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

Genome wide association mapping of yield and agro-morphological traits under drought and heat stress in wheat (Triticum aestivum L.)

Genome-wide association study reveals marker-trait associations for key agronomic and grain quality traits in durum wheat under rainfed and irrigated conditions in Turkish environments

Multi-Environment Multi-Locus Association Mapping Reveals Genomic Regions for Drought-Related Traits in Tropical Maize.

Maize grain yield is frequently constrained by water scarcity, particularly in tropical regions characterized by irregular rainfall patterns. Dissecting the genetic basis of drought-related traits remains challenging because their expression is strongly influenced by environmental conditions. In this study, we applied a multi-environment multi-locus genome-wide association study (MEML-GWAS) to identify genomic regions associated with drought-related traits in tropical maize. The association panel comprised 190 inbred lines from the Embrapa breeding program, which were genotyped with 500,108 GBS-derived SNPs, and crossed with two tester lines. Phenotypic data corresponded to the performance of the testcross hybrids, divided in Dent and Flint heterotic groups, evaluated across two years at two locations in Brazil under well-watered and water-stressed conditions. Traits analyzed included grain yield, anthesis-silking interval, female and male flowering time, and plant and ear height. Drought stress reduced grain yield by approximately 50% and increased the anthesis-silking interval by about two days. A total of 179 significant SNP-trait associations were detected, of which 166 showed significant SNP-by-environment interaction effects, while 13 displayed stable effects across environments. Several associations were detected specifically under water-stressed conditions, highlighting genomic regions potentially involved in drought adaptation. Functional annotation revealed candidate genes previously implicated in abiotic stress responses, including ZmTIP1, which encodes an S-acyltransferase regulating root hair development and drought tolerance. Among the novel candidate genes, GRMZM2G159125, encoding a phospholipase D, emerged as a particularly promising candidate due to its strong association with grain yield and its role in membrane lipid signaling pathways related to stress responses. Although a few associations overlapped genomic regions previously reported for drought tolerance in maize, most loci represent potentially novel genetic factors that may contribute to improving drought resilience in tropical maize breeding programs.

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.

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 and Identification of Core Candidate Genes for Shoot and Root Length in Wheat During Germination

The genetic architecture and core candidate genes for shoot length (SL) and root length (RL) at the germination stage are dissected and seven core candidate genes for SL and 13 for RL are identified, including three pleiotropic genes regulating both traits.