Genetic Mapping and Diversity in Plants and Animals

Phasing and imputation of single nucleotide polymorphism data of missing parents of bi-parental plant populations

The paper introduces a method to phase and impute genotypes of missing parents in bi-parental plant populations, achieving high accuracy for both parents and their descendants.

Genome of Solanum pimpinellifolium provides insights into structural variants during tomato breeding

The paper presents a high-quality genome of Solanum pimpinellifolium and identifies structural variants that underlie important tomato breeding traits.

Dissecting the eQTL micro-architecture in Caenorhabditis elegans

This study maps eQTL in C. elegans RILs across environments, showing higher reproducibility of local eQTL and environmental effects on eQTL micro-architecture.

Genome sequence of Hydrangea macrophylla and its application in analysis of the double flower phenotype

This study sequenced the Hydrangea macrophylla genome to identify DNA markers and causative genes for the double flower phenotype.

A systems genetics approach reveals environment-dependent associations between SNPs, protein co-expression and drought-related traits in maize

This study identifies environment-dependent SNP-protein co-expression and trait associations in maize under drought conditions, revealing pleiotropic loci and candidate genes for drought tolerance.

Accumulation of mutations in genes associated with sexual reproduction contributed to the domestication of a vegetatively propagated staple crop, enset.

The paper analyzes genetic differences between wild and cultivated enset to show that domestication reduced sexual reproduction traits through vegetative propagation.

Genetic control of tracheid properties in Norway spruce wood

The paper uses GWAS to identify genetic loci controlling tracheid properties in Norway spruce, finding 31 loci and 26 novel candidate genes.

Inferring the Allelic Series at QTL in Multiparental Populations

This study introduces a Bayesian framework to infer allelic series in multiparental populations, distinguishing biallelic from multiallelic QTL and improving haplotype effect estimation.

A new approach of dissecting genetic effects for complex traits

This paper introduces an iterative screen regression (ISR) method for GWAS that improves power and accuracy in detecting genetic associations while correcting for population structure.

Genotype identification and diversity analysis in Kiwifruit (Actinidia spp.) using RAPD markers

This study uses RAPD markers to analyze genetic diversity and identify genotypes in kiwifruit, revealing distinct clusters and potential sex-specific markers.

A novel mapping strategy utilizing mouse chromosome substitution strains identifies multiple epistatic interactions that regulate complex traits

This study uses mouse chromosome substitution strains to identify both additive and epistatic genetic loci influencing complex traits and gene expression.

Discovery of novel haplotypes for complex traits in landraces

The paper identifies novel haplotypes in maize landraces associated with quantitative traits and demonstrates their superior performance compared to breeding lines.

Genome-wide SNP genotyping of DNA pools identifies untapped landraces and genomic regions that could enrich the maize breeding pool

The paper uses SNP genotyping of DNA pools to identify landraces and genomic regions with untapped genetic diversity for maize breeding.

Development of diagnostic PCR and LAMP markers for MALE STERILITY 1 (MS1) in Cryptomeria japonica D. Don

The paper develops PCR and LAMP markers to detect mutant alleles of the MS1 gene in Cryptomeria japonica for pollen-free cultivar production.

Grain Fe and Zn Contents Linked SSR Markers Based Genetic Diversity Reveal Perspective for Marker Assisted Biofortification Breeding in Rice

The paper assesses genetic diversity in rice grain Fe and Zn content using SSR markers and identifies significant marker-trait associations for biofortification breeding.

Genomic prediction informed by biological processes expands our understanding of the genetic architecture underlying free amino acid traits in dry Arabidopsis seeds

The paper uses genomic prediction to identify biological processes influencing free amino acid traits in Arabidopsis seeds, revealing new trait-pathway associations and improving predictive ability for specific amino acids.

Population sequencing enhances understanding of tea plant evolution

This study uses population sequencing to analyze tea plant evolution, revealing stronger selection for disease resistance and flavor in C. sinensis var. sinensis compared to C. sinensis var. assamica.

High Throughput Computational Mouse Genetic Analysis

The paper applies haplotype-based computational genetic mapping to large-scale mouse phenotypic datasets to identify genetic factors affecting biomedical traits.

A Maize Practical Haplotype Graph Leverages Diverse NAM Assemblies

The paper constructs a maize pangenome haplotype graph (PHG) to improve genotype imputation accuracy across diverse germplasm using WGS and GBS data.

Application of Pedimap -- a pedigree visualization tool -- to facilitate the decisioning of rice breeding in Sri Lanka

The paper applies Pedimap, a pedigree visualization tool, to rice breeding in Sri Lanka to improve decision-making using phenotypic, molecular, and pedigree data.

Large scale genome-wide association study reveals that drought induced lodging in grain sorghum is associated with plant height and traits linked to carbon remobilisation

This study identifies 213 QTL associated with drought-induced lodging in grain sorghum, showing strong links to plant height and carbon remobilisation traits.

Brassica napus L. dwarfing gene: Determining candidate intervals of dwarfing genes by BSA and SNP typing

This paper identifies a candidate interval for the dwarfing gene DW871 in Brassica napus using BSA and SNP typing, narrowing it to 15.51-16.60Mb on ChrA10.

Genome-wide mapping and prediction of plant architecture in a sorghum nested association mapping population

The paper identifies quantitative trait loci (QTL) for plant architecture traits in sorghum using a nested association mapping population and evaluates genomic prediction accuracy.

Resynthesis: Marker-based partial reconstruction of elite genotypes in clonally-reproducing plant species

The paper introduces a method to reconstruct elite genotypes in clonally-reproducing plants by selecting marker-based lines that retain the genetic architecture of a top-performing cultivar with agronomically relevant differences.

BSAseq: an interactive and integrated web-based workflow for identification of causal mutations in bulked F2 populations

BSAseq identifies causal mutations in bulked F2 populations using a probabilistic model and interactive web tool.

Rat models of human diseases and related phenotypes: a systematic inventory of the causative genes

The paper systematically inventories rat genes associated with human diseases and phenotypes, highlighting their relevance to human disease susceptibility and therapeutic approaches.

mrMLM v4.0: An R Platform for Multi-locus Genome-wide Association Studies

mrMLM v4.0 is an R platform for multi-locus GWAS that improves detection of important loci by comparing with existing methods and confirming its effectiveness with simulations and real datasets.

Genome-wide association analysis reveals new insights into the genetic architecture of defensive, agro-morphological and quality-related traits in cassava

This study performs a genome-wide association analysis on cassava to identify genetic loci associated with defensive, agro-morphological, and quality traits, uncovering 41 significant associations and candidate genes.

Phylogenetic analysis by SNP and development of SSR marker in Passiflora

The paper analyzes the phylogenetic relationships and develops SSR markers in Passiflora species using RAD-Seq and SNP data.

Reproductive tissues-specific meta-QTLs and candidate genes for development of heat-tolerant rice cultivars

This study identifies 35 meta-QTLs and 45 heat-responsive genes specific to reproductive tissues in rice, providing targets for marker-assisted breeding to develop heat-tolerant cultivars.