High transcriptome plasticity drives phosphate starvation responses in tomato.

Tomato is an important vegetable crop and fluctuating available soil phosphate (Pi) level elicits several morpho-physiological responses driven by underlying molecular responses. Therefore, understanding these molecular responses at the gene and isoform levels has become critical in the quest for developing crops with improved Pi use efficiency. A quantitative time-series RNA-seq analysis was performed to decipher the global transcriptomic changes that accompany Pi starvation in tomato. Apart from changes in the expression levels of genes, there were also alterations in the expression of alternatively-spliced transcripts. Physiological responses such as anthocyanin accumulation, reactive oxygen species generation and cell death are obvious 7 days after Pi deprivation accompanied with the maximum amount of transcriptional change in the genome making it an important stage for in-depth study while studying Pi stress responses (PSR). Our study demonstrates that transcriptomic changes under Pi deficiency are dynamic and complex in tomato. Overall, our study dwells on the dynamism of the transcriptome in eliciting a response to adapt to low Pi stress and lays it bare. Findings from this study will prove to be an invaluable resource for researchers using tomato as a model for understanding nutrient deficiency.

Genome-wide identification and characterization of SPX-domain-containing protein gene family in Solanum lycopersicum.

The SYG1, PHO81, and XPR1 (SPX) domain is named after the suppressor of yeast gpa1 (Syg1), yeast phosphatase (Pho81) and the human Xenotropic and Polytrophic Retrovirus receptor1 (XPR1). SPX-domain-containing proteins play pivotal roles in maintaining phosphate ions (Pi) homeostasis in plant. This study was to genome-wide identification and analysis of Solanum lycopersicum SPX-domain-containing protein gene family. The Solanum lycopersicum genome contains 19 SPX-domain-containing protein genes. These SPX-domain-containing protein genes were located in seven of the 12 chromosomes. According to the different conserved domains, the proteins encoded by those genes could be divided into four SPX-domain-containing protein families, which included SPX Family, SPX-ERD1/XPR1/SYG1(SPX-EXS) Family, SPX-Major Facilitator Superfamily (SPX-MFS) Family and SPX-Really Interesting New Gene (SPX-RING) Family. Phylogenetic analysis of SPX-domain-containing protein genes in Arabidopsis thaliana, Solanum tuberosum, Capsicum annuum and Solanum lycopersicum classified these genes into eight clades. Expression profiles derived from transcriptome (RNA-seq) data analysis showed 19 SPX-domain-containing protein genes displayed various expression patterns. SPX-domain-containing protein may play different roles in phosphate nutrition of Solanum lycopersicum different tissues and development stages. And, this study can provide the selection of candidate genes for functional research and genome editing in Solanum lycopersicum phosphate ions (Pi) nutrition.

A CRISPR/Cas9 deletion into the phosphate transporter SlPHO1;1 reveals its role in phosphate nutrition of tomato seedlings.

In vascular (Arabidopsis thaliana) and non-vascular (Physcomitrella patens) plants, PHOSPHATE 1 (PHO1) homologs play important roles in the acquisition and transfer of phosphate. The tomato genome contains six genes (SlPHO1;1-SlPHO1;6) homologous to AtPHO1. The six proteins have typical characteristics of the plant PHO1 family, such as the three Syg1/Pho81/XPRI (SPX) subdomains in the N-terminal portion and one ERD1/XPR1/SYG1 (EXS) domain in the C-terminal portion. Phylogenetic analysis revealed that the SlPHO1 family is subdivided into three clusters. A pairwise comparison indicated that SlPHO1;1 showed the highest level of sequence identity/similarity (67.39/76.21%) to AtPHO1. SlPHO1;1 deletion mutants induced by clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 displayed typical phenotypes of Pi starvation, such as decreased shoot fresh weight and increased root fresh weight, therefore having a greater root-to-shoot ratio. Mutants also accumulated more anthocyanin and had more soluble Pi content in the root and less in the shoot. These results indicate that SlPHO1;1 plays an important role in Pi transport in the tomato at seedling stage.

