid-density SNP capture panel for breeding applications.

The MexMAGIC population reveals the genetic architecture of clinal trait variation in Mexican native maize

The paper uses a MAGIC population to study genetic architecture of clinal traits in Mexican maize, finding one major QTL for tassel branching and multiple QTL for flowering time with complex environmental associations.

The genetic architecture of leaf vein density traits and its importance for photosynthesis in maize

The paper examines the genetic basis of leaf vein density in maize and links it to photosynthesis, finding that higher vein density correlates with increased photosynthetic rates in small intermediate veins.