Genetic Dissection and Fine-Mapping of QTL for Salinity Tolerance at the Reproductive Stage on Chromosome 2 of Rice Variety Nona Bokra

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 of image-based traits reveals genetic architecture of salt tolerance in rice

Transgenic evaluations confirmed that OsSLT1 acts as a positive regulator of salt tolerance at the seedling stage, and no significant changes in Na+ or K+ accumulation were observed in flag leaves under the tested salt-stress condition, suggesting that OsSLT1 may regulate salt tolerance through mechanisms beyond classical shoot ion accumulation.

[Quantitative trait locus (QTL) mapping and candidate gene analysis of heat tolerance of rice at heading stage].

Dissecting seed oil content QTL and integrating their genetic effects for genomic prediction in Brassica napus

This study bridges the gap between high-resolution genetic dissection and predictive breeding, providing a practical framework to accelerate oil yield improvement in rapeseed.

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

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.