The review, published in Discover Agriculture, synthesizes decades of research and field practice from salt-hit regions spanning South Asia, the Middle East, Australia and beyond. It arrives at a moment when the problem is accelerating. Rising seas, erratic monsoons, and irrigation with poor-quality water are pushing salts into soils faster than nature can flush them out. Ten countries, including Australia, Argentina, China, Kazakhstan, the Russian Federation, the United States, Iran, Sudan and Uzbekistan, account for 70 percent of the world’s salt-affected soils. Bangladesh alone has 1.16 million hectares of saline land, roughly 68 percent of its coastal arable area, with cumulative yield losses across crops estimated in the thousands of metric tons.

The science behind the damage is unforgiving. Dissolved salts in soil solution, dominated by sodium, calcium, magnesium, chloride, sulfate and carbonate ions, create a double bind for plants. First, high concentrations of salts in the soil solution raise its osmotic pressure, making it harder for roots to extract water even when the soil is physically wet. Farmers call this physiological drought: the plant wilts while sitting in moist soil. Second, specific ions, particularly sodium (Na+) and chloride (Cl−), accumulate to toxic levels inside plant tissues, disrupting enzyme function, nutrient uptake and photosynthesis. The osmotic stress also forces plants to divert energy into defensive chemistry, producing abscisic acid signaling, closing stomata, and activating genes and proteins that regulate ionic homeostasis, all of which cost the crop yield.

Salinity’s fingerprint extends beyond the plant itself. Sodium’s positive charge makes it cling to clay particles, dispersing them and clogging the pores through which water and air move. Saline soils become firm and compact, resisting root penetration and infiltration, so even a fertile field behaves like an infertile one. Below ground, the microbial community suffers too: salinity suppresses microbial diversity and enzymatic activity, slowing the decomposition of organic matter and the cycling of nutrients. Only halophytic microbes, those evolutionarily adapted to salty conditions, continue functioning at moderate salinity. Meanwhile, nitrogenous fertilizers applied to saline soils leak away more rapidly as gaseous losses of nitrous oxide and ammonia, because nitrification activity is impaired. Research on cotton has even documented lower phenol and proline content in plants grown on saline versus non-saline soils, a biochemical signature of chronic stress.

Not all salt is created equal, and the review draws a careful distinction between two chemically distinct salinity regimes. Chloride-dominated salinity, driven by sodium chloride along with calcium, magnesium and potassium chlorides, is the more aggressive form. Chlorides make up an estimated 50 to 80 percent of salts in many affected soils, and because sodium chloride is highly soluble, electrical conductivity in the soil spikes sharply, intensifying the osmotic stress on crops. Chloride can be directly toxic to glycophytic crops such as potato, citrus and beans, which lack the evolutionary machinery to filter, regulate or safely compartmentalize these ions. Sulfate-dominated salinity, common in gypsum-rich geological formations across Pakistan, India, Iran, Iraq, the southwestern United States and North Africa, is generally less toxic, particularly when calcium sulfate is the dominant salt. Its lower solubility translates to lower electrical conductivity, weaker osmotic effects, and reduced sodium uptake by plants. Ironically, gypsum in sulfate-affected soils can actually improve soil structure and reduce sodicity, the condition where a high sodium adsorption ratio destroys soil architecture.

The severity of the problem is quantified by electrical conductivity (EC), measured in deci-Siemens per meter. Soils below 2 dS/m are considered non-saline and ideal for growth. From 2 to 4 dS/m, only sensitive crops begin to suffer. Between 4 and 8 dS/m, only salt-tolerant species can be expected to yield well, and above 8 dS/m, cultivation becomes genuinely challenging. Beyond 16 dS/m, only halophytes survive, and reclamation becomes a long-term project. It is against this gradient that the review evaluates its two great families of solutions.

