Dissecting the genetic basis underlying drought tolerance at different development stages in soybean

Identification of QTLs for Yield and Yield Related Traits under Reproductive Stage Drought Stress

Reproductive-stage drought stress can substantially reduce rice productivity, making the identification of drought-responsive loci relevant to breeding. This study aimed to detect phenotypic variation and identify QTLs associated with yield and yield-related traits under reproductive-stage drought stress. Drought stress is one of the major challenges in agriculture, particularly in rice production, and has significant negative impacts on rice growth and yield. Reproductive-stage drought stress is an important yield-reducing factor in rain-fed rice production. Therefore, identifying grain yield-related quantitative trait loci (QTLs) during the reproductive stage may provide additional benefits for marker-assisted breeding. This experiment was carried out at the Department of New Genetics, Yezin Agricultural University, Nay Pyi Taw, from August 2025 to January 2026 using a randomized complete block design (RCBD) with three replications under two conditions: 100% field capacity (control) and 50% field capacity (drought). Significant differences were observed in yield and yield-attributing variables. Eleven QTLs were identified for six traits: plant height, panicle length, days to 50% flowering, spikelets per panicle, filled grain percentage, and 1000-grain weight. Two QTLs for plant height were identified on chromosomes 1 and 5, with R2 values of 44.58% and 9.79% and LOD values of 11.12 and 3.68, respectively. The QTL for panicle length, qPL5, was identified on chromosome 5, with an R2 value of 16.25%. Four QTLs (qDTF1.1, qDTF1.2, qDTF6, and qDTF10) were identified on chromosomes 1, 6, and 10 for days to 50% flowering. One QTL each was identified for spikelets per panicle and filled grain percentage (qSPP5 and qFGP8, respectively). For 1000-grain weight, two QTLs, qTGW1 and qTGW3, were identified on chromosomes 1 and 3. These QTLs may be useful for marker-assisted breeding of rice with improved resilience to climate change, particularly drought.

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.

Genomic and genetic dissection underlying seedling drought resilience in oats

Drought threatens global crop yields, and common oat, a vital nutritional source for food and feed, is particularly constrained in the semi‑arid regions where it is widely cultivated. Here, we report two high-quality genome assemblies for drought-resilient (Borris37) and drought-sensitive (XymC06) oat accessions with distinct seedling survival rates and genome sizes of 10.92 Gb and 10.96 Gb, and construct comprehensive landscapes of insertion‑deletions (InDels) and structural variants (SVs). Integrating population-level genomic, transcriptomic and phenotypic (seedling survival rate), we demonstrate that InDels and SVs underpin divergent drought resilience and identify 52 candidate genes associated with drought resistance whose expression is significantly modulated by these variants. Borris37 accumulates 36 favorable alleles of these genes. An InDel in the AsNF-YB3 promoter enhances binding to AsARF1, upregulating AsNF‑YB3 under drought, and overexpression of AsNF‑YB3 reduces ROS accumulation. Our findings provide resources and targets for drought‑resistance breeding in oat, thereby supporting global food security. Drought severely constrains common oat production. By generating genome assemblies for oat accessions with contrasting drought tolerance, the authors identify genetic variants and candidate genes underlying drought resistance, including an NF-Y transcription factor and its putative upstream regulator.

Unravelling genetic variation in drought QTL pyramided lines to identify key traits for drought tolerance in rice

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 Identifies Candidate Genes for Salt Tolerance in Soybean at Emergence and Seedling Stages

Simple Summary Soil salinization is an expanding threat to soybean production worldwide. Resolving the genetic basis of salt tolerance at early growth stages supports the development of resilient cultivars. In this study, we evaluated 256 soybean accessions for salt tolerance at emergence and seedling stages and conducted genome-wide association analysis (GWAS) using a high-density single nucleotide polymorphism (SNP) array. We identified 19 genomic regions (quantitative trait loci, QTLs) associated with salt tolerance, including 16 at the emergence stage and 3 at the seedling stage, along with four putative candidate genes with predicted functions in stress responses. Salt tolerance at the two developmental stages was weakly correlated, indicating that tolerance is stage-specific and that at each stage requires separate selection. These findings provide genetic targets for breeding salt-tolerant soybean varieties.