Genetic Mapping and Diversity in Plants and Animals

High-throughput SNP discovery, development and validation of a 30 K target SNP genotyping tool for cultivated flax (Linum usitatissimum) breeding and germplasm characterization

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

Regulation of heterosis-associated gene expression complementation in maize hybrids

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.

Optimizing selection of restriction enzymes for complexity-reduced genome sequencing in plants

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.

Stacking of anthocyanin related QTLs in the chromosome 10 and postulation of SmNac-like gene to be involve in anthocyanin biodhynthesis

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

Tests for segregation distortion in higher ploidy F1 populations

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

Genomic prediction models based on a large-scale recombinant population allow rapid breeding of desired genotypes

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

HERITABILITY AND QTL MAPPING OF AERIAL ROOTS AND OTHER YIELD COMPONENT TRAITS WITH IMPLICATIONS FOR N2 FIXATION IN ZEA MAYS

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

Two mutations in the same MYC-bHLH transcription factor cause segregation of purple coloration of stolons and seed heads in Zoysia japonica x Zoysia matrella F2 and F1 populations

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

Origin, domestication, and diversity of the climate resilient Ethiopian cereal teff

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

Evaluating the Effectiveness of Data Reduction Techniques in QTL Mapping

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.

An Axiom SNP genotyping array for potato: development, evaluation and applications

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

Effects of using deep learning to predict the geographic origin of barley genebank accessions on genome-environment association studies

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.

Genetic variation at transcription factor binding sites largely explains phenotypic heritability in maize

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

Mapping of genotype-by-environment interaction loci for Metabolic Syndrome-like traits using the multi-parent Drosophila Synthetic Population Resource determines that main genetic effects are distinct from environment dependent plastic loci

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

From aerial drone to QTL: Leveraging next-generation phenotyping to reveal the genetics of color and height in field-grown Lactuca sativa

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.

Developing future resilience from signatures of adaptation across the sorghum pangenome

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

Genome-wide Association Study of Rice Vegetative Biomass under Different Inorganic Nitrogen Forms: Ammonium or Nitrate

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

Meta-Analysis of Wild Relatives and Domesticated Species of Rice, Tomato, and Soybean Using Publicly Available Transcriptome Data

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.

Uncovering Genes Essential in Domestication and Breeding of Sugar Beet

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

PlantVarFilter: A Comprehensive Pipeline for Variant Filtering and Genome-Wide Association Analysis in Plant Genomics

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

Exploring phenotypic and genetic variation in Lactuca with GWAS in L. sativa and L. serriola

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.

Resequencing and phenotyping of the first highly inbred eggplant multiparent population reveal SmLBD13 as a key gene associated with root morphology

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

Trans-regulatory loci shape natural variation of gene expression plasticity in Arabidopsis

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.

The utility of environmental data from traditionalvarieties for climate-adaptive maize breeding

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.

Identifying Agronomic, Nutrition and Leaf Vein Quantitative Trait Loci in the Orphan Crop Gynandropsis gynandra

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

A maize near-isogenic line population designed for gene discovery and characterization of allelic effects

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

Genetic determinants of aerial root traits that support biological nitrogen fixation in maize

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.

Genetic Mapping in Diversity Outbred Mice Identifies Novel Loci and Candidate Genes for Anxiety-Like Behavior and Genetic Subgroups Predictive of Ethanol Consumption

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

Population genomics uncover loci for trait improvement in the indigenous African cereal tef (Eragrostis tef)

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.

Whole genome resequencing of a global collection of Napier grass (Cenchrus purpureus) to explore global population structure and QTL governing yield and feed quality traits

This study resequences 450 Napier grass individuals to assess genetic diversity and identify QTL for yield and feed quality traits.