Editorial: Genomics-driven advances in crop productivity and stress resilience

Parimalan Rangan^1,2*Robert Henry²Ambika Baldev Gaikwad¹

• ¹National Bureau of Plant Genetic Resources, Indian Council of Agricultural Research (ICAR), New Delhi, India
• ²Queensland Alliance for Agriculture and Food Innovation, Saint Lucia, Australia

Scaling-up crop productivity in response to climate change is critical to feed sustainably the ever-growing population. The rate of genetic gain being achieved in recent decades needs to be augmented to satisfy this demand (van Dijk et al., 2021;Hunter et al., 2017). Genomic selection and gene editing strategies for de novo domestication or breaking linkage drag and genetic incompatibility barriers are genomics-driven tools demonstrated to enhance crop productivity and stress resilience. Strategies like landscape genomics, that accommodates environmental variables too, enhance the potential utilization of genebank collections, including crop wild relatives (CWRs) and 'exotic genetic libraries' through identification of appropriate accessions for utilization (Bohra et al., 2022;Campbell et al., 2025;Shrestha et al., 2025).Genomics tools also help gain novel insights on the genetic and epigenetic mechanism associated with stress resilience traits and the factors to be targeted for enhanced crop productivity (Bailey-Serres et al., 2019;Gupta, 2025;Lohani et al., 2025;Miryeganeh, 2025). Understanding the role of the interplay of various components such as the transposable elements (Tossolini et al., 2025) or secondary metabolites (Khan, 2025) or small peptides (Xiao et al., 2025) in influencing stress resilience will help devise strategies to utilize genomics tools for improving crop plants and crop diversification (Wang et al., 2025).Here, Krishnan et al. have demonstrated the applicability of genomics assisted tools in a wide-hybridization program involving a heat tolerant diploid wild wheat Aegilops speltoides accession and a Triticum durum accession to derive a backcross introgression line (BIL) population. Using this population for a marker-assisted-selection (MAS), the research group identified 30 QTLs for heat stress tolerance using molecular breeding and genotyping-by-sequencing (GBS) approaches involving both SSR and SNP markers to map the QTLs. Linkage disequilibrium (LD) decay values calculated using Tasselv5.0 helped them to target 21 candidate genes associated with heat stress tolerance. The most prominent targets based on functional annotation were: cytochrome P450, ABC transporters, E3 ubiquitin-protein ligase, Alcohol dehydrogenase, F-box family, and MYB family. Similarly, in grapevine berries, Heinekamp et al. used a mapping population (Calardis Musque x Villard Blanc) and important cultivars like 'Calardis Blanc' (sunburn resilient cultivar) totaling to a population of 150 for phenotypic evaluation for sunburn resilience in addition to fungal resistance of grapevine cultivars. Using composite interval mapping (CIM) approach with five years' phenotypic data, along with a genetic map for grapevine, they successfully identified two QTLs that explains roughly 40% of the phenotypic variance and were found to be on chromosome 10 and 11. With a greater number of heat waves in recent years, climate-change adapted cultivars that are resistant to fungus and are sunburn resilient are required for sustained viticulture to ensure high yield and wine quality.Using a population genomics approach, Zhang et al. demonstrated the influence of low temperature in exerting selection pressure on various plant traits during adaptation in a Kandelia obovata population. To accomplish this, the team introduced a population of K. obovata from Zhangzhou (ZZ) to two different locations, Quanzhou (QZ, 2003) and Wenzhou (WZ, 2005). Morphological differences were observed at the two sites. To understand the underlying genetics for this variation, they used a whole genome resequencing approach and identified the SNPs that varied between the original habitat and the introduced habitat. The positive selection for genes associated with the SNPs (from the northern province WZ) were analyzed to reveal candidate genes linking especially to cold tolerance traits and glutathione metabolism. Analysis of their promoter sequence (extracted upto 2 kbp) showed enrichment of elements mostly linked to stress tolerance like stress-responsive, low temperature-responsive, wound-responsive, and abscisic acid (ABA)-responsive elements.To achieve drought stress resilience in tropical maize and lettuce, de Pontes et al. and Medina-Lozano et al. utilized different genomics tools to identify candidate genes in these crops.Using 360 maize inbred