Petunia hybrida is a popular bedding plant that has a long history as a genetic model system. We report the whole-genome sequencing and assembly of inbred derivatives of its two wild parents, P. axillaris N and P. inflata S6. The assemblies include 91.3% and 90.2% coverage of their diploid genomes (1.4 Gb; 2n = 14) containing 32,928 and 36,697 protein-coding genes, respectively. The genomes reveal that the Petunia lineage has experienced at least two rounds of hexaploidization: the older gamma event, which is shared with most Eudicots, and a more recent Solanaceae event that is shared with tomato and other solanaceous species. Transcription factors involved in the shift from bee to moth pollination reside in particularly dynamic regions of the genome, which may have been key to the remarkable diversity of floral colour patterns and pollination systems. The high-quality genome sequences will enhance the value of Petunia as a model system for research on unique biological phenomena such as small RNAs, symbiosis, self-incompatibility and circadian rhythms.

Climate change is causing soil salinization, resulting in crop losses throughout the world. The ability of plants to tolerate salt stress is determined by multiple biochemical and molecular pathways. Here we discuss physiological, biochemical, and cellular modulations in plants in response to salt stress. Knowledge of these modulations can assist in assessing salt tolerance potential and the mechanisms underlying salinity tolerance in plants. Salinity-induced cellular damage is highly correlated with generation of reactive oxygen species, ionic imbalance, osmotic damage, and reduced relative water content. Accelerated antioxidant activities and osmotic adjustment by the formation of organic and inorganic osmolytes are significant and effective salinity tolerance mechanisms for crop plants. In addition, polyamines improve salt tolerance by regulating various physiological mechanisms, including rhizogenesis, somatic embryogenesis, maintenance of cell pH, and ionic homeostasis. This research project focuses on three strategies to augment salinity tolerance capacity in agricultural crops: salinity-induced alterations in signaling pathways; signaling of phytohormones, ion channels, and biosensors; and expression of ion transporter genes in crop plants (especially in comparison to halophytes).

The value of organic greenhouse production in the United States is $112 million, and organic floriculture production has increased 40% in greenhouses since 2008. The U.S. National Organic Program (NOP) guidelines allow organic production in containers. One of the primary concerns for current and potential organic container growers is managing container substrate and plant fertility. This manuscript provides a review of current literature on organic substrates and fertilizers for container grown herbs, vegetables and herbaceous ornamentals according to NOP guidelines. Organic-approved substrates can be purchased from commercial suppliers or produced in house. Many organic substrate components are similar to those used in conventional production (peat moss, pine bark, perlite, vermiculite, rice hulls, and whole pine tree) but lack a synthetic wetting agent. Growers who mix their own substrates often add compost at percentages ranging from 20 to 50%. Compost has high water holding and cation exchange capacity. It is often locally or regionally produced and purchased, which impacts variability and quality. For this reason, growers often need to manage substrates with compost more carefully. Single source or blended organic fertilizers may be incorporated in substrates prior to planting. These are derived from a variety of plant and animal based sources. A small number of mined components may be added to substrate-incorporated fertilizers (i.e. limestone). These fertilizers will typically last for four to five weeks, and are often supplemented with liquid fertilizers for longer-term crops or species with high nitrogen requirements. Liquid fertilizers also tend to be more quickly plant available compared to substrate-incorporated fertilizers. With careful management, it is possible to grow container plants in organic production systems that are comparable to those produced in conventional production systems.

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BackgroundTrehalose-6-phosphate synthase (TPS) serves important functions in plant desiccation tolerance and response to environmental stimuli. At present, a comprehensive analysis, i.e. functional classification, molecular evolution, and expression patterns of this gene family are still lacking in Solanum tuberosum (potato).ResultsIn this study, a comprehensive analysis of the TPS gene family was conducted in potato. A total of eight putative potato TPS genes (StTPSs) were identified by searching the latest potato genome sequence. The amino acid identity among eight StTPSs varied from 59.91 to 89.54%. Analysis of dN/dS ratios suggested that regions in the TPP (trehalose-6-phosphate phosphatase) domains evolved faster than the TPS domains. Although the sequence of the eight StTPSs showed high similarity (2571-2796 bp), their gene length is highly differentiated (3189-8406 bp). Many of the regulatory elements possibly related to phytohormones, abiotic stress and development were identified in different TPS genes. Based on the phylogenetic tree constructed using TPS genes of potato, and four other Solanaceae plants, TPS genes could be categorized into 6 distinct groups. Analysis revealed that purifying selection most likely played a major role during the evolution of this family. Amino acid changes detected in specific branches of the phylogenetic tree suggests relaxed constraints might have contributed to functional divergence among groups. Moreover, StTPSs were found to exhibit tissue and treatment specific expression patterns upon analysis of transcriptome data, and performing qRT-PCR.ConclusionsThis study provides a reference for genome-wide identification of the potato TPS gene family and sets a framework for further functional studies of this important gene family in development and stress response.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4298-x) contains supplementary material, which is available to authorized users.

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Salinity and drought stress are the primary cause of crop losses worldwide. In sodic saline soils sodium chloride (NaCl) disrupts normal plant growth and development. The complex interactions of plant systems with abiotic stress have made RNA sequencing a more holistic and appealing approach to study transcriptome level responses in a single cell and/or tissue. In this work, we determined the Petunia transcriptome response to NaCl stress by sequencing leaf samples and assembling 196 million Illumina reads with Trinity software. Using our reference transcriptome we identified more than 7,000 genes that were differentially expressed within 24 h of acute NaCl stress. The proposed transcriptome can also be used as an excellent tool for biological and bioinformatics in the absence of an available Petunia genome and it is available at the SOL Genomics Network (SGN) http://solgenomics.net. Genes related to regulation of reactive oxygen species, transport, and signal transductions as well as novel and undescribed transcripts were among those differentially expressed in response to salt stress. The candidate genes identified in this study can be applied as markers for breeding or to genetically engineer plants to enhance salt tolerance. Gene Ontology analyses indicated that most of the NaCl damage happened at 24 h inducing genotoxicity, affecting transport and organelles due to the high concentration of Na+ ions. Finally, we report a modification to the library preparation protocol whereby cDNA samples were bar-coded with non-HPLC purified primers, without affecting the quality and quantity of the RNA-seq data. The methodological improvement presented here could substantially reduce the cost of sample preparation for future high-throughput RNA sequencing experiments.

MicroRNAs (miRNAs) are endogenous non-coding RNAs with important regulatory functions in plant development and stress responses. However, their population abundance in lotus (Nelumbo nucifera Gaertn) has so far been poorly described, particularly in response to stresses. In this work, submergence-related miRNAs and their target genes were systematically identified, compared, and validated at the transcriptome-wide level using high-throughput sequencing data of small RNA, Mrna, and the degradome. A total of 128 known and 20 novel miRNAs were differentially expressed upon submergence. We identified 629 target transcripts for these submergence-responsive miRNAs. Based on the miRNA expression profiles and GO and KEGG annotation of miRNA target genes, we suggest possible molecular responses and physiological changes of lotus in response to submergence. Several metabolic, physiological and morphological adaptations-related miRNAs, i.e., NNU_far-miR159, NNU_gma-miR393h, and NNU_aly-miR319c-3p, were found to play important regulatory roles in lotus response to submergence. This work will contribute to a better understanding of miRNA-regulated adaption responses of lotus to submergence stress.