Forsythia suspensa extract attenuates lipopolysaccharide-induced inflammatory liver injury in rats via promoting antioxidant defense mechanisms.

Reactive oxygen species (ROS) have been shown to have a role in inflammation. We investigated whether Forsythia suspensa extract (FSE) could exert its antioxidant potential against lipopolysaccharide (LPS)-induced inflammatory liver injury in rats. Rats were orally fed FSE once daily for 7 consecutive days prior to LPS (Escherichia coli, serotype O55:B5) injection. LPS treatment caused liver dysfunction as evidenced by massive histopathological changes and increased serum alanine aminotransferase and aspartate aminotransferase activities which were ameliorated by FSE pretreatment. FSE attenuated LPS-induced depletion of cytosolic nuclear factor-erythroid 2-related factor 2 (Nrf2) and suppression of Nrf2 nuclear translocation in liver, and the generation of ROS and malondialdehyde in serum and liver. FSE increased the Nrf2-mediated induction of heme oxygenase-1 in liver, as well as superoxide dismutase and glutathione peroxidase activities in serum and liver. Importantly, FSE attenuated LPS-induced nuclear factor-кB (NF-кB) nuclear translocation in liver, and subsequently decreased tumor necrosis factor-α, interleukin (IL)-1ß and IL-6 levels in serum and liver, which were associated with FSE-induced activation of Nrf2 in liver. These results indicate that the protective mechanisms of FSE may be involved in the attenuation of oxidative stress and the inhibition of the NF-кB-mediated inflammatory response by modulating the Nrf2-mediated antioxidant response against LPS-induced inflammatory liver injury.

Effect of Forsythia suspensa extract and chito-oligosaccharide alone or in combination on performance, intestinal barrier function, antioxidant capacity and immune characteristics of weaned piglets.

We investigated the effects of Forsythia suspensa extract (FSE) and chito-oligosaccharide (COS), alone or together, on performance and health status of weaned piglets. The treatments included a basal diet and three diets with 160 mg/kg COS, 100 mg/kg FSE, or 100 mg/kg FSE and 160 mg/kg COS. Supplementation with COS or FSE alone improved (P < 0.01) average daily gain and feed conversion ratio compared with the basal diet in the first 2 weeks. On day 14, COS or FSE supplementation separately produced stronger (P < 0.01) serum total antioxidant capacity and glutathione peroxidase activities and lower serum endotoxin (P < 0.05) and malondialdehyde (P < 0.01) concentrations, generated higher (P < 0.01) serum complement 4 concentration, peripheral blood lymphocyte proliferation and serum-specific ovalbumin antibody level than the basal diet. No differences in oxidative injury and immunity indices were detected on day 28. The combined FSE and COS produced similar results compared with FSE or COS when given alone. These data indicate FSE or COS can increase performance by modulating intestinal permeability, antioxidant status and immune function in younger pigs. There appears to be similar advantage in feeding the additives in combination over those obtained from feeding them separately.

Dissecting stylar responses to self-pollination in wild tomato self-compatible and self-incompatible species using comparative proteomics.

Self-incompatibility (SI), a phenomenon that is widespread among flowering plants (angiosperms), promotes outbreeding, resulting in increased genetic diversity and species survival. SI is also important in establishing intra- or interspecies reproductive barriers, such as those that are evident in the tomato clade, Solanum section Lycopersicon, where they limit the use of wild species inbreeding programs to improve cultivated tomato. However, the molecular mechanisms underlying SI are poorly understood in the tomato clade. In this study, an SI (Solanum chilense, LA0130) and a self-compatible (SC, Solanum pimpinellifolium, LA1585) tomato species were chosen to dissect the mechanism of SI formation using a comparative proteomics approach. A total of 635 and 627 protein spots were detected in two-dimensional electrophoresis (2-DE) maps of proteins from the SI and SC species, respectively. In the SC species, 22 differently expressed proteins (DEPs) were detected in SCP versus SCUP (self-pollination versus non-pollination in SC species). Of these, 3 and 18 showed an up-or down-regulated expression in the SCP protein sample, respectively, while only one DEP (MSRA, Solyc03g111720) was exclusively expressed in the SCP sample. In the SI species, 14 DEPs were found between SIP/SIUP, and 5 of these showed higher expression in SIP, whereas two DEPs (MLP-like protein 423-like, gene ID, 460386008 and (ATP synthase subunit alpha, gene ID, Solyc00g042130) were exclusively expressed in SIP or SIUP, respectively. Finally, two S-RNases (gene IDs, 313247946 and 157377662) were exclusively expressed in the SI species. Sequence homology analysis and a gene ontology tool were used to assign the DEPs to the 'metabolism', 'energy', 'cytoskeleton dynamics', 'protein degradation', 'signal transduction', 'defence/stress responses', 'self-incompatibility' and 'unknown' protein categories. We discuss the putative functions of the DEPs in different biological processes and how these might be associated with the regulation of SI formation in the tomato clade.