lines, SNP-array genotype data from an Affymetrix platform and GBS approaches, the researchers identified drought associated SNPs and in turn the underlying candidate genes through genome-wide association studies (GWAS). The candidate genes were annotated to be associated with key pathways like ethylene biosynthesis, jasmonic acid biosynthesis, gibberellin biosynthesis, ABA biosynthesis, and specific protein families like TPR and PPR family, PR protein family, MYB family, and genes like shoot gravitrophism 5, and circadian clock genes. These findings will contribute to improve maize cultivars tailored with drought resilience for sustained yield improvement. In the case of lettuce, the authors used an RNA-seq approach to study the differential expression between the lettuce cultivar 'Romired' and a lettuce wild relative Lactuca homblei. The latter is known to significantly over-express the anthocyanins during drought. Through this study, they have identified 36 genes and roughly 50% of them were linked with the phenylpropanoid-flavonoid pathway. The other genes were annotated to be associated with stomatal closure, phospholipases, and transcription factors like MYB, NAC56, PRA1, HSC70, and ZAT1. This gives an understanding of the drought-mediated anthocyanin pathway regulation for use in imparting drought resilience from the wild species into cultivated lettuce.In order to promote molecular breeding and marker-assisted development of newer cultivars for the ornamental plant Cymbidium ensifolium, Shen et al. utilized the double digest restriction site-assisted DNA sequencing (ddRAD-seq) technique to sequence 50 commercially available cultivars and identified around 1.2 million high-quality SNPs. From these SNPs, kompetitive allele-specific PCR (KASP) primers were designed and used it to screen the cultivars and found that 11 of the final 28 KASP markers are sufficient to distinguish the 83 cultivars tested.In an effort to generate a single circular mitochondrial genome for a decaploid (octaploids are also available) species, Camellia hainanica, Zhang et al. had used Illumina shortread and Nanopore long-read sequencing technologies to generate raw After initial filters of raw data using fastpv0.20.0 and filtlongv0.2.1, the data were mapped against plant mitochondrial core genes using Minimap2 to extract the mitochondrial sequences for assembly using SPAdesv3.15.4, yielding a single circular mitochondrial genome of length 902,617 bp.The mitochondrial genome was annotated for genes (protein-coding and non-coding) and SSR markers.The value of conserving germplasm is realized when it is practically utilized in a breeding program to develop cultivars introgressed with key desirable traits from germplasm which are otherwise difficult to introduce. He et al. evaluated 361 soybean germplasm accessions, comprising six maturity groups, for 100-seed weight (100SW) and seed oil content (SOC) variability. Using a restricted two-stage multi-locus genome-wide association study (RTM-GWAS) approach, LD blocks comprising 230 and 299 alleles, respectively for 100SW and SOC were identified. Gene annotation studies revealed 87 and 132 candidate genes for 100SW and SOC traits, respectively. Promising genes for 100SW were vacuolar proton ATPase A3 and clathrin adaptor complexes. The most promising gene for SOC was identified to be a HAD superfamily phosphatase gene. Genomic selection models using the data for 361 soybean germplasm helped predict the recombination potential for the two traits of study, 100SW (upto 30.43 g) and SOC (upto 27.73%). The model that fits based on priority traits can be chosen for implementing in a breeding program to improve oil yield. Zhernova et al. reviewed the genetic markers available for the improvement of flax (Linum usitatissimum), being widely grown for oil and fiber. This review underscores the markers identified for various traits of interest including biotic and abiotic stress tolerance. This compiled information will be a ready-to-use for markerassisted flax improvement.To conclude, the enormous growth in data generation and computational power that drives accelerated crop improvement has transformed genomics applications for innovations.Notable advances include, the move from a single-reference to a pan-genome reference (Ruperao et al., 2025), understanding the synergy of microbiome for crop improvement with special reference to yield and stress resilience (Xu et al., 2025;Ge and Wang, 2025), identification of susceptibility genes (Baruah et al., 2025), and de novo domestication and rational redomestication (Wang et al., 2025); will lead research for the upcoming decades to address the challenges of sustainable agriculture.