Genetic Mapping and Diversity in Plants and Animals

The paper applies genome-wide mediation analysis to maize data, identifying 736 mediating genes that explain 12.7% of phenotypic variance, with pleiotropic effects observed in 11% of genes.

The paper uses whole-genome sequencing on 220 alfalfa accessions to identify SNPs associated with fall dormancy height, finding a SNP linked to the DREB1C gene.

The paper characterizes traditional Assam rice genotypes using SSR markers and identifies heterotic groups to improve hybrid yield through genetic divergence and heterosis analysis.

The paper develops MNP DNA markers and MNP-Seq method for accurate and efficient genotyping, showing high polymorphism and accuracy in rice and cotton.

The paper uses a multi-parental recombinant inbred line population in C. elegans to study gene expression variation and identifies eQTLs and trans-bands affecting gene expression.

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.

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

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.

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.

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

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.

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.

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

This study identifies QTLs for bioenergy-related traits in sweet sorghum using genotyping-by-sequencing and maps them to specific chromosomes.

The paper identifies genetic loci influencing fruit color in strawberry by analyzing QTLs and mQTLs, revealing the dominant role of the F. vesca subgenome in anthocyanin production.

This study identifies favorable gene haplotypes associated with rice grain quality traits through genome-wide association analysis and shows their benefits in hybrid breeding.

The paper uses genome resources from Setaria viridis to identify loci associated with climate response, seed shattering, and leaf angle, and validates a novel domestication gene.

The paper identifies SNP loci associated with female re-mating rate in Drosophila pseudoobscura using bulk segregant analysis and finds fewer fixed SNPs than expected by simulation.

This paper introduces FlxQTL, a flexible multivariate linear mixed model for genetic mapping of multiple correlated traits, adjusting for relatedness and modeling multiple environments or timepoints.

The paper analyzes genetic diversity in Japonica rice using the 3K RG dataset, identifying multiple introgression streams from different geographic regions and subgroups.

SR4R provides a processed SNP database for rice, offering four reference SNP panels for population genetics and genomic breeding.

The paper introduces a genomic structural equation model to examine relationships between phenotypic plasticity and local environments using Bayesian networks and mixed-effects SEM.

PyBSASeq is a new algorithm for BSA-Seq data analysis that improves sensitivity and reduces sequencing costs by identifying trait-associated SNPs with lower coverage.

The paper addresses ghost QTL and hotspots in QTL mapping by introducing an extended mixed model with nonzero mean random effects to improve detection accuracy.

This study uses marker stability to predict agronomic traits and perform association mapping in rice landraces, showing improved performance over GEMMA for simulated traits and identifying markers in known QTL regions.

The paper analyzes recombination patterns in cassava using pedigree and GBS data, finding sexual dimorphism in crossover frequency and introgression effects on recombination.

This paper introduces a method to estimate chromosome-wide recombination rates using marker selected pools and validates it with simulations and empirical data.