Genetic Mapping and Diversity in Plants and Animals

Genetic analysis of bone morphometry and ivory vertebrae in threespine stickleback

This study identifies genetic loci influencing bone microstructure and a disease-like phenotype in threespine stickleback fish.

Genetic Dissection of Grain Yield and Correlated Proxy Traits Under Suboptimal Conditions

The paper develops a maize MAGIC population to dissect grain yield and proxy traits under stress, identifying QTL and improving genomic prediction models.

Population genomics of the rice landrace Acuce reveals exceptional dynamics of immune receptors

The paper analyzes genomic diversity in the rice landrace Acuce to understand its resistance to pathogens and agricultural traits, finding high diversity and selection pressures in immunity genes.

Genome Sequencing of Rice Landraces from the Yuanyang Terraces Uncovers Ancient and Diverse Lineages of Indica Rice

This study analyzes genetic diversity in rice landraces from the Yuanyang Terraces, finding high genetic variation and differences in immune gene evolution between traditional and modern rice varieties.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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 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.