The first family is genetic. Plant breeders have developed varieties that either tolerate salt internally or escape its worst effects. In rice, the review catalogs a remarkable roster of tolerant cultivars: BRRI dhan67, BRRI dhan112, BRRI dhan97, BRRI dhan99, Binadhan-8, Binadhan-9, Binadhan-10, BRRI dhan47, BRRI dhan53, BRRI dhan54, and the hybrid Hira-2 from Bangladesh, alongside the CSR series (CSR56, CSR60, CSR36, CSR23, CSR13, CSR27, CSR10, CSR52, CSR49, CSR46, CSR43) from India’s Central Soil Salinity Research Institute. Wheat varieties such as GAU Wheat-1, BARI Gom-25, BARI Gom-28, and the KRL series (KRL 1-4, KRL 19, KRL 210, KRL 213, KRL 283) offer similar protection. Salt-tolerant releases now exist for potato (BARI Alu-72), tomato, brinjal (BARI Begun-1 and BARI Hybrid 2), mustard (CS 52, CS 54, CS 56, CS 58, CS 60, plus mutants RM-13 and RM-14), and lentil (PDL-1, PSL-9). Beyond bred varieties, the authors note intrinsic tolerance patterns across species: date palm, barley, sugar beet, cotton and spinach are highly salt-tolerant, while wheat, maize, onion, olive and grape occupy the moderate tier. The biological machinery underlying this tolerance is increasingly well understood, from ancestral sodium transporter genes that improve wheat yields on saline soils to the SOS2 signaling pathway in Arabidopsis, where phytochromes phosphorylate and degrade growth regulators to prioritize survival.

The second family is agronomic, and this is where the review becomes most vividly practical. Farm-pond technology, a technique proven in coastal Bangladesh, carves a mini pond occupying 10 to 15 percent of a plot, typically 3 to 4 meters deep, to harvest fresh rainwater for irrigating vegetables and pulses. The excavated soil is used to raise the surrounding plot, improving drainage simultaneously. Pitcher irrigation, a traditional method now refined by researchers, buries an earthen pot of 10 to 15 liters with jute-fiber-plugged holes near pit crops such as sweet gourd, watermelon and bitter gourd, delivering water slowly and efficiently, keeping root-zone salinity within 3.0 to 4.0 dS/m even where ambient soil salinity ranges from 5.0 to 8.0 dS/m. Double-layer mulching places organic materials such as straw, sawdust or water hyacinth both below and above the seed zone, physically blocking the capillary rise of saline water and returning salinity levels of 3 to 4 dS/m back to productivity. The shallow ridge-furrow system shapes heavy-textured saline soils into low ridges, keeping crops above the worst salt accumulation and safe from sudden waterlogging, allowing earlier planting.

More ingenious still are the land-shaping strategies borrowed from farming communities across the Bay of Bengal. On the raised banks of shrimp and fish ponds, farmers grow tomatoes, beans, gourds and chili with zero tillage and minimal crop protection costs, exploiting the fertile basin soil and the elevated position that keeps salts away from the root zone. Economic analyses from Bangladesh report returns of around 20,395 taka per hectare from a single vegetable cycle on shrimp pond banks, rising to 35,457 taka with simultaneous culture, and 127,000 taka when rice, prawn and dike vegetables are combined. Sorjan farming, an Indonesian technique now spreading through coastal Bangladesh, alternates deep furrows with high raised beds; the beds host upland crops while the furrows store dry-season water, and farmers routinely scoop organic-matter-rich sediment from the canals back onto the beds. Flying bed cropping goes further still, suspending growing beds above the soil surface to escape capillary salt rise entirely, enabling year-round cultivation of high-value crops on otherwise hopeless land.

Where fresh water is scarce, timing and blending become weapons. The rice variety BRRI dhan47 tolerates up to 12 dS/m at the seedling stage but only 6 dS/m when mature, so farmers can alternate saline and fresh water according to the crop’s sensitivity window. Mapping and characterization using remote sensing and machine learning identifies which polygons of a landscape carry which salinity levels, guiding crop selection before seed touches soil. Microbial management deploys halotolerant bacteria such as Bacillus, Pseudomonas and Azospirillum, and commercial bio-formulations like CSR-BIO, a consortium of Bacillus pumilus, B. thuringiensis and Trichoderma harzianum, which mobilize nutrients, synthesize phytohormones and restore ionic balance in the rhizosphere. Endophytic bacteria boost extracellular enzymes such as amylase, protease and cellulase while mitigating potassium imbalances. Chemical amendments, chiefly gypsum, elemental sulfur and sulfuric acid, displace sodium from the exchange complex with calcium, leaching the harm out of the root zone. Organic amendments, including compost, green manure, biochar, straw and corn husk, restore the roughly 5 percent organic matter content that healthy soil needs to buffer salts, hold water and house microbes. Leaching with fresh water works best on light-textured soils over deep water tables, while sound surface and subsurface drainage prevents the waterlogging that breeds salinity in the first place. Regular monitoring of soil electrical conductivity lets farmers anticipate peak salt risk and act before damage occurs.

