Genetic Mapping and Diversity in Plants and Animals

RIL-StEp: epistasis analysis of recombinant inbred lines (RILs) reveals candidate interacting genes that control rice seed hull color

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

Genetic diversity, population structure and selection signature in Ethiopian Sorghum (Sorghum bicolor L. ) germplasm

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

Genome-wide mediation analysis: bridging the dividebetween genotype and phenotype via transcriptomicdata in maize

The paper applies genome-wide mediation analysis to maize data, identifying 736 mediating genes that explain 12.7% of phenotypic variance, with pleiotropic effects observed in 11% of genes.

Integration of Infinium and Axiom SNP array data in the outcrossing species Malus x domestica and causes for seemingly incompatible calls

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

A Genomics Resource for Genetics, Physiology, and Breeding of West African Sorghum

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

Whole-Genome Sequencing on 220 Alfalfa (Medicago sativa L.) Accessions Identified Association of DREB1C Gene with Fall Dormancy Height

The paper uses whole-genome sequencing on 220 alfalfa accessions to identify SNPs associated with fall dormancy height, finding a SNP linked to the DREB1C gene.

K-seq, an affordable, reliable, and open Klenow NGS-based genotyping technology

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 recombination landscape and multiple QTL mapping in a Solanum tuberosum cv. 'Atlantic'-derived F1 population

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.

Characterization and Heterotic Grouping of Traditional Assam rice (Oryza sativa L.)

The paper characterizes traditional Assam rice genotypes using SSR markers and identifies heterotic groups to improve hybrid yield through genetic divergence and heterosis analysis.

Multiple nucleotide polymorphism DNA markers for the accurate evaluation of genetic variations

The paper develops MNP DNA markers and MNP-Seq method for accurate and efficient genotyping, showing high polymorphism and accuracy in rice and cotton.

Enhancing backcross programs through increased recombination

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.

The genetics of gene expression in a C. elegans multi parental recombinant inbred line population.

The paper uses a multi-parental recombinant inbred line population in C. elegans to study gene expression variation and identifies eQTLs and trans-bands affecting gene expression.

Accurate, ultra-low coverage genome reconstruction and association studies in Hybrid Swarm mapping populations

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: A Memory-efficient, Visualization-enhanced, and Parallel-accelerated tool for Genome-Wide Association Study

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

A Statistical Framework for QTL Hotspot Detection

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 phenotyping and machine learning enable discovery of loci regulating daily floral opening in lettuce

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

The influence of QTL allelic diversity on QTL detection in multi-parent populations: a simulation study in sugar beet

This study simulates QTL detection in multi-parent populations of sugar beet, finding that fewer, larger crosses improve detection power, while more parents help detect rare alleles with large effects when population size increases.

Integration of high-density genetic mapping with transcriptome analysis uncovers numerous agronomic QTL and reveals candidate genes for the control of tillering in sorghum

The paper integrates genetic mapping with transcriptome analysis to identify QTL and candidate genes for tillering control in sorghum using a recombinant inbred line population.

Genetic diversity of maize landraces from the South-West of France

This study analyzes the genetic diversity of 194 maize landraces from South-West France using a 50K SNP array, identifying two genetic groups and a longitudinal gradient shaped by genetic drift and restricted gene flow.

Neighbor GWAS: incorporating neighbor genotypic identity into genome-wide association studies of field herbivory

This paper introduces Neighbor GWAS, a method that incorporates neighbor genotypic identity into GWAS to better capture spatial genetic effects, finding that neighbor effects explain 8% more phenotypic variation in field herbivory data.

Neighbor QTL: an interval mapping method for quantitative trait loci underlying plant neighborhood effects

This paper introduces Neighbor QTL, a method for mapping quantitative trait loci that account for neighbor effects in plants, and demonstrates its application to herbivory in Arabidopsis thaliana.

Treatment of the X chromosome in mapping multiple quantitative trait loci

The paper extends a penalized likelihood method for multiple-QTL analysis to handle the X chromosome appropriately, demonstrating its performance through simulation and eQTL data.

Deciphering the genetic diversity of landraces with high-throughput SNP genotyping of DNA bulks: methodology and application to the maize 50k array

The paper develops a DNA bulk SNP genotyping method for landraces and applies it to maize, showing accurate allelic frequency estimation and low ascertainment bias.

Genetic Diversity of Dianthus Plants Revealed by SRAP Markers

This study uses SRAP markers to analyze genetic diversity in 44 Dianthus plants, revealing interspecific diversity and intraspecific variation linked to geography and habitat.

Black Rice Developed Through Interspecific Hybridization (O. sativa x O. rufipogon): Origin of Black Rice Gene from Indian Wild Rice

This paper reports the development of aromatic black rice through interspecific hybridization between O. sativa and O. rufipogon, identifying genetic mechanisms underlying black pericarp formation.

Genome-wide association study of flowering time reveals complex genetic heterogeneity and epistatic interactions in rice

This study performs a GWAS on rice flowering time, identifying hundreds of loci and epistatic interactions that contribute to genetic heterogeneity and missing heritability.

fullsibQTL: an R package for QTL mapping in biparental populations of outcrossing species

The paper introduces fullsibQTL, an R package for QTL mapping in outcrossing species, which considers multilocus genetic maps and different segregation patterns.

Eleven biosynthetic genes explain the majority of natural variation for carotenoid levels in maize grain

The paper identifies eleven biosynthetic genes explaining most of the natural variation in carotenoid levels in maize grain through QTL analysis and expression correlation.

Genome-wide SNP detection in Darjeeling tea: unravelling genetic structure, functional impact and trait associations

This study identifies 54,206 SNPs in Darjeeling tea cultivars, links them to 8 traits, and identifies 57 significant marker-trait associations.

First results on diversity patterns and selective sweeps in a Southeast European panel of maize inbred lines as combined with two West European panels

The paper analyzes diversity patterns and selective sweeps in a Southeast European maize panel combined with two West European panels to identify genomic regions under selection for adaptation to SEE conditions.