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

Genome-wide association identifies and validates genomic region controlling grain yield and agronomic traits in extra-early orange maize inbred lines under drought

In order to meet the expected maize yield by 2050, breeders must work to improve breeding program efficiency by intensifying the implementation of new and improved technologies such as marker-assisted selection (MAS). Dissecting the genomic regions associated with drought tolerance is the first step forward in MAS program deployment for maize improvement under drought stress. Genome-wide association studies (GWAS) were used to investigate and identify quantitative trait loci (QTLs) associated with six traits under drought stress. One hundred and eighty-seven extra-early orange maize inbred lines were evaluated under managed drought stress at Ikenne, in Nigeria, during the 2022 and 2023 dry seasons. The materials were also genotyped using 9355 DArTseq SNP markers and analyzed using the enriched compressed mixed linear model (ECMLM). Enriched compressed mixed linear model was used for association-trait analysis. The ECMLM-based GWAS identified 45 candidate genomic loci associated with the six traits, including five for grain yield, with R2 ranging from 8.79 to 25.3%. Independent validation using the multi-locus 3VmrMLM approach confirmed seven high-confidence genomic loci consistently detected by both methods across grain yield, anthesis-silking interval, ear aspect, and ears per plant, providing additional statistical support for these genomic regions. Candidate gene annotation identified biologically relevant genes underlying the validated loci, including Zm00001eb238250 (protein-serine/threonine phosphatase), Zm00001eb040940 (trehalose-phosphatase), Zm00001eb117820 (homeobox protein knotted-1-like 4), Zm00001eb145560 (zinc ion-binding protein), and Zm00001eb294180 (WRKY DNA-binding domain protein), suggesting their potential roles in drought adaptation and grain productivity. These findings improve our understanding of the genetic architecture of drought tolerance in extra-early orange maize and provide valuable genomic resources for accelerating drought-resilient maize breeding.

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.

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.

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

Mapping the genetic architecture of flowering and maturity in soybean [Glycine max (L.) Merr.] using multi-locus genome-wide association studies under Ethiopian conditions

Evaluating the stability and drought tolerance of maize hybrids using multi-environment and multi-trait analyses

Abstract Drought remains a major constraint on maize productivity in tropical environments. Consequently, maize requires the identification of hybrids that combine high yield with stability across variable conditions. Ten tropical maize hybrids (eight promising candidates and two commercial checks) were evaluated across five environments (three optimal and two drought-stressed) using a randomized complete block design. Significant genotype, environment, and G × E effects (p < 0.01) were detected for nearly all traits, confirming substantial phenotypic variability. Drought stress reduced grain yield by 32.34%, primarily due to declines in ear weight and kernel size. Based on stress tolerance indices, GGE biplot, and WAASB analysis, hybrids G01, G02, and G08 were identified as the most drought-tolerant genotypes with broad stability. MGIDI further confirmed these selections, with G01 specifically achieving the lowest multi-trait distance to the ideotype under both optimal (1.12) and drought conditions (0.56). These results support the recommendation of these superior hybrids for deployment in tropical maize production systems prone to water deficit.