The authors conclude that saline soil management is inherently site-specific, spatial and sometimes transient, and that the agronomic toolkit, however effective up to 8.0 dS/m and occasionally 16.0 dS/m, offers temporary relief while genetic solutions are durable but slow and expensive to develop. Climate change, sea-level rise and unpredictable weather will keep raising the stakes. What they call for, ultimately, is a global technology transfer mechanism, a shared knowledge bank that would let Bangladesh’s pitcher irrigation, India’s CSR-BIO microbes and Indonesia’s Sorjan beds flow freely to the farmers who need them, reducing monetary investment and, in the process, protecting the world’s food supply from one of its most patient and pervasive enemies.

The scale of the underlying problem is difficult to overstate. According to recent global assessments, including the Food and Agriculture Organization’s 2024 report on salt-affected soils and a 2021 modeling study in Nature Communications predicting widespread primary soil salinization under climate change, hundreds of millions of hectares of arable land are degraded by excess salts and alkaline salts. Unlike pure salinity stress, saline-alkali stress combines osmotic pressure, sodium toxicity, and high soil pH, which disrupts nutrient uptake and root development in tandem. Rapeseed (Brassica napus L.), one of the world’s most important oilseed crops and a major source of vegetable oil, is known to tolerate these conditions better than many staple crops, making it a prime candidate for the sustainable utilization and rehabilitation of saline-alkaline soils. Yet breeding improved cultivars has remained slow, relying overwhelmingly on conventional hybridization combined with phenotype-based selection, a process that can take many years to achieve meaningful gains.

To overcome this bottleneck, the research team assembled a catalog of previously reported saline-alkali tolerance genes not only from rapeseed itself but from rice, maize, wheat, sorghum, and the model plant Arabidopsis. This cross-species strategy reflects a growing recognition that the molecular machinery of salt tolerance, including sodium transporters, ion homeostasis regulators, and osmotic adjustment pathways, is broadly conserved across plants. Classic examples include the rice quantitative trait locus encoding a sodium transporter identified in Nature Genetics in 2005, and decades of physiological work by researchers such as Munns and Tester, who dissected the mechanisms by which plants exclude sodium, compartmentalize ions in vacuoles, and maintain potassium nutrition under salt stress. By gathering homologous candidate genes from across these species, the team built a target list that could be mined for natural variation within the rapeseed genome.

The core of the study was a candidate gene-based association analysis. Using resequencing data aligned to the rapeseed reference genome, the researchers identified genetic variants, including single nucleotide polymorphisms and insertion-deletion (InDel) polymorphisms, within and around the candidate genes, then tested whether specific variants were statistically associated with saline-alkali tolerance traits in a diverse rapeseed population. Association analyses of this kind rely on mixed-model statistical frameworks, such as those implemented in widely used tools like GEMMA and PLINK, to correct for population structure and relatedness that would otherwise produce spurious correlations. The team’s rigorous approach, incorporating false discovery rate control using methods descended from the Benjamini-Hochberg procedure, paid off: 483 genes were found to be significantly associated with tolerance, and among these, 355 genes contained favorable haplotypes, meaning particular combinations of alleles linked to better performance under saline-alkali conditions.

From these significantly associated genes, the researchers successfully developed molecular markers for 275 genes. The marker set comprises 746 KASP marker pairs and 201 InDel marker pairs. KASP, or Kompetitive Allele-Specific PCR, is a fluorescence-based genotyping chemistry that distinguishes allele variants using allele-specific primers carrying distinct fluorophore tags, allowing a simple end-point readout of an individual plant’s genotype at each locus. It has become a workhorse of modern crop breeding because it is relatively inexpensive, highly accurate, and amenable to high-throughput automation, particularly when coupled to scoring systems that separate samples into clean genotype clusters. InDel markers, by contrast, exploit small insertions and deletions in the genome and provide a complementary, often co-dominant means of tracking chromosome segments during crossing. Four marker pairs were randomly selected from the newly developed set and experimentally validated, confirming that the markers faithfully distinguish the intended alleles.

