Genetic Mapping and Diversity in Plants and Animals

Exploring the genetic factors of nitrogen use efficiency in potato

This study identifies 21 QTNs and 750 candidate genes associated with nitrogen use efficiency in potato through GWAS, contributing to understanding its genetic basis.

Natural variation in chalcone isomerase defines a major locus controlling radial stem growth variation among Populus nigra populations

Variant filters using segregation information improve mapping of nectar-production genes in sunflower (Helianthus annuus L.)

This paper improves variant calling in sunflower by using segregation-based filtering, leading to better QTL mapping and identification of nectar-related genes.

Quantitative genetics of photosynthetic trait variation in maize

This study identifies genetic variants associated with photosynthetic traits in maize by controlling environmental and spatial confounders, revealing high-confidence GWAS signals and validating candidate genes through insertion alleles.

Development and application of a genotyping by target sequencing SNP array panel in Salix suchowensis

The paper develops a SNP array panel for Salix suchowensis to improve genotyping and identifies SNPs associated with growth traits.

QTL identification and characterization of the recombination landscape of the mountain pine beetle (Dendroctonus ponderosae)

The paper identifies a QTL for generation time in mountain pine beetles and characterizes recombination patterns, including sex-biased inheritance of X chromosomes.

Powerful one-dimensional scan to detect heterotic QTL

This study introduces hQTL-ODS, a one-dimensional scan method for detecting heterotic QTLs, showing improved computational efficiency and reduced false positives in wheat hybrids.

Transcripts and genomic intervals associated with variation in metabolite abundance in maize leaves under field conditions

The paper identifies genomic intervals and transcripts associated with metabolite abundance variation in maize under field conditions using GWAS and transcriptome-wide association studies.

Discovery and characterisation of gene by environment and epistatic genetic effects in a vertebrate model

The paper uses medaka fish to study genetic and environmental interactions in heart rate, identifying QTLs and validating genes, while showing limitations of GWAS in capturing complex genetic effects.

Investigating the genetic architecture of biotic stress response in stone fruit tree orchards under natural infections with a multi-environment GWAS approach

Multi-environment GWAS of 206 peach and 150 apricot accessions under natural infection finds mostly environment-specific or interactive loci, 60 high confidence QTLs and 87 candidate genes.

Selective breeding for determinacy and photoperiod sensitivity in common bean (Phaseolus vulgaris L.)

This study identifies QTLs for determinacy and photoperiod sensitivity in common bean, linking them to population structure and providing insights for breeding and genetic research.

The genetic architecture of cell-type-specific cis-regulation in maize

The paper identifies cell-type-specific cis-regulatory variants in maize using single-cell genomics and population genetics, revealing their role in local adaptation and flowering.

A spectral framework to map QTLs affecting joint differential networks of gene co-expression

The paper introduces snQTL, a network-based method to map QTLs affecting gene co-expression networks, demonstrating its effectiveness in stickleback data by uncovering missed candidate genes.

Genome-wide association study in European beech (Fagus sylvatica L.) for drought stress traits

The paper conducts a GWAS in European beech to identify genetic markers associated with drought stress traits, finding significant SNPs linked to stomatal density and water use efficiency.

New QTLs involved in the control of stigma position in tomato

The paper identifies new QTLs associated with stigma position in tomato and validates previously reported QTLs, supporting the role of multiple genes in controlling herkogamy.

Extremely Early Flowering and Large Grain Isogenic Japonica Rice Koshihikari Integrated with Gene e1 and GW2

This paper describes the development of an isogenic rice line with early flowering and large grain by integrating the e1 and GW2 alleles into Koshihikari.

Omics-driven Identification of Candidate Genes and SNP markers in a Major QTL Controlling Early Heading in Rice

This study identifies a major QTL for early heading in rice and links it to candidate genes and SNP markers that can improve climate resilience and yield.

Population and adaptation history of 739 Thlaspi arvense natural accessions

The paper analyzes 739 Thlaspi arvense accessions to uncover genetic variation and adaptation mechanisms, identifying genomic regions linked to agronomic traits and climate resilience.

Dissecting the molecular basis of variability for flowering time in Camelina sativa

This study identifies molecular mechanisms underlying flowering time variation in Camelina sativa using transcriptomic and genetic analyses.

Genome-Wide Associations within Diverse Wild Apple Germplasm for Postharvest Blue Mold Resistance to Penicillium expansum

The paper identifies SNPs associated with postharvest blue mold resistance in wild apple germplasm using genomic sequencing and association mapping.

A Theory of Heterosis

The paper develops a theoretical framework to analyze heterosis by estimating QTL effects and applies it to maize and rice datasets, finding dominance primarily drives heterosis in both.

Local selection shaped the diversity of European maize landraces

This study examines how maize introduction to Europe shaped genetic diversity and differentiation, finding landraces maintain high diversity despite selection pressures and modern breeding accumulating genetic load.

The influence of heavy metal stress on the evolutionary transition of teosinte to maize

This study investigates how heavy metal stress influenced the evolutionary transition from teosinte to maize by analyzing gene expression and genetic diversity in response to copper and cadmium exposure.

Recombinant inbred line panels inform the genetic architecture and interactions of adaptive traits in Drosophila melanogaster

This study uses Drosophila melanogaster recombinant inbred lines to analyze the genetic architecture and interactions of adaptive traits, finding detectable alleles and gene-by-environment interactions but limited epistasis.

EasyOmics-A graphical interface for population-scale omics data association, integration and visualization

EasyOmics provides a user-friendly R Shiny interface for population-scale omics data association, integration, and visualization without requiring advanced programming skills.

Epistasis and cryptic QTL identified using modified bulk segregant analysis of copper resistance in budding yeast

The paper identifies epistatic QTLs in budding yeast using a modified bulk segregant analysis approach that fixes one chromosome to detect genetic interactions.

System genomics of salinity stress response in rice

The paper examines gene expression variation in rice under salinity stress, finding trans-eQTLs dominate and cis-trans reinforcement is more common than compensation.

A pan-gene catalogue of Asian cultivated rice

The paper develops a pan-gene catalogue for Asian cultivated rice by creating a reference panel of 16 cultivars and identifying core and cultivar-specific genes.

Structural variants contribute to phenotypic variation in maize

The paper identifies structural variants in maize using whole genome alignment and short-read sequencing, linking them to life history traits and genotype-by-environment interactions.

Association analyses reveal both anthropic and environmental selective events during eggplant domestication

This study identifies anthropic and environmental selective events during eggplant domestication using genome-wide association and genotype-environment association analyses.