Comparative Leaf and Root Transcriptomic Analysis of two Rice Japonica Cultivars Reveals Major Differences in the Root Early Response to Osmotic Stress

Background Rice (Oryza sativa L.) is one of the most important crops cultivated in both tropical and temperate regions and is characterized by a low water-use efficiency and a high sensitivity to a water deficit, with yield reductions occurring at lower stress levels compared to most other crops. To identify genes and pathways involved in the tolerant response to dehydration, a powerful approach consists in the genome-wide analysis of stress-induced expression changes by comparing drought-tolerant and drought-sensitive genotypes. Results The physiological response to osmotic stress of 17 japonica rice genotypes was evaluated. A clear differentiation of the most tolerant and the most sensitive phenotypes was evident, especially after 24 and 48 h of treatment. Two genotypes, which were characterized by a contrasting response (tolerance/sensitivity) to the imposed stress, were selected. A parallel transcriptomic analysis was performed on roots and leaves of these two genotypes at 3 and 24 h of stress treatment. RNA-Sequencing data showed that the tolerant genotype Eurosis and the sensitive genotype Loto mainly differed in the early response to osmotic stress in roots. In particular, the tolerant genotype was characterized by a prompt regulation of genes related to chromatin, cytoskeleton and transmembrane transporters. Moreover, a differential expression of transcription factor-encoding genes, genes involved in hormone-mediate signalling and genes involved in the biosynthesis of lignin was observed between the two genotypes. Conclusions Our results provide a transcriptomic characterization of the osmotic stress response in rice and identify several genes that may be important players in the tolerant response

Improving seed germination of the eggplant rootstock Solanum torvum by testing multiple factors using an orthogonal array design

[EN] Solanum torvum is a highly vigorous relative of eggplant that is resistant to a number of harmful soil-borne diseases and is compatible for grafting with eggplant. Being a potential rootstock, this plant frequently presents poor and erratic germination, which makes its practical use difficult. We used an L8 (2(7)) orthogonal array design to evaluate the primary effects of seven factors (soaking of seeds, scarification with sodium hypochlorite (NaClO), application of gibberellic acid (GA(3)), use of potassium mitrate (KNO3) as a moistening agent, cold stratification, application of a heatshock, and light irradiation during germination) at two levels (L0 and L1) using four germination parameters (early and final germination, germination rate and vigour index) in fresh S. torvum seeds. S. torvum seeds had a strong dormancy with no germination in the untreated seeds and high early and final germination (approximately 100%) in certain treatments. An evaluation of the main effects revealed highly positive effects on germination from seed soaking, and the use of GA(3), KNO3, and light irradiation, whereas NaClO scarification had a negative effect. The application of cold stratification and heat shock treatments also had a positive effect on seed germination but to a lesser extent than the other treatments. An improved proposed protocol that consisted of subjecting seeds to soaking, the application of GA(3) and KNO3, cold stratification, heat shock, and light irradiation was validated and demonstrated to be highly effective, with seed germination success greater than 60% being observed at 3 days and final germination reaching a plateau at 6 days. A second validation experiment using a commercial growing substrate also showed a high emergence (approximately 50%) at 7 days and a final germination of approximately 80% was recorded with application of the improved protocol. The seed germination protocol that we have developed will facilitate the use of S. torvum as a rootstock for eggplant and its use in breeding programmes. Our results also reveal that orthogonal array designs are a powerful tool for establishing improved protocols for seed germination. (C) 2015 Elsevier B.V. All rights reserved.This work was completed as part of the initiative "Adapting Agriculture to Climate Change: Collecting, Protecting and Preparing Crop Wild Relatives", which is supported by the Government of Norway. The project is managed by the Global Crop Diversity Trust with the Millennium Seed Bank of the Royal Botanic Gardens, Kew and is implemented in partnership with national and international gene banks and plant breeding institutes. For further information see the project website: http://www.cwrdiversity.org/. Isabel Andujar and Pietro Gramazio are grateful to Universitat Politecnica de Valencia for their post-doctoral (PAID-10-14) and pre-doctoral (Programa FPI de la UPV-Subprograma 1) contracts, respectively.Ranil, RH.; Niran, HML.; Plazas Ávila, MDLO.; Fonseka, R.; Hemal Fonseka, H.; Vilanova Navarro, S.; Andújar Pérez, I.... (2015). Improving seed germination of the eggplant rootstock Solanum torvum by testing multiple factors using an orthogonal array design. Scientia Horticulturae. 193:174-181. https://doi.org/10.1016/j.scienta.2015.07.030S17418119

