Genetic Mapping and Diversity in Plants and Animals

CannSelect: A High-Quality Genotyping Platform for Cannabis sativa

CannSelect is a genotyping platform for Cannabis sativa that maps day-neutrality to the Autoflower1 locus with 88.5% capture efficiency.

Multi-Trait Meta-QTL Analysis Reveals Genomic Hotspot Classes for Strategic Maize Improvement

This paper integrates maize QTL data to identify genomic hotspots for multi-trait breeding, revealing functional classes and environmental influences on trait associations.

PlantOmicsGWAS: An end-to-end, reproducible framework for plant genome-wide association and genomic prediction using linear and pan-genome references

PlantOmicsGWAS provides a reproducible framework for plant GWAS and genomic prediction, supporting both linear and pan-genome references to improve analysis of structural variations.

A haplotype-based breeding framework for the precise pyramiding of elite QTL alleles: a lettuce case study

This paper introduces HAPBDB, a haplotype-based breeding framework that translates regional haplotypes into breeding decisions, demonstrating its effectiveness in lettuce for QTL pyramiding.

Historical rice seeds from the 1950s reveal pre-modern genetic structure in indica landraces of mainland Southeast Asia

The paper analyzes historical rice seeds from the 1950s to show pre-modern genetic structure in indica landraces, revealing a distinct northern Vietnamese lineage and a genetic continuum in southern Vietnam, Cambodia, and Thailand.

From Field Photosynthesis to Genetic Architecture: Insights from the First Dedicated Photosynthesis Hackathon

The paper reports findings from a photosynthesis hackathon that identified key insights into genetic architecture using field photosynthesis data across four crop species.

Genetic Diversity and Population Structure of Maize Doubled Haploid Lines from Drought and Low Nitrogen Tolerant Populations

This study analyzes genetic diversity and population structure of 250 maize doubled haploid lines from drought and low nitrogen tolerant populations, revealing moderate diversity and clear clustering.

Genotype imputation and error estimation in connected multiparental populations

This paper introduces MagicImpute, a genotype imputation tool for multiparental populations that improves computational efficiency and error handling, showing accuracy across real datasets with missing parents and sequencing errors.

Development of an open-pollinated genetic mapping framework to facilitate the identification of QTL in apples

The paper develops an open-pollinated genetic mapping framework for apples to identify QTL, showing that MLMM outperforms MLM and demonstrating the feasibility of OP-based mapping for faster QTL discovery.

SABER: A Multiparental Tomato Population Leveraging Wild Relative Diversity for High-Resolution QTL Mapping

The paper introduces SABER, a multiparental tomato population incorporating wild relatives for high-resolution QTL mapping, identifying known and novel QTL for agronomic traits.

Genome-wide dissection of tillering responsiveness to neighbour proximity in sorghum

This study identifies genetic loci controlling tillering responsiveness to neighbour proximity in sorghum using GWAS and a diversity panel.

Flywheel Genomics: Simultaneous trait discovery and genetic gain in plant breeding

This paper introduces Flywheel Genomics, a framework that integrates trait discovery with rapid cycling breeding to improve plant breeding efficiency and genetic gain.

Multi-environment GWAS analysis for photosynthetic light use efficiency in Arabidopsis thaliana

This study performs multi-environment GWAS on photosynthetic light use efficiency in Arabidopsis thaliana, identifying robust and conditional quantitative trait loci.

Cis-regulatory variation and transcription factor binding contribute to allelic genotype-by-environment interactions for gene expression in maize

An industry perspective on whole genome-informed hybrid maize disease resistance characterization to improve breeding decisions

This paper introduces a genome-informed method to improve disease resistance characterization in hybrid maize using whole genome ordered probit regression, validated with field trial data.

AI-enabled simultaneous phenotyping of leaf vein and stomatal traits uncovers independent genetic control in maize

The paper uses AI to phenotype leaf vein and stomatal traits in maize, finding independent genetic control between these traits.

GAMETE maps the genetic architecture of chromatin accessibility in rice pollen at single-nucleus resolution

GAMETE maps chromatin accessibility genetic architecture in rice pollen using single-nucleus ATAC-seq and genotype inference, revealing cell-type-specific caQTLs and chromatin dynamics.

Pedigree-reconciled pan-genomics reveals megabase-scale hitchhiking after a century of canola breeding

The paper traces the inheritance of a genomic haplotype linked to oil quality in canola over a century of breeding, revealing its pre-existing origin and long-term persistence through hitchhiking.

When Does Reaction Norm GWAS Discover Plasticity? The Residual Channel in Environmental Index-Based Genetic Dissection

The paper shows that using climate-derived indices in GWAS to detect phenotypic plasticity is flawed, as the index's correlation with environmental means limits the ability to detect plasticity-specific genetic variation.

Prioritizing Non-coding Variants in Rice GWAS Loci with a Chromatin-Informed DNA Language Model

This paper introduces a method to prioritize non-coding variants in rice GWAS loci using a chromatin-informed DNA language model, demonstrating its utility through case studies.

Shared QTLs underlie loss of a conserved trait in replicate mapping populations of Arabidopsis thaliana

The paper identifies shared QTLs for stamen number, ovule number, and flowering time in Arabidopsis thaliana RILs, showing some QTLs are consistent across crosses while others are unique.

PanvaR: An R package for fine-mapping and visualizing results from genome-wide association studies

PanvaR integrates GWAS and fine-mapping in one tool, providing LD analysis, SNP effect predictions, and candidate gene lists with visualizations.

Assembling and annotating the Tainung 67 rice genome to trace its japonica and indica ancestries

The paper assembles and annotates the Tainung 67 rice genome, tracing its japonica and indica ancestries through gene analysis and repeat composition.

Shaping of developmental gradients through selection on multiple loci in Antirrhinum

The paper shows how natural selection shapes molecular gradients by acting on multiple loci in snapdragons, with cis and trans regulatory variation influencing flower color gradients.

Integrating Genome-Wide Association Analysis, Functional Annotation and Regulatory Genomics for the Prioritization of Candidate Variants Associated with Grain Yield in Upland Rice

This paper identifies genomic variants associated with grain yield in upland rice and develops an integrative framework to prioritize candidate variants by combining GWAS, functional annotation, and regulatory genomics.

SNPstar: A Web Server Linking Allelic Variation to Protein Structure and Function in Arabidopsis thaliana

SNPstar links SNPs in Arabidopsis thaliana to protein structure and function using AlphaFold3 predictions, enabling variant characterization and geographic mapping.

Integrated pangenome and population genomics reveal selection on standing genetic variation driving fiber flax-linseed divergence

This study identifies selection on standing genetic variation driving divergence between fiber flax and linseed using pangenome and population genomic analyses.

Multi-tissue metabolic GWAS and drought-responsive multi-omics reveal the genetic basis of the quinoa metabolome

This study integrates multi-omics data from quinoa to identify genetic factors controlling its metabolome and stress response, revealing key genes involved in metabolite biosynthesis.

A newly arisen indel governs a leaf shape polymorphism in the Ivy Leaf Morning Glory (Ipomoea hederacea)

The paper identifies a 117 kb indel associated with leaf shape polymorphism in Ipomoea hederacea and shows it is a novel genetic mechanism distinct from related species.

Diversity Assessment with SNP, SSR, AFLP, and RAPD Markers in Plants: A Systematic Review and Meta-Analysis

This study compares SNP, SSR, AFLP, and RAPD markers for plant genetic diversity metrics using meta-analysis, finding SSRs outperform SNPs and RAPDs in per-locus diversity.