Regulation of Na+ and K+ homeostasis in plants: towards improved salt stress tolerance in crop plants

Combining GWAS, Genome-Wide Domestication and a Transcriptomic Analysis Reveals the Loci and Natural Alleles of Salt Tolerance in Rice (Oryza sativa L.)

Soil salinity poses a serious threat to the sustainable production of rice (Oryza sativa L.) throughout the world. Thus, the detection of loci and alleles responsible for salt tolerance is fundamental to accelerating the improvement of rice and producing the resilient varieties that will ensure future harvests. In this study, we collected a set of 191 mini-core rice populations from around the world, evaluated their salt tolerance based on plant growth and development phenotypes at the seedling stage, and divided a standard evaluation score (SES) of visual salt injury into five different grades. We used ∼3.82 million single nucleotide polymorphisms (SNPs) to identify 155 significant SNPs and 275 genes associated with salt sensitivity based on a genome-wide association study (GWAS) of SES. In particular, two candidate genes, ZFP179 and OsDSR2, were associated with salt tolerance, and OsHKT1;1 was co-detected in the entire GWAS of all the panels and indica. Additionally, we investigated the transcriptional changes in cultivars 93-11 and PA64s under normal and salinity stress conditions and found 517 co-upregulated and 223 co-downregulated genes. These differentially expressed genes (DEGs) were highly enriched in "response to chemical" and "stress" based on the gene ontology enrichment analysis. Notably, 30 candidate genes that were associated with the salt tolerance analysis were obtained by integrating GWAS and transcriptomic DEG analyses, including 13 cloned genes that had no reports of tolerance to salt and 17 candidate genes whose functions were unknown. To further explore these genes and their alleles, we performed haplotype analysis, genome-wide domestication detection, and transcriptome analysis to breed improved varieties. This data and the genetic resources provided will be valuable for the development of salt tolerant rice varieties.

Biochemical, Physiological and Anatomical Mechanisms of Adaptation of Callistemon citrinus and Viburnum lucidum to NaCl and CaCl2 Salinization

Callistemon citrinus and Viburnum lucidum are appreciated and widespread ornamental shrubs for their abundant flowering and/or brilliant foliage. The intrinsic tolerance to drought/salinity supports their use in urban areas and in xeriscaping. Despite adaptive responses of these ornamental species to sodium chloride (NaCl) have been extensively explored, little is known on the effects of other salt solution, yet iso-osmotic, on their growth, mineral composition and metabolism. The present research was aimed to assess responses at the biochemical, physiological and anatomical levels to iso-osmotic salt solutions of NaCl and CaCl2 to discriminate the effects of osmotic stress and ion toxicity. The two ornamental species developed different salt-tolerance mechanisms depending on the salinity sources. The growth parameters and biomass production decreased under salinization in both ornamental species, independently of the type of salt, with a detrimental effect of CaCl2 on C. citrinus. The adaptive mechanisms adopted by the two ornamental species to counteract the NaCl salinity were similar, and the decline in growth was mostly related to stomatal limitations of net CO2 assimilation rate, together with the reduction in leaf chlorophyll content (SPAD index). The stronger reduction of C. citrinus growth compared to V. lucidum, was due to an exacerbated reduction in net photosynthetic rate, driven by both stomatal and non stomatal limitations. In similar conditions, V. lucidum exhibited other additional adaptive response, such as modification in leaf functional anatomical traits, mostly related to the reduction in the stomata size allowing plants a better control of stomata opening than in C. citrinus. However, C. citrinus plants displayed an increased ability to retain higher Cl- levels in leaves than in roots under CaCl2 salinity compared to V. lucidum, thus, indicating a further attempt to counteract chloride toxicity through an increased vacuolar compartmentalization and to take advantages of them as chip osmotica.