Genetic Mapping and Diversity in Plants and Animals

The paper develops and validates a 30K SNP genotyping tool for flax breeding, showing high polymorphism and genotyping accuracy.

This study shows that single-parent expression complementation explains 29% of heterotic variance in maize hybrids and reveals cis/trans eQTL regulation of SPE patterns.

The paper develops an in silico method to predict restriction enzyme performance for complexity-reduced genome sequencing, finding that MspI and PstI are highly informative for plant genomes.

This study identifies a genomic region on chromosome 10 associated with photosensitivity in eggplants and suggests SmNAC1-like gene involvement in anthocyanin biosynthesis.

The paper develops and validates statistical tests for segregation distortion in higher ploidy F1 populations, showing improved type I error control and power.

The paper presents a genomic breeding strategy using large-scale recombinant populations and prediction models to rapidly develop rice cultivars with desired traits.

This paper estimates heritability and identifies QTL for aerial root traits and yield components in maize, finding genetic overlap with introgression from wild mexicana.

The paper identifies two mutations in a MYC-bHLH transcription factor causing purple coloration in stolons and seed heads of Zoysia grass hybrids.

This study investigates the domestication history and genetic diversity of teff using genomic analyses, identifying key loci associated with seed color and panicle architecture.

The paper compares PCA-based QTL mapping with individual trait hotspots in metabolomic and transcriptomic data from a recombinant inbred line, finding they identify different genomic regions and genetic architectures.

The paper develops and validates a high-density SNP array for potato, demonstrating its utility in genetic diversity analysis, GWAS, and genomic prediction.

This study uses deep learning to predict geographic origins of barley genebank accessions and integrates imputed environmental data into genome-environment association studies, revealing both potential and limitations of this approach.

The paper identifies genetic variants at transcription factor binding sites that explain a large portion of phenotypic heritability in maize under different water conditions.

This study identifies genetic loci for MetS-like traits in Drosophila and finds that main genetic effects are distinct from diet-dependent plastic loci.

This study uses drone-based phenotyping to conduct a GWAS on lettuce, confirming known QTLs and identifying new ones for plant height and color in field conditions.

This paper constructs a sorghum pangenome and identifies trait-associated variants to inform climate-aware genome-enabled breeding strategies.

This study identifies SNP markers associated with rice biomass under different nitrogen sources, revealing genetic mechanisms for nitrogen use efficiency.

This study analyzes gene expression changes in domesticated and wild relatives of rice, tomato, and soybean to understand domestication effects on stress tolerance and other traits.

This study identifies genes associated with monogermity and betalain biosynthesis in sugar beet through genome-wide association analysis of 290 accessions.

PlantVarFilter is a Python pipeline for variant filtering and GWAS in plants, supporting multiple formats and providing statistical analysis and visualization tools.

The paper conducts GWAS on Lactuca species to identify genetic loci associated with phenotypic traits, finding novel QTLs in wild species not detected in domesticated lettuce.

The paper develops a MAGIC population for eggplant, identifies a gene linked to root morphology, and shows its potential for trait mapping and breeding.

The paper identifies trans-regulatory loci influencing gene expression plasticity in Arabidopsis under salicylic acid treatment, showing most loci act in trans and are under-detected in GWAS.

This study evaluates the use of environmental and genomic data to identify climate-adaptive maize varieties, finding that genomic data better predict yield traits than environmental data alone.

The paper identifies QTL associated with agronomic, nutritional, and photosynthetic traits in Gynandropsis gynandra to aid in crop improvement.

This study investigates the evolutionary history of cultivated rice and identifies genomic signatures of heterosis in super-hybrid rice varieties.

The paper characterizes a maize near-isogenic line population to identify introgressions and map disease resistance QTL, revealing allelic variation in traits.

This study identifies genetic factors influencing aerial root traits in maize that support biological nitrogen fixation, finding heritable traits and QTLs from landrace and elite inbred varieties.

This study identifies genetic loci and subgroups in DO mice linked to anxiety-like behavior and ethanol consumption using behavioral assays and QTL analysis.

This study identifies genomic loci associated with agronomic and grain traits in tef, revealing novel marker-trait associations and retrotransposon effects on grain color and size.