Contents Summary 523 I. Introduction 523 II. Sensing salt stress 524 III. Ion homeostasis regulation 524 IV. Metabolite and cell activity responses to salt stress 527 V. Conclusions and perspectives 532 Acknowledgements 533 References 533 SUMMARY: Excess soluble salts in soil (saline soils) are harmful to most plants. Salt imposes osmotic, ionic, and secondary stresses on plants. Over the past two decades, many determinants of salt tolerance and their regulatory mechanisms have been identified and characterized using molecular genetics and genomics approaches. This review describes recent progress in deciphering the mechanisms controlling ion homeostasis, cell activity responses, and epigenetic regulation in plants under salt stress. Finally, we highlight research areas that require further research to reveal new determinants of salt tolerance in plants.

https://nph.onlinelibrary.wiley.com/doi/epdf/10.1111/nph.14920

Elucidating the molecular mechanisms mediating plant salt-stress responses

Soil salinity is a major environmental stress that restricts the growth and yield of crops. Understanding the physiological, metabolic, and biochemical responses of plants to salt stress and mining the salt tolerance-associated genetic resource in nature will be extremely important for us to cultivate salt-tolerant crops. In this review, we provide a comprehensive summary of the mechanisms of salt stress responses in plants, including salt stress-triggered physiological responses, oxidative stress, salt stress sensing and signaling pathways, organellar stress, ion homeostasis, hormonal and gene expression regulation, metabolic changes, as well as salt tolerance mechanisms in halophytes. Important questions regarding salt tolerance that need to be addressed in the future are discussed.

Mechanisms of Plant Responses and Adaptation to Soil Salinity.

Chromatin regulation is essential to regulate genes and genome activities. In plants, the alteration of histone modification and DNA methylation are coordinated with changes in the expression of stress-responsive genes to adapt to environmental changes. Several chromatin regulators have been shown to be involved in the regulation of stress-responsive gene networks under abiotic stress conditions. Specific histone modification sites and the histone modifiers that regulate key stress-responsive genes have been identified by genetic and biochemical approaches, revealing the importance of chromatin regulation in plant stress responses. Recent studies have also suggested that histone modification plays an important role in plant stress memory. In this review, we summarize recent progress on the regulation and alteration of histone modification (acetylation, methylation, phosphorylation, and SUMOylation) in response to the abiotic stresses, drought, high-salinity, heat, and cold in plants.

/pdf/chromatin-changes-in-response-to-drought-salinity-heat-and-553d7ju4c3.pdf

Chromatin changes in response to drought, salinity, heat, and cold stresses in plants.

Salinity is a consistent factor of crop productivity loss in the world and in particular arid and semi-arid areas where the soil salinity and saline water are major problems. Plants employ various mechanisms to cope with salinity stress and activate an array of stress-responsive genes to counteract the salinity-induced osmotic and ionic stresses. Genetic improvement for salinity tolerance is challenging, and thus progress attained over the several decades has been far less than anticipated. The generation of an explosion of knowledge and technology related to genetics and genomics over the last few decades is promising in providing powerful tools for future development of salinity-tolerant cultivars. Despite a major progress in defining the underlying mechanisms of salinity tolerance, there are still major challenges to be overcome in translating and integrating the resultant information at the molecular level into plant-breeding practices. Various approaches have been suggested to improve the eff...

Smart Engineering of Genetic Resources for Enhanced Salinity Tolerance in Crop Plants

DNA methylation is an epigenetic mechanism that play an important role in gene regulation in response to environmental conditions. The understanding of DNA methylation at the whole genome level can provide insights into the regulatory mechanisms underlying abiotic stress response/adaptation. We report DNA methylation patterns and their influence on transcription in three rice (Oryza sativa) cultivars (IR64, stress-sensitive; Nagina 22, drought-tolerant; Pokkali, salinity-tolerant) via an integrated analysis of whole genome bisulphite sequencing and RNA sequencing. We discovered extensive DNA methylation at single-base resolution in rice cultivars, identified the sequence context and extent of methylation at each site. Overall, methylation levels were significantly different in the three rice cultivars. Numerous differentially methylated regions (DMRs) among different cultivars were identified and many of which were associated with differential expression of genes important for abiotic stress response. Transposon-associated DMRs were found coupled to the transcript abundance of nearby protein-coding gene(s). Small RNA (smRNA) abundance was found to be positively correlated with hypermethylated regions. These results provide insights into interplay among DNA methylation, gene expression and smRNA abundance, and suggest a role in abiotic stress adaptation in rice.

