Genetic Mapping and Diversity in Plants and Animals

Marker-assisted selection of trees with MALE STERALITY 1 in Cryptomeria japonica D. Don

This study identifies markers for the male-sterility gene MS1 in Cryptomeria japonica and demonstrates their use in marker-assisted selection across different populations.

Reanalysis of Genome Sequences of tomato accessions and its wild relatives: Development of tomato genomic variation (TGV) database integrating SNPs and INDELs polymorphisms

The paper reanalyzes tomato genome sequences to develop the TGV database, integrating SNPs and INDELs with functional annotations for trait improvement.

Genotyping by sequencing for identification and mapping of QTLs for bioenergy-related traits in sweet sorghum

This study identifies QTLs for bioenergy-related traits in sweet sorghum using genotyping-by-sequencing and maps them to specific chromosomes.

The genetic architecture of fruit colour in strawberry (Fragaria x ananassa) uncovers the predominant contribution of the F. vesca subgenome to anthocyanins and reveals underlying genetic variations

The paper identifies genetic loci influencing fruit color in strawberry by analyzing QTLs and mQTLs, revealing the dominant role of the F. vesca subgenome in anthocyanin production.

The usefulness of multi-parent multi-environment QTL analysis: an illustration in different NAM populations

The paper introduces methods to analyze multi-parent multi-environment QTL data, showing they better estimate QTL effects across environments and sub-populations than single-environment analyses.

Genome-wide development of miRNA-based SSR markers in Cleistogenes songorica with their transferability analysis to gramineae and non- gramineae species

The paper develops miRNA-based SSR markers in Cleistogenes songorica and evaluates their transferability to other species, finding high polymorphism and utility for genetic studies.

Combination of favorable gene haplotypes plays an important role in rice hybrid grain quality traits based on genome-wide association analysis

This study identifies favorable gene haplotypes associated with rice grain quality traits through genome-wide association analysis and shows their benefits in hybrid breeding.

Genetic Mapping in Autohexaploid Sweet Potato with Low-coverage NGS-based Genotyping Data

The paper proposes a cost-effective genetic mapping strategy for autopolyploids using low-coverage NGS data and allele dosage probabilities to detect loci associated with phenotypes.

ZEAMAP, a comprehensive database adapted to the maize multi-omics era

ZEAMAP integrates multi-omics data for maize and teosinte to support genetic research and trait improvement.

Metabolite Quantitative Trait Loci for flavonoids provide new insights into the genetic architecture of strawberry (Fragaria x ananassa) fruit quality

The paper identifies metabolite quantitative trait loci (mQTLs) for flavonoids in strawberries, revealing genetic factors influencing fruit quality traits.

Low additive genetic variation in a trait under selection in domesticated rice

The paper estimates additive genetic variation in rice root growth under selection and finds low marker heritability and no associated loci in a tropical japonica population.

QTG-Finder2: a generalized machine-learning algorithm for prioritizing QTL causal genes in plants

QTG-Finder2 improves QTL causal gene prioritization in plants by using orthologs and additional features, achieving high recall in Sorghum and Setaria species.

Genome-wide variations analysis of special waxy sorghum cultivar Hongyingzi for brewing Moutai liquor

The paper analyzes genome-wide variations in the waxy sorghum cultivar Hongyingzi to identify genetic differences related to liquor-making traits.

Adapting genotyping-by-sequencing and variant calling for heterogeneous stock rats

The paper adapts genotype-by-sequencing for HS rats to call and impute over 3.7 million SNPs with 99% concordance compared to a genotyping array.

The Setaria viridis genome and diversity panel enables discovery of a novel domestication gene

The paper uses genome resources from Setaria viridis to identify loci associated with climate response, seed shattering, and leaf angle, and validates a novel domestication gene.

A single locus underlies variation in Caenorhabditis elegans chemotherapeutic responses

The paper identifies a single gene, scb-1, as a pleiotropic locus underlying variation in Caenorhabditis elegans responses to multiple chemotherapeutics.

Multiple QTL mapping in autopolyploids: a random-effect model approach with application in a hexaploid sweetpotato full-sib population

This paper develops a random-effect model for QTL mapping in autopolyploid sweetpotato, identifying 41 QTL across eight yield traits in a full-sib population.

Development of diagnostic SNP markers for quality assurance and control in sweetpotato breeding programs

The paper develops a 36-SNP marker set for quality assurance and control in sweetpotato breeding programs, showing it can detect mislabeling errors similarly to a high-density SNP set.

Identifying genomic markers associated with female re-mating rate in Drosophila pseudoobscura by replicated bulk segregant analysis.

The paper identifies SNP loci associated with female re-mating rate in Drosophila pseudoobscura using bulk segregant analysis and finds fewer fixed SNPs than expected by simulation.

SMRT sequencing of the Oryza rufipogon genome reveals the genomic basis of rice adaptation

The paper presents a high-quality Oryza rufipogon genome assembly using SMRT sequencing and identifies genomic variants and selected genes related to reproductive traits and adaptation.

Twelve Platinum-Standard Reference Genomes Sequences (PSRefSeq) that complete the full range of genetic diversity of Asian rice

The paper generates 12 new high-quality rice reference genomes to expand the genetic diversity coverage of cultivated rice, forming a comprehensive pan-genome resource with 16 reference sequences.

Development of a multiparent advanced generation intercross (MAGIC) population for genetic exploitation of complex traits in Brassica juncea: glucosinolate content as an example

The paper develops a MAGIC population in B. juncea for QTL mapping of glucosinolate content and identifies three major QTLs associated with different GSL types.

Flexible multivariate linear mixed models for structured multiple traits

This paper introduces FlxQTL, a flexible multivariate linear mixed model for genetic mapping of multiple correlated traits, adjusting for relatedness and modeling multiple environments or timepoints.

Dissecting adaptive traits with nested association mapping: Genetic architecture of inflorescence morphology in sorghum

This study identifies genetic factors controlling inflorescence morphology in sorghum using nested association mapping, revealing QTL associated with precipitation adaptation.

Disentangling group specific QTL allele effects from genetic background epistasis using admixed individuals in GWAS: an application to maize flowering

The paper introduces a GWAS method to identify QTLs with group-specific allele effects in admixed populations, applied to maize flowering time data.

Variance heterogeneity genome-wide mapping for cadmium in bread wheat reveals novel genomic loci and epistatic interactions

This study applies variance heterogeneity genome-wide association mapping to identify novel genomic loci and epistatic interactions influencing grain cadmium concentration in bread wheat.

Gene Expression Networks in the Drosophila Genetic Reference Panel

The paper maps expression quantitative trait loci and constructs sex-specific regulatory networks in Drosophila to understand how genetic variation affects gene expression and transposable element activity.

Choosing the optimal population for a genome-wide association study: a simulation using whole-genome sequences from rice

This study shows that combining target populations with more diverse populations improves GWAS power for detecting QTNs, depending on genetic diversity metrics like FST and He.

Haplotype-based genome wide association study using a novel SNP-set method : RAINBOW

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.

Reconstruction of networks with direct and indirect genetic 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.