Editorial: Utilizing advanced genomics and biochemical tools to strengthen crop adaptation for biotic and abiotic stresses

Abstract

identification of stripe rust resistance loci in wheat, drought-tolerant clones in sugarcane, and pod borer tolerance genetic loci in pigeonpea. Machine learning approaches prioritized stressassociated genes in maize, while comparative transcriptomics in S. miltiorrhiza revealed MAPK cascade roles in pathogen response and metabolite accumulation. Soybean studies identified genes and pathways that enhance tolerance to drought, salinity, and biotic stresses, including the CAM/CML gene family, which confers dual viral and fungal resistance. Additional insights include drought-responsive microRNAs in wheat and waterlogging resilience in B. napus. A review of genotyping in climate-smart breeding emphasizes the use of integrative tools to accelerate genetic improvement. Therefore, this RT demonstrates how integrating genomics, biochemical profiling, and computational biology can accelerate the development of high-yielding, stress-resilient cultivars as well as helps in contributing to sustainable, climate-smart agriculture.Identification of new genetic resources for drought tolerance-related traits from the world Erianthus germplasm collection (doi.org/10.3389/fpls.2025.1684712)A diverse panel of 223 Erianthus germplasm accessions from seven countries were evaluated under field-imposed drought stress to identify donor clones for sugarcane improvement.Physiological screening and multi-year phenotyping enabled the development of a 91-clone drought response association panel. GWAS using 1,044 high-quality SNPs identified 43 QTNs (quantitative trait nucleotides) associated with drought-adaptive traits. Candidate genes analysis from the identified QTL regions revealed the set of genes involved in stress perception and signaling, including TOR2, TMK1, potassium, and nitrate transporters. These drought-tolerant clones, QTNs, and gene targets provide valuable resources for developing drought-resilient sugarcane cultivars through marker-assisted breeding.Genome wide association studies (GWAS) for identification of stripe rust resistance loci in diverse wheat genotypes (doi.org/10.3389/fpls.2025.1687331) Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), remains a major threat of wheat productivity in North India due to rapidly evolving virulent races. To identify durable resistance, a GWAS was conducted on 652 elite wheat genotypes using 1,938 DArTseq SNPs markers and phenotypic data from four locations. The analysis revealed 27 significant genomic regions associated with stripe rust resistance, including loci on chromosomes 2B, 6A, and 6B. Candidate gene analysis from the QTL region identified defense-related genes such as NBLRR, F-box, LRR, and kinase families. These loci provide strong targets for developing user-friendly markers and accelerating breeding of rust-resistant wheat varieties. This study integrated 39,756 RNA-seq datasets from maize under diverse biotic and abiotic stresses to identify candidate genes for stress resilience. Using seven machine learning-based models and WGCNA, 235 top-ranked genes were prioritized, including hub genes such as Zm00001eb176680 (bZIP transcription factor 68), Zm00001eb176940 (glycine-rich structural protein 2), and Zm00001eb179190 (ALDH11). Promoter analysis revealed enrichment for abscisic acid and antioxidant-responsive elements, suggesting regulatory roles in stress adaptation. These findings provide a comprehensive resource for understanding maize stress responses and offer key molecular targets for functional validation, genome editing, and molecular breeding to develop multi-stress-resilient maize cultivars for sustainable agriculture. This study presents a comprehensive analysis of drought-responsive microRNAs (miRNAs) in drought-tolerant (NI5439) and susceptible (WL711) wheat genotypes under control and drought stress conditions at the booting stage. A total of 364 miRNAs (306 known and 58 novel) were identified from four sRNA libraries. 18 miRNAs showed significant changes in expression after stress treatment, with 2,300 predicted target genes involved in signal transduction, epigenetic regulation, and development. Ten novel miRNAs were validated via qRT-PCR, confirming genotype-specific responses. These findings expand the catalog of drought-responsive miRNAs, providing molecular targets for functional genomics and offering future opportunities for genetic engineering and breeding drought-resilient wheat cultivars. This study evaluated the effect of humic acid (HA) on salt tolerance in four synthetic hexaploid (SH) and three bread wheat (BW) genotypes for physiological, biochemical, and genetic traits. HA enhanced chlorophyll content (33.3-100%), photosynthesis (31.2-50%), and antioxidant enzyme activities (SOD, POD, CAT), while reduced Na⁺/K⁺ ratio (33.3-50%), proline (20-28.5%), and glycine betaine (42.8-77.7%) under salt stress. TaHKT1,4,TaAKT1,TaPRX2A,TaSOD,and TaCAT1) were upregulated, whereas TaP5CS was downregulated, in SH wheat lines, indicating superior tolerance. SH genotypes can serve as a bridge to transfer salt tolerance traits into wheat breeding programs. Future studies should conduct field evaluations across diverse soils and climates to optimize HA application and assess long-term impacts on wheat salt resilience. This review highlights the key role of genotyping and integrative tools in climate-smart plant breeding to enhance crop resilience and productivity. Modern approaches, including genome editing, mutation breeding, multi-omics, microRNAs, and digital technologies, enable precise targeting of loci controlling complex traits and support real-time decision-making. Climate-smart plant breeding innovations are relevant for smallholder farmers across diverse agro-climatic zones, helping crops adapt to climate variability, nutritional demands, and consumer preferences. The article also emphasizes responsible adoption, addressing genetic erosion, biodiversity, and intellectual property concerns. Overall, integrating these tools offers a holistic strategy for sustainable, climate-resilient agricultural systems.