Neil S. Mattson

Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida

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.

Transcriptomic Analysis of Petunia hybrida in Response to Salt Stress Using High Throughput RNA Sequencing

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.

Exogenous 24-Epibrassinolide Elevates the Salt Tolerance Potential of Pea (Pisum sativum L.) by Improving Osmotic Adjustment Capacity and Leaf Water Relations

Salinity, as a wide spread problem around the globe, can drastically limits the crop growth and productivity. Therefore, there is a growing need to mitigate the drastic effects of this abiotic stress through the use some sustaiable short-term or long term approaches. An investigation was carried out to assess the potential role of 24-epibrassinolide (EBL) in mitigating the drastic effects of salt stress on growth, water relations, osmolytes, and ions accumulation of salt-tolerant and salt-sensitive pea genotypes. EBL treatment significantly altered the leaf water status and accumulation of osmolytes and various ions in salt-stressed [with sodium chloride (+NaCl)] plants. The plants of both salt-tolerant and salt-sensitive genotypes, subjected to +NaCl conditions had a significant reduction in plant fresh and dry weights, internodal distance, leaf area (LA), leaf water potential (w), leaf osmotic potential (o), leaf turgor potential (t), relative water content (RWC), number of seeds pod−1, seed weight, root/leaf inorganic osmolytes (Ca2+, K+ and Mg2+), while increased the levels of root/leaf proline, glycinebetaine, total free amino acids, total soluble sugars, sodium (Na+), and chloride (Cl−). There was non-significant effect of EBL on number of pods plant−1 both under saline and non-saline conditions. However, the foliar application of EBL significantly alleviated the deleterious effects of salinity by improving the plant biomass, water relations and concentration of organic/inorganic osmolytes and yield attributes. However, EBL minimized the drastic effects of salt stress by limiting the root/leaf Na+ and Cl− contents. It can be concluded that EBL efficiently alleviated the salinity-induced drastic effects by improving the water status of plant tissues, which led to salt dilution within plant tissues, thus minimized the ion-toxicity, ultimately elevated the plant growth by minimizing the toxic action of Na+ and Cl−. Secondly, EBL augmented the salt-tolerance capacity of tested pea genotypes by enhancing their osmotic adjustment potential, in terms of high accumulation of organic and inorganic osmolytes within leaf and root tissues.

Genome-Wide Identification and Evolution Analysis of Trehalose-6-Phosphate Synthase Gene Family in Nelumbo nucifera

Trehalose-6-phosphate synthase (TPS) plays a key role in plant carbohydrate metabolism and the perception of carbohydrate availability. In the present work, the publicly available Nelumbo nucifera (lotus) genome sequence database was analyzed which led to identification of nine lotus TPS genes (NnTPS). It was found that at least two introns are included in the coding sequences of NnTPS genes. When the motif compositions were analyzed we found that NnTPS generally shared the similar motifs, implying that they have similar functions. The dN/dS ratios were always less than 1 for different domains and regions outside domains, suggesting purifying selection on the lotus TPS gene family. The regions outside TPS domain evolved relatively faster than NnTPS domains. A phylogenetic tree was constructed using all predicted coding sequences of lotus TPS genes, together with those from Arabidopsis, poplar, soybean, and rice. The result indicated that those TPS genes could be clearly divided into two main subfamilies (I-II), where each subfamily could be further divided into 2 (I) and 5 (II) subgroups. Analyses of divergence and adaptive evolution show that purifying selection may have been the main force driving evolution of plant TPS genes. Some of the critical sites that contributed to divergence may have been under positive selection. Transcriptome data analysis revealed that most NnTPS genes were predominantly expressed in sink tissues. Expression pattern of NnTPS genes under copper and submergence stress indicated that NNU_014679 and NNU_022788 might play important roles in lotus energy metabolism and participate in stress response. Our results can facilitate further functional studies of TPS genes in lotus.

Identification of Submergence-Responsive MicroRNAs and Their Targets Reveals Complex MiRNA-Mediated Regulatory Networks in Lotus (Nelumbo nucifera Gaertn)

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.

Genome-wide analysis of the Solanum tuberosum (potato) trehalose-6-phosphate synthase (TPS) gene family: evolution and differential expression during development and stress

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.

