In this report, we test the hypothesis that Na+ accumulation in the shoot in maize is negatively correlated with salt tolerance. Salt tolerance is defined as a percentage of the control on a dry weight basis. Two hybrids (Pioneer hybrid 3578 and Pioneer hybrid 3772) differing widely in Na+ accumulation were compared. Plants were treated with two types of salinity for 15 days (80 mol m-3 NaCl or 80 mol m-3 NaCl plus 8.75 mol m-3 CaCl2). Ion concentrations (Na+, K+, Ca2+ and Cl-) were measured in the roots, stalks, sheaths and leaves of plants harvested every third day. Ion concentrations were significantly affected by the treatments. Na+ and Cl- concentrations increased with salinity treatments; K+ and Ca2+ concentrations decreased. Supplemental Ca2+ increased Ca2+ and decreased Na+ concentrations. Hybrid 3772 maintained very low Na+ concentrations in the shoots, whereas 3578 did not. The largest distinction between the hybrids was in the ability to transport Na+ to the shoot; hybrid 3578 transported Na+ at twice the rate of hybrid 3772. In general, ion transport to the shoot appeared to be a function of root ion concentration. This model could account for the effects of NaCl salinity and supplemental Ca2+ on ion transport, although Na+ transport was complicated by an apparent reabsorption mechanism in the root and mesocotyl. The lack of correlation of Na+ accumulation in the shoot and other ion parameters with growth indicated that the mineral nutrition of the plants was not correlated with salt tolerance. It was concluded that the growth response of maize to salinity was primarily affected by osmotic factors.

Background Grapevine is an economically important crop for which yield and berry quality is strongly affected by climate change. Large variations in drought tolerance exist across Vitis species. Some of these species are used as rootstock to enhance abiotic and biotic stress tolerance. In this study, we investigated the physiological and transcriptomic responses to water deficit of four different genotypes that differ in drought tolerance: Ramsey (Vitis champinii), Riparia Gloire (Vitis riparia), Cabernet Sauvignon (Vitis vinifera), and SC2 (Vitis vinifera x Vitis girdiana). Results Ramsey was particularly more drought tolerant than the other three genotypes. Ramsey maintained a higher stomatal conductance and photosynthesis at equivalent levels of moderate water deficit. We identified specific and common transcriptomic responses shared among the four different Vitis species using RNA sequencing analysis. A weighted gene co-expression analysis identified a water deficit core gene set with the ABA biosynthesis and signaling genes, NCED3, RD29B and ABI1 as potential hub genes. The transcript abundance of many abscisic acid metabolism and signaling genes was strongly increased by water deficit along with genes associated with lipid metabolism, galactinol synthases and MIP family proteins. This response occurred at smaller water deficits in Ramsey and with higher transcript abundance than the other genotypes. A number of aquaporin genes displayed differential and unique responses to water deficit in Ramsey leaves. Genes involved in cysteine biosynthesis and metabolism were constitutively higher in the roots of Ramsey; thus, linking the gene expression of a known factor that influences ABA biosynthesis to this genotype’s increased NCED3 transcript abundance. Conclusion The drought tolerant Ramsey maintained higher photosynthesis at equivalent water deficit than the three other grapevine genotypes. Ramsey was more responsive to water deficit; its transcriptome responded at smaller water deficits, whereas the other genotypes did not respond until more severe water deficits were reached. There was a common core gene network responding to water deficit for all genotypes that included ABA metabolism and signaling. The gene clusters and sub-networks identified in this work represent interesting gene lists to explore and to better understand drought tolerance molecular mechanisms.

