Genome-Wide Association Study and Identification of Core Candidate Genes for Shoot and Root Length in Wheat During Germination

Genetic diversity, GWAS, and candidate genes identification for plant architecture traits in maize (Zea mays L.)

Genetic architecture of node-specific leaf length and candidate gene identification in maize revealed by a temperate–tropical multiparental population

Optimizing leaf morphology is essential for improving maize plant architecture, plant density tolerance, and yield. Leaf length is a key agronomic trait controlled by complex genetic mechanisms. In this study, upper leaf length (ULL), ear leaf length (ELL) and lower leaf length (DLL) were evaluated across two environments using a multiparent RIL population derived from crosses between the temperate inbred line Ye107 and three tropical inbred lines. Combined with high-density GBS markers, genome-wide association study (GWAS) and QTL mapping were integrated to dissect the genetic basis of leaf length. Leaf length traits exhibited high heritability (54.85%–76.85%). A total of 133 significant SNPs were identified by GWAS, and 13 candidate regions were detected by QTL localization, among which ql1-17 explained 12.10% of the phenotypic variation. Joint analysis revealed multiple colocalized regions on chromosomes 1, 6 and 8, resulting in the identification of three key candidate genes ZmHUA2 (Zm00001d029223) , ZmCAMTA5 (Zm00001d025235) , and ZmPAT16 (Zm00001d038367) . Haplotype and qRT-PCR analyses showed that favorable haplotypes from tropical parents significantly increased leaf length, and these genes exhibited high expression specificity in the leaf elongation region. This study elucidates the complex genetic architecture of leaf length in temperate × tropical hybrid populations. Through integrated analyses, we identified key genomic loci and prioritized three candidate genes, particularly ZmHUA2 (Zm00001d029223) and ZmCAMTA5 (Zm00001d025235) . These findings provide valuable genomic resources and favorable alleles for marker-assisted selection, establishing a robust theoretical and practical foundation for maize ideotype breeding aimed at optimizing leaf morphology to enhance yield potential under high-density planting conditions.

Genome-wide association study of image-based traits reveals genetic architecture of salt tolerance in rice

Genome-wide association analysis reveals new loci for leaf water status, biomass and plant architectural traits in bread wheat under rainfed conditions

Drought during reproductive development and grain filling is a major constraint to bread wheat productivity in rainfed environments. In the present study, we employed genome-wide association analysis in an untapped diversity panel of wheat genotypes relevant to natural dryland conditions. A total of 186 genotypes were evaluated for drought-related physiological, biomass, and architectural traits under terminal rainfed stress in Azerbaijan. Relative water content, plant height, fresh weight, dry weight, flag leaf length, and flag leaf width were assessed at the milk ripening stage. These data were subjected to genome-wide association analysis using 19,737 SNP markers to identify loci and epistatic interactions involved in the determination of these traits. The panel showed broad phenotypic variation and significant genotypic effects for all traits, with broad-sense heritability ranging from 0.991 for plant height to 0.385 for flag leaf width. GWAS identified a major locus for relative water content on chromosome 2D at SNP marker AX-86184518, which explained 11.94% of the genotypic variation. Candidate-gene analysis highlighted the proximal WEB-family-like gene TraesCS2D03G1001000 as the main candidate gene. Plant height showed strong additive loci, mainly on chromosomes 2A and 4A, whereas biomass and flag leaf traits showed suggestive additive loci and epistatic interactions. These findings provide candidate loci and interaction patterns in the genetic make-up of essential traits, which may facilitate indirect selection in breeding new varieties.

Association Mapping of Seedling Resistance to Fusarium graminearum Root Rot and Development of KASP Assays in Soybean

Soybean root rot caused by Fusarium graminearum is an important soil-borne disease. It hinders seedling establishment and ultimately reduces soybean yield. Resistant germplasm and reliable molecular markers are therefore needed for resistance breeding. In this study, 336 soybean accessions were evaluated for resistance to F. graminearum root rot using the disease severity index (DSI), which ranged from 5.71 to 100.00 across the association panel. Genome-wide association analysis was performed using resequencing-based single nucleotide polymorphism (SNP) data with mixed linear model (MLM) and Fixed and random model Circulating Probability Unification (FarmCPU) models, which detected 117 and 113 candidate resistance-associated SNPs, respectively. Among these, 105 shared SNPs were used to define candidate genomic intervals containing 247 annotated genes. Based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, functional annotation, and allelic-effect analysis, six candidate genes and their associated exonic SNPs were prioritized. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis showed infection-responsive expression patterns for all six candidate genes, with Glyma.17g202500 and Glyma.18g266700 showing stronger induction in the resistant accession. Two SNPs in these genes were converted into Kompetitive allele-specific PCR (KASP) assays. KASP-S17_32244510 and KASP-S18_55105706 were successfully developed for genotype screening, with screening efficiencies of 73.08% and 74.29%, respectively. These findings identify useful genetic targets and molecular markers for improving soybean resistance to root rot caused by F. graminearum.

Integrated Genome-Wide Association and QTL Mapping Elucidate the Genetic Basis of Fruit Yield and Quality Traits in Pepper under Water Stress.

Water deficit is a major constraint on pepper (Capsicum annuum) yield, yet the genetic architecture of reproductive-stage drought tolerance remains poorly resolved. We phenotyped a Balkan C. annuum diversity panel (n = 133) and an interspecific backcross inbred line (BIL) population (n = 76) under well-watered (WW) and water-stress (WS) conditions. WS was applied from anthesis of the second truss as a stepwise reduction in irrigation volume relative to WW (30% for 7 days, then 60% thereafter), maintained for 90 days across the reproductive period. We assessed yield components, soluble solids, and stress-tolerance (STI) and stress-susceptibility (SSI) indices. Genome-wide association study (GWAS) identified 104 SNP-trait associations (P < 1×10-5), and QTL mapping detected 38 significant QTLs (1,000 permutations, α = 0.01), with the QTL intervals defined at LOD ≥ 8. Integrating GWAS and QTL mapping under WS revealed overlapping loci on chromosomes 5 and 6, harboring two consensus intergenic SNPs associated with yield components and soluble solids. Haplotype analysis linked chromosome 5 alleles to higher fruit number and soluble solids. At chromosome 6, the G allele at SNP 6_28348737 was enriched in tolerant lines for fruit number. These regions harbor candidate genes for reproductive development and stress response, including GREEN RIPE-LIKE1 (GRL1), CYP77A19, Endoglucanase-like, and FLOWERING PROMOTING FACTOR 1 (FPF1), possibly through cis-regulatory variation. Together, these results advance understanding of the genetic basis of pepper yield under drought and identify candidate breeding markers.