A computational-based update on microRNAs and their targets in barley (Hordeum vulgare L.)

<p>Abstract</p> <p>Background</p> <p>Many plant species have been investigated in the last years for the identification and characterization of the corresponding miRNAs, nevertheless extensive studies are not yet available on barley (at the time of this writing). To extend and to update information on miRNAs and their targets in barley and to identify candidate polymorphisms at miRNA target sites, the features of previously known plant miRNAs have been used to systematically search for barley miRNA homologues and targets in the publicly available ESTs database. Matching sequences have then been related to Unigene clusters on which most of this study was based.</p> <p>Results</p> <p>One hundred-fifty-six microRNA mature sequences belonging to 50 miRNA families have been found to significantly match at least one EST sequence in barley. As expected on the basis of phylogenetic relations, miRNAs putatively orthologous to those of <it>Triticum </it>are significantly over-represented inside the set of identified barley microRNA mature sequences. Many previously known and several putatively new miRNA/target pairs have been identified. When the predicted microRNA targets were grouped into functional categories, biological processes previously known to be regulated by miRNAs, such as development and response to biotic and abiotic stress, have been highlighted and most of the target molecular functions were related to transcription regulation. Candidate microRNA coding genes have been reported and genetic variation (SNPs/indels) both in functional regions of putative miRNAs (mature sequence) and at miRNA target sites has been found.</p> <p>Conclusions</p> <p>This study has provided an update of the information on barley miRNAs and their targets representing a foundation for future studies. Many of previously known plant microRNAs have homologues in barley with expected important roles during development, nutrient deprivation, biotic and abiotic stress response and other important physiological processes. Putative polymorphisms at miRNA target sites have been identified and they can represent an interesting source for the identification of functional genetic variability.</p

Identification of gene modules associated with low temperatures response in Bambara groundnut by network-based analysis

Bambara groundnut (Vigna subterranea (L.) Verdc.) is an African legume and is a promising underutilized crop with good seed nutritional values. Low temperature stress in a number of African countries at night, such as Botswana, can effect the growth and development of bambara groundnut, leading to losses in potential crop yield. Therefore, in this study we developed a computational pipeline to identify and analyze the genes and gene modules associated with low temperature stress responses in bambara groundnut using the cross-species microarray technique (as bambara groundnut has no microarray chip) coupled with network-based analysis. Analyses of the bambara groundnut transcriptome using cross-species gene expression data resulted in the identification of 375 and 659 differentially expressed genes (p<0.01) under the sub-optimal (23°C) and very sub-optimal (18°C) temperatures, respectively, of which 110 genes are commonly shared between the two stress conditions. The construction of a Highest Reciprocal Rank-based gene co-expression network, followed by its partition using a Heuristic Cluster Chiseling Algorithm resulted in 6 and 7 gene modules in sub-optimal and very sub-optimal temperature stresses being identified, respectively. Modules of sub-optimal temperature stress are principally enriched with carbohydrate and lipid metabolic processes, while most of the modules of very sub-optimal temperature stress are significantly enriched with responses to stimuli and various metabolic processes. Several transcription factors (from MYB, NAC, WRKY, WHIRLY & GATA classes) that may regulate the downstream genes involved in response to stimulus in order for the plant to withstand very sub-optimal temperature stress were highlighted. The identified gene modules could be useful in breeding for low-temperature stress tolerant bambara groundnut varieties