Dissect style response to pollination using metabolite profiling in self-compatible and self-incompatible tomato species.

Tomato style is the pathway for pollen germination and pollen tubes growth from the stigma to the ovules where fertilization occurs. It is essential to supplying the nutrients for pollen tube growth and guidance for the pollen tubes. To our knowledge, style also regulates gametophytic self-incompatibility (SI) in tomato species. This study identified the metabolites and monitored the metabolic changes of self-incompatible and self-compatible tomato with self-pollinated or unpollinated styles by gas chromatography-mass spectrometry (GC-MS). A total of 9 classes of compounds were identified in SI and self-compatibility (SC) self-pollinated and unpollinated styles which included amino acids, sugars, fatty acids/lipids, amines, organic acids, alcohols, nitriles, inorganic acids and other compounds. The contents of d-Mannose-6-phosphate, Cellobiose, Myristic acid, 2,4-Diaminobutyric acid, Inositol and Urea were significantly decreased and the rest did not significantly change in SI styles. But change of metabolites content significantly happened in SC styles. In addition, among the total 9 classes of compounds, the different metabolites accounted for a different proportion in amino acids, sugars, amines, organic acids and alcohols compared SC and SI. The result indicated that the physiological changes of styles existed differences in SC and SI after self pollination.

Dissection of the style's response to pollination using transcriptome profiling in self-compatible (Solanum pimpinellifolium) and self-incompatible (Solanum chilense) tomato species.

BACKGROUND: Tomato (Solanum lycopersicum) self-compatibility (SC) is defined as self-pollen tubes that can penetrate their own stigma, elongate in the style and fertilize their own ovules. Self-incompatibility (SI) is defined as self-pollen tubes that are prevented from developing in the style. To determine the influence of gene expression on style self-pollination, a transcriptome-wide comparative analysis of SC and SI tomato unpollinated/pollinated styles was performed using RNA-sequencing (RNA-seq) data. RESULTS: Transcriptome profiles of 24-h unpollination (UP) and self-pollination (P) styles from SC and SI tomato species were generated using high-throughput next generation sequencing. From the comparison of SC self-pollinated and unpollinated styles, 1341 differentially expressed genes (DEGs) were identified, of which 753 were downregulated and 588 were upregulated. From the comparison of SI self-pollinated and unpollinated styles, 804 DEGs were identified, of which 215 were downregulated and 589 were upregulated. Nine gene ontology (GO) terms were enriched significantly in SC and 78 GO terms were enriched significantly in SI. A total of 105 enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified in SC and 80 enriched KEGG pathways were identified in SI, among which "Cysteine and methionine metabolism pathway" and "Plant hormone signal transduction pathway" were significantly enriched in SI. CONCLUSIONS: This study is the first global transcriptome-wide comparative analysis of SC and SI tomato unpollinated/pollinated styles. Advanced bioinformatic analysis of DEGs uncovered the pathways of "Cysteine and methionine metabolism" and "Plant hormone signal transduction", which are likely to play important roles in the control of pollen tubes growth in SI species.

Super High Dosing with a Novel Buttiauxella Phytase Continuously Improves Growth Performance, Nutrient Digestibility, and Mineral Status of Weaned Pigs.