BackgroundWine grapes are important economically in many countries around the world. Defining the optimum time for grape harvest is a major challenge to the grower and winemaker. Berry skins are an important source of flavor, color and other quality traits in the ripening stage. Senescent-like processes such as chloroplast disorganization and cell death characterize the late ripening stage.ResultsTo better understand the molecular and physiological processes involved in the late stages of berry ripening, RNA-seq analysis of the skins of seven wine grape cultivars (Cabernet Franc, Cabernet Sauvignon, Merlot, Pinot Noir, Chardonnay, Sauvignon Blanc and Semillon) was performed. RNA-seq analysis identified approximately 2000 common differentially expressed genes for all seven cultivars across four different berry sugar levels (20 to 26 °Brix). Network analyses, both a posteriori (standard) and a priori (gene co-expression network analysis), were used to elucidate transcriptional subnetworks and hub genes associated with traits in the berry skins of the late stages of berry ripening. These independent approaches revealed genes involved in photosynthesis, catabolism, and nucleotide metabolism. The transcript abundance of most photosynthetic genes declined with increasing sugar levels in the berries. The transcript abundance of other processes increased such as nucleic acid metabolism, chromosome organization and lipid catabolism. Weighted gene co-expression network analysis (WGCNA) identified 64 gene modules that were organized into 12 subnetworks of three modules or more and six higher order gene subnetworks. Some gene subnetworks were highly correlated with sugar levels and some subnetworks were highly enriched in the chloroplast and nucleus. The petal R package was utilized independently to construct a true small-world and scale-free complex gene co-expression network model. A subnetwork of 216 genes with the highest connectivity was elucidated, consistent with the module results from WGCNA. Hub genes in these subnetworks were identified including numerous members of the core circadian clock, RNA splicing, proteolysis and chromosome organization. An integrated model was constructed linking light sensing with alternative splicing, chromosome remodeling and the circadian clock.ConclusionsA common set of differentially expressed genes and gene subnetworks from seven different cultivars were examined in the skin of the late stages of grapevine berry ripening. A densely connected gene subnetwork was elucidated involving a complex interaction of berry senescent processes (autophagy), catabolism, the circadian clock, RNA splicing, proteolysis and epigenetic regulation. Hypotheses were induced from these data sets involving sugar accumulation, light, autophagy, epigenetic regulation, and fruit development. This work provides a better understanding of berry development and the transcriptional processes involved in the late stages of ripening.Electronic supplementary materialThe online version of this article (doi:10.1186/s12...

Two maize (Zea mays L.) hybrids, differing in their salt tolerance (percentage of control on a dry weight basis) and ability to accumulate Na+ in the shoot, were treated with 80 mol m-3 NaCl salinity or 80 mol m-3 NaCl plus 8.75 mol m-3 CaCl2. Multiple harvests were performed and the interactions of salinity with time were examined with growth analysis. Relative growth rate (RGR) and leaf area ratio (LAR) were significantly reduced by NaCl salinity, but net assimilation rate (NAR) was unaffected. Supplemental Ca2+ improved RGR by maintaining LAR closer to control values. LAR was inhibited in the early stages of salt stress, but was not limiting growth relative to controls in later stages. Salinity also reduced the specific leaf area and leaf weight ratio, which indicates that leaf expansion and carbon allocation were altered. Differences in salt tolerance between the hybrids were small, but significant throughout the lifecycle of the plants. These differences were associated with differences in leaf elongation rates and LAR within the first 9 days of salinity.

Viticulture, like other fields of agriculture, is currently facing important challenges that will be addressed only through sustained, dedicated and coordinated research. Although the methods used in biology have evolved tremendously in recent years and now involve the routine production of large data sets of varied nature, in many domains of study, including grapevine research, there is a need to improve the findability, accessibility, interoperability and reusability (FAIR-ness) of these data. Considering the heterogeneous nature of the data produced, the transnational nature of the scientific community and the experience gained elsewhere, we have formed an open working group, in the framework of the International Grapevine Genome Program (www.vitaceae.org), to construct a coordinated federation of information systems holding grapevine data distributed around the world, providing an integrated set of interfaces supporting advanced data modeling, rich semantic integration and the next generation of data mining tools. To achieve this goal, it will be critical to develop, implement and adopt appropriate standards for data annotation and formatting. The development of this system, the GrapeIS, linking genotypes to phenotypes, and scientific research to agronomical and oeneological data, should provide new insights into grape biology, and allow the development of new varieties to meet the challenges of biotic and abiotic stress, environmental change, and consumer demand.