Genetic Mapping and Diversity in Plants and Animals

This paper introduces Neighbor GWAS, a method that incorporates neighbor genotypic identity into GWAS to better capture spatial genetic effects, finding that neighbor effects explain 8% more phenotypic variation in field herbivory data.

This paper introduces Neighbor QTL, a method for mapping quantitative trait loci that account for neighbor effects in plants, and demonstrates its application to herbivory in Arabidopsis thaliana.

The paper extends a penalized likelihood method for multiple-QTL analysis to handle the X chromosome appropriately, demonstrating its performance through simulation and eQTL data.

The paper develops a DNA bulk SNP genotyping method for landraces and applies it to maize, showing accurate allelic frequency estimation and low ascertainment bias.

This study uses SRAP markers to analyze genetic diversity in 44 Dianthus plants, revealing interspecific diversity and intraspecific variation linked to geography and habitat.

This paper reports the development of aromatic black rice through interspecific hybridization between O. sativa and O. rufipogon, identifying genetic mechanisms underlying black pericarp formation.

This study performs a GWAS on rice flowering time, identifying hundreds of loci and epistatic interactions that contribute to genetic heterogeneity and missing heritability.

The paper introduces fullsibQTL, an R package for QTL mapping in outcrossing species, which considers multilocus genetic maps and different segregation patterns.

The paper identifies eleven biosynthetic genes explaining most of the natural variation in carotenoid levels in maize grain through QTL analysis and expression correlation.

This study identifies 54,206 SNPs in Darjeeling tea cultivars, links them to 8 traits, and identifies 57 significant marker-trait associations.

The paper analyzes diversity patterns and selective sweeps in a Southeast European maize panel combined with two West European panels to identify genomic regions under selection for adaptation to SEE conditions.

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.

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

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

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

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.

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

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

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

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.

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

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

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

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

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

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

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.

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.

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

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