Genetic Mapping and Diversity in Plants and Animals

Genomic analysis of fruit size and shape traits in apple: unveiling candidate genes through GWAS analysis.

This paper performs GWAS on apple fruit size and shape traits using the Apple REFPOP collection, identifying SNPs and candidate genes associated with these traits.

GWAS from Spoken Phenotypic Descriptions: A Proof of Concept from Maize Field Studies

This paper demonstrates using spoken phenotypic descriptions in GWAS to identify genomic regions associated with maize plant height, corroborating known associations and finding novel candidate genes.

A comprehensive overview and benchmarking analysis of fast algorithms for genome-wide association studies

This study benchmarks 33 GWAS algorithms to evaluate their performance in identifying QTLs across plant species and simulated data.

Characterization of popcorn temperate and tropical populations and GWAS for zeins and starch contents

The paper characterizes temperate and tropical popcorn populations and identifies candidate genes for zein and starch content, proposing new quantification methods for breeding programs.

RecView: an interactive R application for viewing and locating recombination positions using pedigree data

RecView identifies recombination positions in pedigrees using genotype data and visualizes grandparent-of-origin of alleles.

QTL analysis of floral morphology polymorphisms between Gilia yorkii and G. capitata

The paper analyzes QTLs for floral morphology differences between Gilia yorkii and G. capitata, identifying colocalized QTL intervals on chromosomes 6 and 9.

Genomic and phenotypic characterization of finger millet indicates a complex diversification history

This study characterizes genomic and phenotypic variation in finger millet using SNP and trait data, revealing complex diversification patterns and geographic differentiation.

Cell morphology QTL reveal gene by environment interactions in a genetically diverse cell population

The paper identifies cell morphology quantitative trait loci (cmQTL) in fibroblasts exposed to arsenic, revealing gene-environment interactions and genetic regulation of oxidative stress responses.

Prediction of plant complex traits via integration of multi-omics data

This study integrates multi-omics data to predict complex traits in Arabidopsis, showing that transcriptome- and methylome-based models perform comparably to genome-based models and reveal novel gene interactions.

Insights into spinach domestication from genomes sequences of two wild spinach progenitors, Spinacia turkestanica and S. tetrandra

The paper reports genome assemblies of two wild spinach progenitors and identifies structural variants and introgression events associated with spinach domestication.

Improving selection efficiency in C. americana x C. avellana interspecific hybrids through the development of an indel-based genetic map

This paper develops an indel-based genetic map for hazelnut hybrids to improve breeding efficiency using next-generation sequencing.

The genetic architecture of the pepper metabolome provides insights into the regulation of capsianoside biosynthesis

This study identifies genetic loci and candidate genes involved in capsianoside biosynthesis in pepper, providing insights into the regulation of these beneficial metabolites.

LsTT2 encoding R2R3-MYB transcription factor is responsible for a shift from black to white in lettuce seed

This study identifies LsTT2, an R2R3-MYB transcription factor gene, as responsible for the shift from black to white seed color in lettuce through genetic mapping and genome editing validation.

SEQUENCE VARIATIONS ASSOCIATED WITH NOVEL PURPLE-PERICARP SUPER-SWEETCORN COMPARED TO ITS PURPLE-PERICARP MAIZE AND WHITE SUPER-SWEETCORN PARENTS

The paper identifies sequence variations in anthocyanin biosynthesis and sweetcorn genes between a novel purple-pericarp super-sweetcorn line and its parents.

Genomic signatures of adaptation to abiotic stress from a geographically diverse collection of chile peppers (Capsicum spp.) from Mexico

The paper identifies fifteen priority loci associated with abiotic stress tolerance in chile peppers using environmental association analysis and outlier detection.

Comprehensive analyses of 1771 transcriptome from seven tissues enhance genetic and biological interpretations of maize complex traits

The paper analyzes 1771 RNA-seq datasets from seven maize tissues to build a gene regulation atlas and link tissue-specific expression variation to agronomic traits.

Homoeologous non-reciprocal translocation explains a major QTL for seed lignin content in oilseed rape (Brassica napus L.)

The paper identifies a homoeologous non-reciprocal translocation in a major QTL for reduced seed lignin content in oilseed rape, leading to the deletion of the lignin biosynthesis gene PAL4.

Genome-Wide Association Study for Yield and Yield related traits reveals MarkerTrait Associations in Germplasm lines of Rice

This study performs a genome-wide association study on rice germplasm lines to identify marker-trait associations linked to yield and yield-related traits.

Polygenic basis of strong and rapid flowering time response to environment perturbations in wild Arabidopsis thaliana population

The paper identifies polygenic basis and environmental interactions underlying rapid flowering time response in Arabidopsis thaliana across diverse environments.

The irregular fruit green netting: An eggplant domestication trait controlled by the SmGLK2 gene with implications in fruit colour diversification

The paper identifies SmGLK2 as the gene controlling fruit green netting in eggplants, showing mutations that disrupt chlorophyll biosynthesis and contribute to fruit color diversity.

Dark side of the honeymoon: reconstructing the Asian x European rose breeding history through the lens of genomics

The paper traces the genetic changes in European rose breeding during the 19th century by analyzing phenotypic and genetic data from 204 rose accessions, revealing a shift to an Asian genetic background and reduced diversity.

Development of the First High-Density Linkage Map in the Maize Weevil, Sitophilus zeamais

The paper develops the first genetic linkage map for the maize weevil, Sitophilus zeamais, using flow cytometry to determine genome size and SNP markers to construct the map.

Genetic diversity of North American popcorn germplasm and the effect of population structure on nicosulfuron response

The paper analyzes genetic diversity in North American popcorn germplasm, identifies two distinct populations, and links population structure to nicosulfuron response.

QTL Mapping of Seed Fe Concentration in an Interspecific RIL Population Derived from Lens culinaris x Lens ervoides

This study maps QTLs for seed Fe concentration in a lentil interspecific RIL population, identifying two genomic regions explaining 11.9-20.5% of phenotypic variation.

Genetic mapping of genotype-by-ploidy effects in Arabidopsis thaliana

The paper maps genotype-by-ploidy effects in Arabidopsis thaliana by analyzing haploid and diploid offspring from a late flowering cross, identifying ploidy-specific QTLs and pleiotropic effects.

Genomics and Phenomics Enabled Prebreeding Improved Early-Season Chilling Tolerance in Sorghum

This study uses phenomics and genomics to improve early-season chilling tolerance in sorghum through marker-assisted breeding, showing up to 24% performance improvement in lines with the CT allele.

Saturating the eQTL map in Drosophila melanogaster: genome-wide patterns of cis and trans regulation of transcriptional variation in outbred populations

The paper maps eQTLs in Drosophila melanogaster using an outbred panel, identifying cis and trans regulatory loci for most expressed genes and revealing non-modular gene co-expression networks.

Genome-wide association studies reveal novel loci controlling tuber flesh color and oxidative browning in Dioscorea alata

This study uses GWAS to identify genetic loci controlling tuber flesh color and oxidative browning in Dioscorea alata, finding 14 and 4 significant associations with phenotypic variance explained up to 18.04%.

QTL mapping of the narrow-branch "Pendula" phenotype in Norway spruce (Picea abies L. Karst.)

The paper identifies a single QTL associated with the Pendula phenotype in Norway spruce using QTL mapping across two F1 progenies.

The effect of developmental variation on expression QTLs in a multi parental C. elegans population

This study investigates how developmental age variation affects eQTL patterns in C. elegans using dynamical eQTL mapping and compares it to classical methods.