Genetic Mapping and Diversity in Plants and Animals

Joint QTL mapping reveals patterns of pleiotropy across structured environments in budding yeast

The paper uses joint QTL mapping to analyze pleiotropy patterns across structured environments in budding yeast, revealing genetic interactions influenced by environmental relationships.

Interpreting Short Tandem Repeat Variations with Genomic Foundation Models in Olive

The paper identifies STR variation in olive and evaluates how genomic language models respond to natural STR length changes, finding consistent embedding perturbations and prioritizing candidate loci linked to oil composition.

LDscnR: LD-aware complexity reduction for genome scans

LDscnR reduces genome scan tests by grouping correlated markers using LD decay, improving precision while maintaining recall, and showing structure can explain outlier regions.

Haplotype-resolved genetic mapping using selfed progeny enables simultaneous genome assembly validation and trait dissection in a heterozygous plant

This paper introduces HRGM, a method that uses selfed progeny and haplotype-resolved assemblies to create genetic maps and validate genome assemblies in plants, identifying loci associated with root development.

Genotype imputation improves GWAS resolution and facilitates candidate gene identification in pearl millet

The paper improves GWAS resolution in pearl millet by imputing missing genotypes using a whole-genome sequencing reference panel, leading to more localized association signals and candidate gene identification.

Haplotype-rich cis-regulation underlies transcriptomic diversity across the breeding history of maize (Zea mays)

This study identifies cis-regulatory variants in maize using RNA-seq and genome-wide data, showing that haplotype-rich variants explain most expression diversity and that single-variant summaries are incomplete.

Uncovering genetic determinants of rice root anatomy using genome wide analysis

This study identifies genetic determinants of rice root anatomy through genome-wide association analysis of 185 Vietnamese rice landraces, uncovering 24 SNPs linked to anatomical traits and drought tolerance.

Microscale bulk segregant analysis

This paper introduces a 96-well liquid format for high-throughput QTL mapping in yeast, enabling efficient analysis of multiple crosses and environmental conditions.

ZmPMI3 phosphomannose isomerase kinetics is associated with natural variation of watersoluble carbohydrate content in mature maize stem

The paper associates natural variation in ZmPMI3 phosphomannose isomerase kinetics with differences in water-soluble carbohydrate content in mature maize stems.

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.

Genomic SEM reveals shared genetic architecture and expands locus discovery for locomotor activity in heterogeneous stock rats

The paper uses Genomic SEM to identify loci underlying locomotor activity in rats, finding 31 loci compared to fewer from other methods.

QTL analysis of essential oil, seed shattering, thousand-grain weight and stalk attachment rate in Carum carvi

This study identifies QTLs for essential oil, seed shattering, thousand-grain weight, and stalk attachment rate in Carum carvi using F2 populations and develops diagnostic markers for fine-mapping.

Pangenome and transcriptome analyses reveal extensive diversity and breeding signatures in the oat GDSL-esterase/lipase gene family

The paper analyzes the genomic and transcriptomic diversity of the GDSL-esterase/lipase gene family in oat, identifying candidate genes and regions associated with agronomic traits and breeding signatures.

GWAS of flag leaf primary metabolites uncovers metabolic QTL hubs linked to grain yield stability under drought in field-grown indica rice

This study identifies metabolic QTL hubs in indica rice linked to grain yield stability under drought by analyzing metabolomics and GWAS data from field-grown plants.

Deciphering the genetic basis of phytoplankton traits through genome-wide association studies

This study uses GWAS to identify genetic loci associated with pigment and lipid metabolism in the microalga Tisochrysis lutea, revealing previously unknown genomic regions linked to these traits.

Parental Genome Assemblies of Suyunuo1 Reveal Structural Variation Underlying Edible Waxy Maize Evolution, Superior Hybrid Performance and Yield - Flavor Balance

The paper assembles high-quality genomes of two waxy maize inbreds, identifies structural variations contributing to yield and flavor traits, and highlights their role in hybrid performance.

BSA101: Unlocking Historical Mutant Collections with BSA-Seq

This paper develops a BSA-Seq framework to map mutations in genetically heterogeneous populations, successfully identifying known and novel candidate regions in maize mutants.

Pangenomics and machine learning reveal genetic variation to optimize carotenoids in sorghum grain

This study uses pangenomics and machine learning to identify genetic markers associated with carotenoid accumulation in sorghum, revealing structural variation and multi-locus genetic architecture.

A telomere-to-telomere genome of Mojiang purple rice resolves a rare three-copy structural allele upstream of Kala4/OsB2

The paper reports a telomere-to-telomere genome of Mojiang purple rice, identifying a rare three-copy structural allele upstream of Kala4/OsB2 and its association with pigmentation traits.

Additive genes contribute to yield heterosis in rice

This study identifies additive genes as key contributors to yield heterosis in rice by analyzing their effects in homozygous and heterozygous backgrounds.

Multi-omic integration using interpretable machine learning reveals genetic mechanisms of trait variation and phenotypic plasticity in switchgrass

This study integrates multi-omic data with interpretable machine learning to identify genetic mechanisms underlying trait variation and phenotypic plasticity in switchgrass across environments.

Genetic dissection of a Solanum elaeagnifolium tertiary genepool introgression associated with 4-O-caffeoylquinic acid accumulation in eggplant

This study identifies a 4-O-caffeoylquinic acid (4-CQA) accumulation trait from S. elaeagnifolium introgressions in eggplant through fine mapping and metabolite analysis.

A reusable neural approach to recombination mapping for model and non-model species

The paper introduces fastrho, a neural network for recombination mapping that works across species and scenarios, showing it can produce accurate recombination maps and detect selection effects.

Multiparental RNA-seq driven eQTL screening identifies loci underlying host plant fitness in a generalist herbivore

The paper identifies trans-eQTL hotspots in T. urticae linked to host plant fitness using a multiparental RNA-seq approach.

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.

Reference-guided comparative genomics of seven Indonesian rice cultivars identifies conserved gene space and trait-associated sequence candidates

The paper generates consensus genomes for seven Indonesian rice cultivars, identifies conserved gene space, and prioritizes trait-associated sequence candidates for functional validation.

Natural Variation in Maize Shikimate Dehydrogenase Alters Enzyme Activity and Kernel Homoserine Accumulation.

The paper identifies genetic variants in the shikimate dehydrogenase gene Sad1 that affect enzyme activity and homoserine accumulation in maize kernels through integrated metabolite profiling and genome-scale modeling.

A genomewide association study for bristle number variation in Drosophila melanogaster

The paper performs a GWAS on bristle number variation in Drosophila melanogaster, identifying significant genomic regions and candidate genes associated with abdominal and sternopleural bristle numbers.