This study was conducted to evaluate the efficacy of a novel Buttiauxella phytase to pigs fed P-deficient, corn-soybean meal diets. One hundred and twenty crossbred piglets (9.53 ± 0.84 kg) were allocated to one of five treatments which consisted of four low P diets (0.61 % Ca and 0.46 % total P) supplemented with 0, 500, 1,000, or 20,000 FTU/kg phytase as well as a positive control diet (0.77 % Ca and 0.62 % total P). Each treatment had six replicated pens with four pigs per pen. Pigs were fed the experimental diets for 28 days. Phytase supplementation linearly improved (P < 0.05) average daily gain (ADG), feed conversion ratio (FCR), and apparent total tract digestibility (ATTD) of dry matter, gross energy, crude protein, Ca, and P in weaned pigs. Super high dosing with phytase (20,000 FTU/kg) further increased (P < 0.05) ADG compared with 500 FTU/kg phytase inclusion group, as well as ATTD of Ca and P. Metacarpal bone characteristics and several trace mineral concentration in bone, plasma, or organ tissues were linearly (P < 0.05) improved at increasing dose of phytase. Super high dosing with phytase (20,000 FTU/kg) supplementation improved (P < 0.05) Mn and Zn concentration in bone compared to normal dose of phytase supplementation (500 or 1,000 FTU/kg). In conclusion, supplementation of 500 FTU of Buttiauxella phytase/kg and above effectively hydrolyzed phytate in a low-P corn-soybean diet for pigs. In addition, a super high dosing with phytase (20,000 FTU/kg) improved macro- or micro mineral availability and growth performance.

Effects of essential oil supplementation of a low-energy diet on performance, intestinal morphology and microflora, immune properties and antioxidant activities in weaned pigs.

A total of 144 weaned piglets were used to evaluate the effects of essential oil (EO) supplementation of a low-energy diet on performance, apparent nutrient digestibility, small intestinal morphology, intestinal microflora, immune properties and antioxidant activities in weaned pigs. Pigs received a low-energy diet (negative control, NC, digestible energy = 3250 kcal/kg), NC plus 0.025% EO or a positive control diet (PC, digestible energy = 3400 kcal/kg) for 28 days. Growth performance was similar between the EO group and PC group. However, EO supplementation increased (P < 0.05) average daily gain and the apparent digestibility of dry matter, crude protein and energy compared with pigs fed the NC diet. Greater (P < 0.05) villus height and lower (P < 0.05) counts of Escherichia coli and total anaerobes in the rectum in the EO group were observed compared with NC or PC groups. Pigs fed EO diet had higher (P < 0.05) concentrations of albumin, immunoglobulin A (IgA), IgG and total antioxidant capacity and lower fecal score than pigs fed the PC and NC diets. Above all, this study indicates that supplementation of EO to a low-energy pig diet has beneficial results and obtains similar performance compared with normal energy (PC) diet.

Fine mapping of RppP25, a southern rust resistance gene in maize.

Southern rust (Puccinia polysora Underw.) is a major disease that can cause severe yield losses in maize (Zea mays L.). In our previous study, a major gene RppP25 that confers resistance to southern rust was identified in inbred line P25. Here, we report the fine mapping and candidate gene analysis of RppP25 from the near-isogenic line F939, which harbors RppP25 in the genetic background of the susceptible inbred line F349. The inheritance of resistance to southern rust was investigated in the BC1 F1 and BC3 F1 populations, which were derived from a cross between F939 and F349 (as the recurrent parent). The 1:1 segregation ratio of resistance to susceptible plants in these two populations indicated that the resistance is controlled by a single dominant gene. Ten markers, including three simple sequence repeat (SSR) markers and seven insertion/deletion (InDel) markers, were developed in the RppP25 region. RppP25 was delimited to an interval between P091 and M271, with an estimated length of 40 kb based on the physical map of B73. In this region, a candidate gene was identified that was predicted to encode a putative nucleotide-binding site leucine-rich repeat (NBS-LRR) protein. Two co-segregated markers will aid in pyramiding diverse southern rust resistance alleles into elite materials, and thereby improve southern rust resistance worldwide.