Foliar treatment with Lolium perenne (Poaceae) leaf extract alleviates salinity and nickel-induced growth inhibition in pea

Abstract The plants of pea (Pisum sativum L.) were grown under NaCl and/or NiCl2 stress, to comparatively evaluate stress-mitigating effects of pure proline and naturally proline-enriched Lolium perenne (L.) aqueous leaf extract. Both stress factors (salinity and nickel) significantly reduced plant biomass, chlorophyll content, photosynthetic activity, stomatal conductance, intercellular carbon dioxide (CO2) level, number of stomata, stomatal size, water-use efficiency, relative water content (RWC), and the membrane stability index (MSI). However, the proline and glycinebetaine contents, lipid peroxidation, electrolyte leakage, and activities of antioxidant enzymes (superoxide dismutase, peroxidase, catalase, ascorbate peroxidase, guaiacol peroxidase, and glutathione reductase) were significantly increased. Exogenously applied proline and Lolium perenne (LP) leaf extracts significantly overcame the nickel and/or salinity-induced toxic effects on growth, RWC, and various photosynthetic attributes. However, follow-up treatment with proline and LP-leaf-extract detoxified the stress caused by NiCl2 and/or NaCl, by suppressing lipid peroxidation and electrolyte leakage, accelerating the antioxidant enzyme activities, and improving the MSI, leaf/root proline, and glycinebetaine contents. LP-leaf-extract proved to be better than pure proline for improving growth, gas exchange parameters, osmolytes, RWC, and antioxidant enzyme activities. As LP-leaf-extract was enriched with a substantial amount of proline along with many other essential osmoprotectants, it was found to be as effective as pure proline in ameliorating growth, some major physiological attributes, and non-enzymatic and enzymatic antioxidant activities in the pea, under nickel and/or salinity stress. Thus, it could be used as an alternative inexpensive source of proline, to be used as a mitigating agent for protecting plants against the deleterious effects of nickel and/or salinity stress.

Nitrate: ammonium ratio affects growth and development of Oxalis regnellii in hydroponic culture.

Nitrogen (N)-source ratio (NO3 -:NH4 +) effects on growth and development of oxalis have not been investigated previously. An experiment was conducted to establish an optimum NO3 -:NH4 + ratio for oxalis in a hydroponic system. Five NO3 --N:NH4 +-N ratio treatments consisting of 100:0, 75:25, 50:50, 25:75, and 0:100 were tested. Increasing proportions of NO3 --N increased total leaf, root, flower, and bottom shoot biomasses. New rhizome biomass increased with increasing NO3 --N rates until 50 and 75%, after which, new rhizome biomass decreased. Plants that received increasing amounts of NO3 --N were greener or had a greater chlorophyll index at the end of the experiment. On a dry weight basis, N, B, Fe, and Al concentrations decreased as NO3 --N levels increased, whereas K, Ca, and Mn concentrations increased. Tissue P, Mo, and Cu increased with increasing NO3 --N levels up to 50% NO3 --N supplied, and then decreased. No significant relationship was found with NO3 -: NH4 + ratios for Mg, Zn, and Na.

Genome-Wide Associations with Resistance to Bipolaris Leaf Spot (Bipolaris oryzae (Breda de Haan) Shoemaker) in a Northern Switchgrass Population (Panicum virgatum)

Switchgrass (Panicum virgatum L.), a northern native perennial grass, suffers from yield reduction from Bipolaris leaf spot caused by Bipolaris oryzae (Breda de Haan) Shoe-maker. This study aimed for determining the resistant populations via multiple phenotyping approaches and identifying potential resistance genes to the disease from genome-wide association studies in the switchgrass northern association panel. The disease resistance was evaluated from both natural (field evaluations in NY and PA) and artificial inoculations (detached leaf and leaf disk assays). There are ten out of the 66 populations showed the most resistant based on a combination of detached leaf, leaf disk, and mean from two locations. The GWAS from five subgroups from the association panel to different disease evaluation combinations yielded 27 significant SNPs on 12 chromosomes: 1K, 2K, 2N, 3K, 3N, 4N, 5K, 5N, 6N, 7K, 7N, and 9N accumulatively explaining phenotypic variance of BLUPs of detached leaf percent lesion via image analysis 26.52% at most and BLUPs of leaf disk percent lesion via image analysis 3.28% at least. Within linkage disequilibrium of 20 kb, these SNP markers linked with the potential resistance genes including genes encoding for NBS-LRR, PPR, cell wall related proteins, homeostatic proteins, anti-apoptotic proteins, and ABC transporters.

Genome-wide transcriptional analysis of submerged lotus reveals cooperative regulation and gene responses

Flooding severely limits plant growth even for some aquatic plants. Although much work has been done on submergence response of some important crop plants, little is known about the response mechanism of aquatic plants, i.e. lotus (Nelumbo nucifera). In this study, we investigated the genome-wide regulation lotus genes in response to submergence stress by high-throughput mRNA sequencing. A total of 4002 differentially expressed genes (DEGs) in lotus upon submergence stress. Among them, 1976 genes were up-regulated and 2026 down-regulated. Functional annotation of these genes by Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis revealed that they were mainly involved in processes of oxidation-reduction, abiotic stimuli, cellular metabolism and small molecule metabolism. Based on these data, previous work and quantitative RT-PCR (RT-qPCR) validation, we constructed a cooperative regulation network involved in several important DEGs in regards to the antioxidant system, disease resistance, hypoxia resistance and morphological adaptation. Further work confirmed that several innate immunity genes were induced during submergence and might confer higher resistance to lotus rot disease. In conclusion, these results provide useful information on molecular mechanisms underlying lotus responses to submergence stress.