Comparative Functional Genomics of Salt Stress in Related Model and Cultivated Plants Identifies and Overcomes Limitations to Translational Genomics

One of the objectives of plant translational genomics is to use knowledge and genes discovered in model species to improve crops. However, the value of translational genomics to plant breeding, especially for complex traits like abiotic stress tolerance, remains uncertain. Using comparative genomics (ionomics, transcriptomics and metabolomics) we analyzed the responses to salinity of three model and three cultivated species of the legume genus Lotus. At physiological and ionomic levels, models responded to salinity in a similar way to crop species, and changes in the concentration of shoot Cl− correlated well with tolerance. Metabolic changes were partially conserved, but divergence was observed amongst the genotypes. Transcriptome analysis showed that about 60% of expressed genes were responsive to salt treatment in one or more species, but less than 1% was responsive in all. Therefore, genotype-specific transcriptional and metabolic changes overshadowed conserved responses to salinity and represent an impediment to simple translational genomics. However, ‘triangulation’ from multiple genotypes enabled the identification of conserved and tolerant-specific responses that may provide durable tolerance across species

Shoot chloride exclusion and salt tolerance in grapevine is associated with differential ion transporter expression in roots

BACKGROUND: Salt tolerance in grapevine is associated with chloride (Cl-) exclusion from shoots; the rate-limiting step being the passage of Cl- between the root symplast and xylem apoplast. Despite an understanding of the physiological mechanism of Cl- exclusion in grapevine, the molecular identity of membrane proteins that control this process have remained elusive. To elucidate candidate genes likely to control Cl- exclusion, we compared the root transcriptomes of three Vitis spp. with contrasting shoot Cl- exclusion capacities using a custom microarray. RESULTS: When challenged with 50 mM Cl-, transcriptional changes of genotypes 140 Ruggeri (shoot Cl- excluding rootstock), K51-40 (shoot Cl- including rootstock) and Cabernet Sauvignon (intermediate shoot Cl- excluder) differed. The magnitude of salt-induced transcriptional changes in roots correlated with the amount of Cl- accumulated in shoots. Abiotic-stress responsive transcripts (e.g. heat shock proteins) were induced in 140 Ruggeri, respiratory transcripts were repressed in Cabernet Sauvignon, and the expression of hypersensitive response and ROS scavenging transcripts was altered in K51-40. Despite these differences, no obvious Cl- transporters were identified. However, under control conditions where differences in shoot Cl- exclusion between rootstocks were still significant, genes encoding putative ion channels SLAH3, ALMT1 and putative kinases SnRK2.6 and CPKs were differentially expressed between rootstocks, as were members of the NRT1 (NAXT1 and NRT1.4), and CLC families. CONCLUSIONS: These results suggest that transcriptional events contributing to the Cl- exclusion mechanism in grapevine are not stress-inducible, but constitutively different between contrasting varieties. We have identified individual genes from large families known to have members with roles in anion transport in other plants, as likely candidates for controlling anion homeostasis and Cl- exclusion in Vitis species. We propose these genes as priority candidates for functional characterisation to determine their role in chloride transport in grapevine and other plants.Sam W Henderson, Ute Baumann, Deidre H Blackmore, Amanda R Walker, Rob R Walker and Matthew Gilliha

An enigma in the genetic responses of plants to salt stresses

Soil salinity is one of the main factors restricting crop production throughout the world. Various salt tolerance traits and the genes controlling these traits are responsible for coping with salinity stress in plants. These coping mechanisms include osmotic tolerance, ion exclusion, and tissue tolerance. Plants exposed to salinity stress sense the stress conditions, convey specific stimuli signals, and initiate responses against stress through the activation of tolerance mechanisms that include multiple genes and pathways. Advances in our understanding of the genetic responses of plants to salinity and their connections with yield improvement are essential for attaining sustainable agriculture. Although a wide range of studies have been conducted that demonstrate genetic variations in response to salinity stress, numerous questions need to be answered to fully understand plant tolerance to salt stress. This chapter provides an overview of previous studies on the genetic control of salinity stress in plants, including signaling, tolerance mechanisms, and the genes, pathways, and epigenetic regulators necessary for plant salinity tolerance

Chloride transport and compartmentation within main and lateral roots of two grapevine rootstocks differing in salt tolerance

Root Cl⁻ transport was investigated using ³⁶Cl⁻ flux analysis in two grapevine (Vitis sp.) rootstock hybrids differing in salt tolerance; 1103 Paulsen (salt-tolerant) and K 51–40 (salt sensitive). Initial ³⁶Cl⁻ influx to the root was greater in Paulsen than K 51–40. This flux, attributed to the Cl⁻ influx to the cytoplasm (Φ ₒc) increased with increasing external concentrations of Cl⁻ for plants adapted to growth in 30� mM NaCl. The concentration kinetics in this high concentration range could be fit to a Michaeils–Menton equation. There was no significant difference between genotypes in Km (28.68� ±� 15.76 and 24.27� ±� 18.51� mM for Paulsen and K 51–40, respectively), but Paulsen had greater V ₘₐₓ (0.127� ±� 0.042) compared to K 51–40 (0.059� ±� 0.026� μm� g⁻¹� FW� min⁻¹). In Paulsen, the main root had greater contribution to ³⁶Cl⁻ uptake than lateral roots, there being no significant difference in lateral root influx between the genotypes. ³⁶Cl⁻ transport to the shoot of K 51–40 was greater than for Paulsen. It was estimated that efflux rate from the xylem parenchyma cells to the xylem vessels (Φ cₓ) in K 51–40 was twice that of Paulsen. Compartmental analysis from ³⁶Cl⁻ efflux kinetics confirmed the larger Φ ₒc and the higher ratio of main to lateral root Φ ₒc for Paulsen. Efflux from the cytoplasm (Φ cₒ) was higher than 95� % of Φ ₒc indicating a high degree of cycling across the plasma membrane in roots at these high external Cl⁻ concentrations. Paulsen appears to keep the cytoplasmic Cl⁻ concentration in roots lower than K 51–40 via greater efflux to the vacuole and to the outside medium. The difference in salt tolerance between the genotypes can be attributed to different Cl⁻ transport properties at the plasma membrane and tonoplast and particularly in Cl⁻� efflux to the xylem.Nasser Abbaspour, Brent Kaiser, Stephen Tyerma