Genetic Mapping and Diversity in Plants and Animals

The genomic basis of local adaptation to photoperiod across altitude in a self-fertilizing monkeyflower

The paper identifies genomic regions associated with photoperiod adaptation in Mimulus laciniatus using QTL analysis, finding shared and unique loci related to gibberellin pathways.

Cosmopolitan inversions have a major impact on trait variation and the power of different GWAS approaches to identify associations

This study investigates how genomic inversions affect trait variation and the effectiveness of GWAS methods in detecting associations within inverted regions in Drosophila melanogaster.

Genomic and pan-genomic insight into longan domestication and improvement

This study presents a T2T genome and graph-based pan-genome of longan, identifying structural variants and QTLs associated with maturity period and providing resources for genetic improvement.

3D-Manhattan: An interactive visualization tool for multiple GWAS results

3D-Manhattan visualizes multiple GWAS results in 3D to compare genetic associations across traits, time points, or conditions.

Diversity and genetic structure within a Mexican maize race reveal consistent biocultural processes across geographic scales.

The paper examines genetic diversity and structure within the Olotillo maize race in Mexico, finding that genetic clusters align with geographic origin rather than race identity, and highlights inbreeding and directional selection across scales.

KineticGP: a computational framework for genomic prediction of leaf photosynthesis traits

KineticGP improves prediction of leaf photosynthesis traits in maize by integrating genomic data with kinetic models of C4 photosynthesis.

Haplotype Bias Detection Using Pedigree-Based Transmission Simulation: Traces of Selection That Occurred in Apple Breeding

The paper develops a method to detect haplotype bias using pedigree-based gene drop simulations in apple cultivars, identifying SNPs associated with fruit traits and potential selection signals.

QTLIT: A user-friendly Shiny app for Quantitative Trait Loci (QTL) analysis

QTLIT is a Shiny app that simplifies QTL analysis by integrating SNP identification and visualization tools for plant breeders using DNA sequence data.

Novel major loci shape habitat-associated flowering time variation in Yellowstone monkeyflowers

The paper identifies two novel QTLs associated with extreme flowering time variation in Yellowstone monkeyflowers, linking them to environmental factors like soil temperature.

Identification of QTLs for Internode Length and Diameter Associated with Lodging Resistance in Rice

This study identifies QTLs for internode length and diameter linked to lodging resistance in rice using a recombinant inbred line population and RNA-Seq analysis.

Contemporary hybridization among Arabis floodplain species creates opportunities for adaptation

The paper investigates hybridization between Arabis nemorensis and A. sagittata, identifying QTLs associated with phenotypic traits and hybrid fitness, revealing both challenges and opportunities for adaptation.

Chromosome-Scale Assemblies of Flowering Dogwood Cultivars Enable Identification of Candidate Genes Regulating Anthocyanin Biosynthesis in Leaves and Bracts

Structural variations contribute to subspeciation and yield heterosis in rice

This study identifies structural variants (SVs) contributing to subspeciation and heterosis in rice, showing their role in gene expression and agronomic traits.

High-resolution genome and genetic map of tetraploid Allium porrum expose pericentromeric recombination

The paper presents a high-quality reference genome and genetic map of Allium porrum, revealing pericentromeric recombination patterns and genomic relationships within the Allium genus.

Multiparent Recombinant Inbred lines crossed to a tester provide novel insights into sources of cis and trans regulation of gene expression

The paper introduces a method using multi-parent RILs crossed to a tester to dissect cis and trans regulation of gene expression in Drosophila, finding environmental and genetic trans effects in 31% and 19% of loci respectively.

Genome-wide association mapping for grain and forage quality traits in a subtropical oat germplasm collection adapted to highland regions of Eastern Africa

This study maps genome-wide associations for grain and forage quality traits in a subtropical oat germplasm collection, identifying SNPs and candidate genes linked to yield and resilience.

A Nextflow pipeline for molecular quantitative trait loci mapping in small sample size datasets with an application in Atlantic salmon

The paper introduces nf-RASQUAL, a Nextflow pipeline for molQTL mapping in small datasets, applied to Atlantic salmon to identify expression and chromatin accessibility QTLs.

Whole-genome polymorphisms and relatedness of rice varieties circulating in the Mediterranean market

The paper analyzes whole-genome polymorphisms of high-value rice cultivars in the Mediterranean market to assess genetic relationships and identify variants linked to quality and drought traits.

A novel allele of Sh1 underlines the conversion of waxy corn to wx-sweet corn

The paper identifies a novel Sh1 allele in corn that synergizes with waxy1 to alter carbohydrate metabolism, resulting in a waxy-sweet texture in maize kernels.

Hybridization Reveals Cell Type-Specific Regulatory Variation Driving Brain Transcriptomic Divergence

The paper investigates how hybridization affects gene expression in brain tissues by identifying cell type-specific regulatory variation in interspecies fish hybrids.

The dominance of gene expression controlled by trans-eQTL hotspots contributes to phenotypic heterosis in maize

The paper investigates how trans-eQTL hotspots contribute to phenotypic heterosis in maize by regulating non-additive gene expression through transcription factors.

Genomic Prediction and SNP Importance Analysis for Agronomic Traits in Two Coffea canephora Populations

This study identifies population-specific genetic strategies for agronomic traits in Coffea canephora using genomic analysis and machine learning, revealing distinct biological pathways in two populations.

Unravelling the Genetic Architecture of Field Traits through Multi-Omics Platform Data integration

This study integrates multi-omics data to identify genes influencing yield in maize, showing improved resolution and predictive power compared to GWAS.

Pervasive context-dependent effects in the genetic architecture of complex and quantitative traits revealed by a powerful multiparent mapping population in yeast

The paper uses a multiparent yeast population to identify QTL for growth rates across environments, revealing context-dependent genetic architectures and allelic heterogeneity.

The first nested association mapping (NAM) population for outbreeding Italian ryegrass reveals candidate genes for seed shattering and related traits

This paper establishes the first NAM population in Italian ryegrass to identify candidate genes for seed shattering and related traits using ddRAD and whole genome sequencing.

Optimizing core collections for genetic studies: a worldwide flax germplasm case study

The paper develops optimized core collections for genetic studies using a worldwide flax germplasm, balancing genetic diversity and representativeness for improved QTL detection in GWAS.

Composite interval mapping and genomic prediction of nut quality traits in American and American-European interspecific hybrid hazelnuts

This paper uses composite interval mapping and genomic prediction to identify QTL and improve prediction accuracy for nut quality traits in American and interspecific hybrid hazelnuts.

Integrative metabolome-genome analysis reveals the genetic architecture of metabolic diversity in sorghum grain

This study integrates metabolomics and genomics in sorghum to uncover the genetic basis of metabolic diversity, identifying millions of SNP-metabolite associations and gene clusters.

Hybrids reveal accessible chromatin trans genetic associations

The paper identifies trans-regulatory variants associated with chromatin accessibility in maize hybrids, revealing their role in heterosis and gene expression.

Signatures in domesticated beet genomes pointing at genes under selection in a sucrose-storing root crop

The paper identifies selection signatures in domesticated beet genomes, highlighting genes related to root development and sucrose storage.