Genetic Mapping and Diversity in Plants and Animals

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.

AFLAP constructs high-density genetic maps and improves genome assemblies using k-mers from whole genome sequencing data without requiring a reference genome.

RIL-StEp identifies epistatic gene interactions in rice seed hull color using SNP data from recombinant inbred lines.

This study characterizes genetic diversity, population structure, and selection signatures in Ethiopian sorghum germplasm using GBS, identifying 40 genomic regions under selection.

This paper integrates Infinium and Axiom SNP array data in apple, identifies compatible SNPs, and highlights challenges in data integration.

The paper develops a genomic resource for West African sorghum by characterizing a diverse panel and identifying QTLs for flowering time and plant height.

K-seq is a cost-effective genotyping method using Klenow amplification and Illumina sequencing, showing comparable genetic results to WGS and GBS with higher SNP detection.

The paper constructs a genetic map and identifies QTL in a tetraploid potato population, finding co-located QTL for multiple traits on linkage group 5.

This study simulates how increasing recombination rate affects introgression efficiency in backcross programs, showing it reduces linkage drag in cold regions but is harmful in hot regions.

This study develops a computational pipeline to reconstruct genomes from ultra-low coverage data in Hybrid Swarm populations and evaluates its effectiveness for genetic association studies.

rMVP improves GWAS computation by offering memory efficiency, visualization tools, and parallel acceleration for faster and more scalable analysis.

The paper introduces a statistical framework for detecting QTL hotspots that handles both individual-level and summarized data, addresses correlation structure and computational cost, and improves hotspot identification.

Drone-based remote phenotyping combined with machine learning and Bayesian analysis identified two loci regulating daily floral opening time in lettuce.