Genetic Mapping and Diversity in Plants and Animals

The paper presents a high-quality reference genome for tomato, revealing genomic fragments linked to human selection during domestication.

The paper develops a 50K SNP genotyping array for Scots pine to enable genome-wide analyses and improve genetic research and breeding programs.

This paper modifies a BSA-Seq analysis method to identify trait-associated genomic regions without requiring parental genome sequences, demonstrating its effectiveness on a public dataset.

This study uses GWAS to identify candidate genes for drought tolerance in coast redwood and giant sequoia, finding 78 and 6 marker-trait associations respectively.

This study identifies seed storability-related loci in Dongxiang wild rice using BSA-seq and confirms their effects through metabolic and cellular analysis.

The paper introduces a generic hidden Markov model for genotype reconstruction in multi-parent populations and demonstrates its application using R/qtl2 on mouse data.

The paper examines recombination patterns in cassava, finding higher female recombination rates and suppressed recombination in wild introgression segments.

The paper combines data from two independent mouse studies to identify genetic loci for traits, finds poor replication rates, and proposes a method to assess confidence in associations.

The paper maps transcriptome variation in Mimulus guttatus to cis- and trans-acting mutations, finding differing patterns of selection and showing that gene expression modules predict allele frequencies and traits.

This study sequenced 300 Thai rice accessions to identify SNP variants and infer population structure, revealing five subpopulations grouped by location with unique genetic and agronomic traits.

This paper introduces an automated SNP-based method to identify contaminants in polyploid plant progenies using PCA, Mendelian segregation analysis, and clustering, validated on simulated and real data.

This paper introduces HARE, a method for imputing cis haplotype-associated RNA expression to improve genomic prediction of complex traits across maize populations.

The paper analyzes liver proteomes across three genetically diverse mouse populations to understand how genetic variation influences protein abundance and its relationship to phenotypes.

The paper presents a high-quality genome assembly of maize inbred line A188, revealing structural variations and candidate genes associated with embryonic callus induction.

The paper evaluates MAGIC population designs and introduces a tool to create and test them, showing that certain designs improve haplotype diversity without requiring large crossing programs.

The paper develops GPU-accelerated algorithms for fast eQTL scans in BXD mice, reducing runtime to seconds for large transcriptome datasets.

The paper introduces polyqtlR, a tool for QTL analysis in polyploid crops, enabling detection of QTL, exploration of allelic composition, and analysis of meiotic processes.

This paper develops software for QTL mapping in tetraploid and diploid diallel populations, demonstrating its effectiveness in detecting QTLs and improving model fit through non-additive effects.

The paper assesses genetic purity and diversity in maize inbred lines and hybrids using SNP markers, finding 67% of inbreds are pure and identifying promising hybrids for release.

The paper develops a statistical framework for haplotype reconstruction in tetraploid F1 populations and implements it in the software PolyOrigin, demonstrating its effectiveness on a potato dataset.

This study identifies 10 salt stress-responsive QTL in a sorghum population, linking them to genes involved in ionic, tissue, and osmotic tolerance.

The paper reanalyzes a GWAS peak in Arabidopsis thaliana and proposes that the association with flowering time is due to genetic heterogeneity rather than the previously suggested gene cluster.

The paper identifies edQTLs in rice under field conditions and shows they can predict gene expression in different environments and complex genotypes.

This study develops a sorghum pan-genome to explore its functional utility in accelerating genetic gain by identifying genes and SNPs associated with agronomic traits and drought tolerance.

This study identifies genetic factors influencing zinc and cadmium concentrations in sweet corn kernels through genome-wide association analysis.

The paper examines heritable gene expression under salt stress in rice, identifying condition-specific heritable genes and their chromosomal distribution patterns.

The paper identifies genetic factors influencing maize rind strength through divergent selection and transcriptome analysis, revealing key genes and pathways related to cell wall composition.

MultiGWAS is a tool that performs GWAS for diploid and tetraploid organisms by integrating multiple software, improving reproducibility and model selection.

This study examines how kinship correction affects genetic interaction test statistics in mouse populations, finding no inflation in interaction tests but recommending reduced kinship matrices for better correction.