/pdf/divergent-dna-methylation-patterns-associated-with-gene-3wvo4fpenp.pdf

Divergent DNA methylation patterns associated with gene expression in rice cultivars with contrasting drought and salinity stress response

Cytosine methylation is a well recognized epigenetic mark. Here, the methylation status of a salinity-tolerant wheat cultivar (cv. SR3, derived from a somatic hybridization event) and its progenitor parent (cv. JN177) was explored both globally and within a set of 24 genes responsive to salinity stress. A further comparison was made between DNA extracted from plants grown under control conditions and when challenged by salinity stress. The SR3 and JN177 genomes differed with respect to their global methylation level, and methylation levels were reduced by exposure to salinity stress. We found the genetic stress- (triggered by a combination of different genomes in somatic hybridization) induced methylation pattern of 13 loci in non-stressed SR3; the same 13 loci were found to undergo methylation in salinity-stressed JN177. For the salinity-responsive genes, SR3 and JN177 also showed different methylation modifications. C methylation polymorphisms induced by salinity stress were present in both the promoter and coding regions of some of the 24 selected genes, but only the former were associated with changes in transcript abundance. The expression of both TaFLS1 (encoding a flavonol synthase) and TaWRSI5 (encoding a Bowman-Birk-type protease inhibitor), which showed both a different expression and a different DNA methylation level between SR3 and JN177, enhanced the salinity tolerance of Arabidopsis thaliana. C methylation changes appear to be a common component of the plant response to stress, and methylation changes triggered by somatic hybridization may contribute to the superior salinity tolerance of SR3.

/pdf/induced-and-constitutive-dna-methylation-in-a-salinity-1ui35fea57.pdf

Induced and Constitutive DNA Methylation in a Salinity-Tolerant Wheat Introgression Line

WRKY proteins constitute a large family of transcription factors in higher plants, and are involved in the regulation of development, senescence and stress resistance. However, little is known with respect to the constitution and function of WRKY genes in bread wheat (Triticum aestivum). We identified a set of 92 wheat WRKY genes from publicly available sequence databases, and constructed a phylogeny map based on the conserved WRKY domain peptide sequences. The wheat sequences were classified into the standard set of WRKY groups and sub-groups established from plant model genomes. Our results show the WRKY orthologues of wheat and rice are more similar compared to their Arabidopsis counterparts. Therefore, we argue some expansion of the WRKY family occurred following the divergence of these three species. The induction of sequence variation in a subset of 18 TaWRKY genes via somatic hybridization was studied by comparing the sequences from cv. JN177 and its derivative cv. SR3. We also analyzed the responses of these 18 genes to imposed salinity, PEG, ABA and SA using quantitative real time PCR. Nine of the 18 TaWRKY genes were up-regulated by exogenous SA. Six genes were up-regulated by salinity or PEG treatment, and their expression was also induced by exogenous ABA. Interestingly, induction by salinity or PEG was impaired when ABA biosynthesis was inhibited. The indication was that most of the TaWRKY genes involved in the abiotic stress response acted in an ABA-dependent manner.

WRKY Transcription Factors in Wheat and Their Induction by Biotic and Abiotic Stress

Broad phenotypic variations were induced in derivatives of an asymmetric somatic hybridization of bread wheat (Triticum aestivum) and tall wheatgrass (Thinopyrum ponticum Podp); however, how these variations occurred was unknown. We explored the nature of these variations by cytogenetic assays and DNA profiling techniques to characterize six genetically stable somatic introgression lines. Karyotyping results show the six lines similar to their wheat parent, but GISH analysis identified the presence of a number of short introgressed tall wheatgrass chromatin segments. DNA profiling revealed many genetic and epigenetic differences, including sequences deletions, altered regulation of gene expression, changed patterns of cytosine methylation, and the reactivation of retrotransposons. Phenotypic variations appear to result from altered repetitive sequences combined with the epigenetic regulation of gene expression and/or retrotransposon transposition. The extent of genetic and epigenetic variation due to the maintenance of parent wheat cells in tissue culture was assessed and shown to be considerably lower than had been induced in the introgression lines. Asymmetric somatic hybridization provides appropriate material to explore the nature of the genetic and epigenetic variations induced by genomic shock.

https://www.genetics.org/content/genetics/199/4/1035.full.pdf

Genetic and Epigenetic Changes in Somatic Hybrid Introgression Lines Between Wheat and Tall Wheatgrass

The Ns genome of the genus Psathyrostachys possesses superior traits useful for wheat improvement. However, very little is known about the high molecular weight (HMW) subunits of glutenin encoded by the Ns genome. In this paper, we report the isolation of four alleles of HMW glutenin subunit gene from Psathyrostachys juncea. Sequence alignment data shows the four alleles have similar primary structure with those in wheat and other wheat-related grasses, with some unique modifications. All four sequences more closely resemble y-type, rather than x-type, glutenins. However, our results show three of the subunits (1Ns2-4) contain an extra glutamine residue in the N-terminal region not found on typical y-type subunits, as well as the x-type subunit specific sequence LAAQLPAMCRL. These three subunits likely represent an intermediate state in the divergence between x- and y-type subunits. Results also indicate that the Ns genome is more closely related to the St genome of Pseudoroegneria than any other Triticeae genomes.

Lina Kong

Papers

Induced and Constitutive DNA Methylation in a Salinity-Tolerant Wheat Introgression Line

WRKY Transcription Factors in Wheat and Their Induction by Biotic and Abiotic Stress

Genetic and Epigenetic Changes in Somatic Hybrid Introgression Lines Between Wheat and Tall Wheatgrass

Characterization of high molecular weight glutenin subunit genes from the Ns genome of Psathyrostachys juncea.

Genetic and Epigenetic Changes in Somatic Hybrid Introgression Lines between