Transcriptional profiling of two contrasting genotypes uncovers molecular mechanisms underlying salt tolerance in alfalfa.

Alfalfa is an important forage crop that is moderately tolerant to salinity; however, little is known about its salt-tolerance mechanisms. We studied root and leaf transcriptomes of a salt-tolerant (G03) and a salt-sensitive (G09) genotype, irrigated with waters of low and high salinities. RNA sequencing led to 1.73 billion high-quality reads that were assembled into 418,480 unigenes; 35% of which were assigned to 57 Gene Ontology annotations. The unigenes were assigned to pathway databases for understanding high-level functions. The comparison of two genotypes suggested that the low salt tolerance index for transpiration rate and stomatal conductance of G03 compared to G09 may be due to its reduced salt uptake under salinity. The differences in shoot biomass between the salt-tolerant and salt-sensitive lines were explained by their differential expressions of genes regulating shoot number. Differentially expressed genes involved in hormone-, calcium-, and redox-signaling, showed treatment- and genotype-specific differences and led to the identification of various candidate genes involved in salinity stress, which can be investigated further to improve salinity tolerance in alfalfa. Validation of RNA-seq results using qRT-PCR displayed a high level of consistency between the two experiments. This study provides valuable insight into the molecular mechanisms regulating salt tolerance in alfalfa.

Linking diverse salinity responses of 14 almond rootstocks with physiological, biochemical, and genetic determinants.

Fourteen commercial almond rootstocks were tested under five types of irrigation waters to understand the genetic, physiological, and biochemical bases of salt-tolerance mechanisms. Treatments included control (T1) and four saline water treatments dominant in sodium-sulfate (T2), sodium-chloride (T3), sodium-chloride/sulfate (T4), and calcium/magnesium-chloride/sulfate (T5). T3 caused the highest reduction in survival rate and trunk diameter, followed by T4 and T2, indicating that Na and, to a lesser extent, Cl were the most toxic ions to almond rootstocks. Peach hybrid (Empyrean 1) and peach-almond hybrids (Cornerstone, Bright's Hybrid 5, and BB 106) were the most tolerant to salinity. Rootstock's performance under salinity correlated highly with its leaf Na and Cl concentrations, indicating that Na+ and Cl- exclusion is crucial for salinity tolerance in Prunus. Photosynthetic rate correlated with trunk diameter and proline leaf ratio (T3/T1) significantly correlated with the exclusion of Na+ and Cl-, which directly affected the survival rate. Expression analyses of 23 genes involved in salinity stress revealed that the expression differences among genotypes were closely associated with their performance under salinity. Our genetic, molecular, and biochemical analyses allowed us to characterize rootstocks based on component traits of the salt-tolerance mechanisms, which may facilitate the development of highly salt-tolerant rootstocks.

Characterization of natural genetic variation identifies multiple genes involved in salt tolerance in maize.

Progressive decline in irrigation water is forcing farmers to use brackish water which increases soil salinity and exposes the crop plants to salinity. Maize, one of the most important crops, is sensitive to salinity. Salt tolerance is a complex trait controlled by a number of physiological and biochemical processes. Scant information is available on the genetic architecture of salt tolerance in maize. We evaluated 399 inbred lines for six early vigor shoot and root traits upon exposure of 18-day seedlings to salinity (ECiw = 16 dS m-1) stress. Contrasting response of shoot and root growth to salinity indicated a meticulous reprogramming of resource partitioning by the plants to cope with the stress. The genomic analysis identified 57 single nucleotide polymorphisms (SNP) associated with early vigor traits. Candidate genes systematically associated with each SNP include both previously known and novel genes. Important candidates include a late embryogenesis protein, a divalent ion symporter, a proton extrusion protein, an RNA-binding protein, a casein kinase 1, and an AP2/EREBP transcription factor. The late embryogenesis protein is associated with both shoot and root length, indicating a coordinated change in resource allocation upon salt stress. Identification of a casein kinase 1 indicates an important role for Ser/Thr kinases in salt tolerance. Validation of eight candidates based on expression in a salt-tolerant and a salt-sensitive inbred line supported their role in salt tolerance. The candidate genes identified in this investigation provide a foundation for dissecting genetic and molecular regulation of salt tolerance in maize and related grasses.

Molecular characterization and expression analysis of the Na+/H+ exchanger gene family in Medicago truncatula.

One important mechanism plants use to cope with salinity is keeping the cytosolic Na+ concentration low by sequestering Na+ in vacuoles, a process facilitated by Na+/H+ exchangers (NHX). There are eight NHX genes (NHX1 through NHX8) identified and characterized in Arabidopsis thaliana. Bioinformatics analyses of the known Arabidopsis genes enabled us to identify six Medicago truncatula NHX genes (MtNHX1, MtNHX2, MtNHX3, MtNHX4, MtNHX6, and MtNHX7). Twelve transmembrane domains and an amiloride binding site were conserved in five out of six MtNHX proteins. Phylogenetic analysis involving A. thaliana, Glycine max, Phaseolus vulgaris, and M. truncatula revealed that each individual MtNHX class (class I: MtNHX1 through 4; class II: MtNHX6; class III: MtNHX7) falls under a separate clade. In a salinity-stress experiment, M. truncatula exhibited ~ 20% reduction in biomass. In the salinity treatment, sodium contents increased by 178 and 75% in leaves and roots, respectively, and Cl- contents increased by 152 and 162%, respectively. Na+ exclusion may be responsible for the relatively smaller increase in Na+ concentration in roots under salt stress as compared to Cl-. Decline in tissue K+ concentration under salinity was not surprising as some antiporters play an important role in transporting both Na+ and K + . MtNHX1, MtNHX6, and MtNHX7 display high expression in roots and leaves. MtNHX3, MtNHX6, and MtNHX7 were induced in roots under salinity stress. Expression analysis results indicate that sequestering Na+ into vacuoles may not be the principal component trait of the salt tolerance mechanism in M. truncatula and other component traits may be pivotal.