Genomics-Assisted Breeding for Drought Tolerance in Wheat (Triticum aestivum L.): Recent Advances and Future Prospects

Phenotypic variation in drought response for a double-haploid population of bread wheat (Triticum aestivum)

Emerging molecular strategies to improve drought tolerance in barley Hordeum vulgare L.)

The validated hub genes may serve as promising candidate targets for the development of functional markers in marker-assisted selection (MAS), potentially facilitating early-stage screening and pyramiding of drought-tolerant alleles in barley breeding programs, pending experimental validation.

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.

A systems breeding framework integrating pangenomics multiomics phenomics and precision genome editing for reproductive stage drought resilience in rice

Rice (Oryza sativa L.) is highly vulnerable to drought during the reproductive phase, with yield losses exceeding 50% due to spikelet sterility, pollen abortion, and impaired grain filling. Progress through conventional breeding has been constrained by the polygenic nature of drought tolerance and by strong genotype × environment (G × E) interactions. This review proposes a systems breeding strategy integrating five complementary approaches rice pangenomics, genome-wide association studies (GWAS), genomic selection (GS), high-throughput phenomics, and precision genome editing to strengthen drought resilience at the reproductive stage. Structural variants identified through pangenome analyses across diverse Oryza accessions have been implicated in abscisic acid (ABA) signalling, osmolyte biosynthesis, antioxidant defence, and root system architecture pathways central to reproductive-stage drought adaptation. Multi-omics-informed GWAS, combined with co-localisation of eQTLs and protein QTLs in drought-stressed reproductive tissues, highlights high-confidence candidate genes including OsNAC14, OsbZIP23, and DRO1 that help explain the physiological basis of water-deficit adaptation. Incorporating envirotyping data into GS models has been shown to improve predictive accuracy across diverse rainfed environments. Alongside marker-assisted selection, base editing and prime editing enable targeted allelic refinement with minimal off-target effects. We present a proposed tiered candidate prioritisation pipeline that advances loci supported by convergent genomic, transcriptomic, proteomic, and field-level evidence toward practical breeding deployment. Translating these discoveries into climate-resilient varieties will require FAIR data sharing, coordinated phenotyping networks, and multi-environment validation platforms linking genomic discovery to scalable breeding pipelines for drought-resistant, high-yielding rice in rainfed systems.

Exploring genetic diversity and stress adaptation in bread wheat (Triticum aestivum L.) under terminal heat stress

Integrated BSA-seq and RNA-seq analyses reveal CmRABE1c as a negative regulator of drought tolerance and enable the development of a promoter SNP marker in Chinese chestnut

Drought stress severely limits both yield and nut quality of Chinese chestnut (Castanea mollissima Blume), an economically and ecologically important woody grain species native to China. However, the genetic basis of drought tolerance in Chinese chestnut remains a research gap. Our study fills this gap by identifying novel drought-responsive genes, which represents the first comprehensive molecular characterization of drought adaptation in this species. To dissect the genetic basis of drought tolerance and develop functional markers, we investigated 316 F1 seedlings derived from the cross between the drought-tolerant ‘Yanlong’ cultivar and the drought-sensitive ‘Shuofeng’. Bulked segregant analysis coupled with next-generation sequencing (BSA-seq) identified 80 drought-associated quantitative trait loci (QTLs) across 12 chromosomes. Integration of BSA−seq, RNA-seq, and parental resequencing resulted in the identification of a core candidate gene, CmRABE1c, encoding a ras-related protein. CmRABE1c overexpression in tobacco and poplar confirmed its negative regulatory role in drought tolerance. Notably, a GG-to-AA substitution at -312/-313 bp in the CmRABE1c promoter disrupted the GT1-motif and was significantly associated with drought tolerance across 60 chestnut accessions. Furthermore, transgenic tobacco and poplar assays proved this SNP may be diagnostic by showing that the AA allele confers superior drought tolerance compared to the GG allele. This diagnostic marker likely can be directly applied in marker-assisted selection (MAS) to screen and develop drought-tolerant chestnut cultivars, thereby accelerating breeding efficiency. In summary, this study provides valuable genetic resources and a robust functional SNP marker for drought resistance breeding in Chinese chestnut.