Genomics-assisted breeding for designing salinity-smart future crops

Climate change induces many abiotic stresses, including soil salinity, significantly challenging global agriculture. Salinity stress tolerance (SST) is a complex trait, both physiologically and genetically, and is conferred at various levels of plant functional organization. As both the sustainability and profitability of agricultural production systems are critically dependent on SST, plant breeders are trying to design and develop salinity-smart crop plants capable of thriving under high salinity conditions. The accessibility of extreme-quality reference genomes for cultivated crops, naturally salinity-smart plants, and crop wild relatives has fast-tracked the discovery of key genes and quantitative trait loci (QTLs), marker development, genotyping assays and molecular breeding products with improved SST. Employing fast-forward breeding tools, namely genomic selection (GS), haplotype-based breeding (HBB), artificial intelligence (AI) and high-throughput phenotyping (HTP), has shown influence not only for fast-tracking genetic gains but also for reducing the time and cost of developing commercial cultivars with enhanced SST and yield stability. This review discusses the advancement and prospects of various genomics-assisted breeding (GAB) tools, including genome sequencing, QTL mapping, GWAS, GS, HBB, pan-genomics, single-cell/tissue genomics and phenotyping, epigenomics and transgenomics, to exploit the genetic landscape for improving SST. Additionally, we explore the integration of HTP and AI, which demonstrates how these innovative approaches can optimize breeding efficiency and guide large-scale breeding efforts for designing salinity-smart crops to ensure sustainable agriculture and global food security. The collective adoption of these tools suggests bridging the gap between research and field application to deliver stress-smart varieties designed for saline-affected regions worldwide.