In parallel with the marker development, the team constructed a 5K cGPS liquid-phase genotyping chip, designated HZSW-cGPS-BRNAP-04. Unlike traditional silicon-based solid chips, liquid-phase chips rely on targeted sequencing of a predefined panel of loci, in this case roughly 5,000 informative sites distributed across the rapeseed genome and concentrated in regions relevant to saline-alkali tolerance. The performance testing showed a high call rate, meaning the proportion of loci successfully genotyped in each sample, and excellent reproducibility, indicating that repeated genotyping of the same material yields consistent results. These quality metrics are essential for a breeding tool: a chip that fails to call genotypes reliably at low cost cannot support the routine screening of thousands of seedlings. Liquid-phase designs also offer flexibility, since marker panels can be updated as new tolerance loci are discovered, and they sidestep some of the manufacturing rigidity and cost constraints of fixed microarray platforms.

The practical payoff lies in marker-assisted selection, or MAS. In a conventional rapeseed breeding program, a breeder crosses a tolerant parent with a high-yielding elite cultivar, then spends generations measuring performance in saline field nurseries, an expensive and weather-dependent process complicated by the fact that tolerance is a quantitative trait influenced by many genes and strongly affected by the environment. With the new marker set, breeders can instead screen seedlings in trays with a few drops of DNA extract, identifying which individuals carry the favorable alleles at 275 tolerance-associated genes within days of germination. This early-generation evaluation allows breeders to discard susceptible material before it ever reaches the field, stack multiple favorable haplotypes in a single line through repeated crossing, and dramatically compress the timeline for delivering tolerant cultivars to farmers. The approach also lays the groundwork for molecular design breeding, in which crosses are planned computationally by combining known favorable alleles across the genome, and the study’s data on haplotypes and associated genes provide a functional framework for such designs.

The choice of rapeseed is itself a strategic one. The crop has emerged as a leading candidate for “green rehabilitation” of degraded land, because a crop that tolerates saline-alkali conditions both produces oil on otherwise unproductive soil and can contribute to improving soil properties through cultivation. Prior work by some of the same groups, including genome-wide association studies of salt tolerance traits in rapeseed and transcriptomic and metabolomic dissection of the elite salt-tolerant cultivar Huayouza 62, had accumulated the genetic and mechanistic knowledge that made marker development feasible. The new study consolidates that dispersed knowledge, much of it scattered across candidate gene reports from six species, into a single, validated, breeding-ready toolkit. The pan-genome resources now available for B. napus, built from multiple high-quality assemblies, further ensured that the markers capture the allelic diversity present in the species rather than the variants of a single reference line.

Funding for the work came from China’s agricultural science and technology renovation programs, the STI 2030 major project, and the Natural Science Foundation of China, reflecting the national priority placed on reclaiming saline-alkaline land, a matter of acute significance given that China alone holds tens of millions of hectares of salt-affected soils, with substantial acreage in the Xinjiang region where co-authors from the Xinjiang Academy of Agricultural Sciences are based. The authors note that the markers and the HZSW-cGPS-BRNAP-04 chip are expected to improve the breeding efficiency of saline-alkaline-tolerant rapeseed cultivars, and the supplementary data accompanying the paper, released as a downloadable file, should allow breeding programs in other countries to adopt the tools directly.

More broadly, the study illustrates how the pieces of modern plant genetics can be assembled into a working pipeline: conserved candidate genes from comparative genomics, dense sequence variation from resequencing, statistical association mapping, and high-throughput genotyping chemistry, all converging on a single agronomic goal. As climate change accelerates soil salinization and pressure mounts to feed a growing population without expanding cropland, tools that let breeders select for resilience in a petri dish rather than a salt field may prove among the most consequential innovations in crop improvement. For rapeseed, the path from laboratory marker to a saline-alkali-tolerant cultivar standing in a rehabilitated field just became considerably shorter.