Genetic Mapping and Diversity in Plants and Animals

RAINBOW is a novel SNP-set GWAS method that improves detection of causal variants and controls false positives, especially for nearby variants with opposite effects.

The paper introduces PCgen, an algorithm that reconstructs genetic networks by incorporating direct and indirect effects, improving accuracy using individual data over genotypic means.

The paper identifies SNPs and INDELs in Indian tomato cultivars using ddRAD-seq to aid in genetic purity analysis and breeding.

This study maps QTLs associated with morpho-physiological traits under reproductive stage drought stress in rice using RIL populations and BSA, identifying novel QTLs for marker-assisted breeding.

WormQTL2 is a database platform that integrates and allows analysis of eQTL datasets in C. elegans to facilitate systems genetics research.

The paper reports the de novo genome sequencing and analysis of the rice variety KitaakeX, identifying genomic variations and providing a high-quality reference for rice functional genomics.

This study constructs an ultra-dense genetic map for hexaploid sweetpotato and characterizes its inheritance system using a new software tool.

The paper develops a high-throughput method to genotype InDels in maize using an Affymetrix Axiom array, achieving high reliability and reproducibility.

This paper uses logistic regression with phenotypic data to classify Asian rice cultivars into indica and japonica with high accuracy.

The paper develops a maize nested association mapping population (TeoNAM) to identify QTLs for domestication and agronomic traits, finding novel teosinte alleles and confirming a rice gene's role in maize tillering.

This study identifies 92 grain size QTL in sorghum through GWAS, showing overlap with rice and maize QTL and supporting common genetic control of grain size across cereals.

This study predicts complex traits in maize using transcriptome and genetic marker data, finding similar performance between both approaches and highlighting transcriptome's role in capturing trait variation not captured by sequence data.

This study identifies QTLs and differentially expressed genes associated with 2-propenyl and 3-butenyl glucosinolate synthesis in Brassica juncea using genetic mapping and RNA-sequencing.

The paper identifies genetic loci associated with chilling tolerance in sorghum using nested association mapping and finds some loci co-localize with historically selected genes.

The paper improves the genome of Aethionema arabicum using long-read sequencing and constructs a genetic map, enhancing genome assembly and enabling comparative genetic studies.

The paper analyzes linkage disequilibrium and haplotype block patterns in maize populations to understand LD decay and its implications for association studies and genomic selection.

This paper introduces SEM-GWAS, a method that incorporates phenotypic networks into GWAS to partition SNP effects into direct and indirect effects, using rice traits as an example.

The paper constructs a high-resolution RAD-Seq linkage map for marine medaka, anchors the reference genome, and identifies a sex trait QTL on the sex chromosome.

The paper integrates transcriptomic network reconstruction and QTL analyses to uncover mechanistic links between genomic architecture and Brassica rapa development in field settings.

This study combines linkage and association mapping to identify QTLs associated with black tea quality and drought tolerance traits, finding additional QTLs related to secondary metabolites and abiotic stress.

Gephebase compiles genotype-phenotype relationships from natural and domesticated eukaryotic variation to support evolutionary genetics research and applications.

The paper presents genome-wide marker datasets and population structure analyses for three minor millets, revealing subpopulations and validating SNP accuracy using phenotype data.

The paper develops a method to convert tetraploid GBS data into diploidized genotype calls and evaluates its performance using Urochloa hybrids.

The paper develops a hidden Markov model-based method to estimate recombination fractions and infer linkage phases in autopolyploid species with high ploidy levels using simulated and real data.

QTG-Finder uses machine learning to prioritize causal genes within QTLs in Arabidopsis and rice by analyzing genomic and functional data.

The paper shows that combining transcriptome-wide association studies (TWAS) with genome-wide association studies (GWAS) improves the detection of genes linked to agronomic and seed quality traits in maize.

The paper compares genotyping-by-sequencing and microarrays for detecting QTLs, showing they complement each other by tagging different haplotypes and improving detection power and localization.

The paper identifies genetic loci associated with seed fatty acid composition in oat using multivariate GWAS approaches, finding more significant SNPs than univariate analyses.

The paper identifies 746k polymorphic sites in Capsicum species and finds four novel loci associated with fruit shape, including a mutation in the Longifolia 1-like gene.

ViVa is a webtool that enables researchers to mine natural variation from genomic data, demonstrating its utility in analyzing the auxin signaling pathway in Arabidopsis thaliana.