Internodes of grass stems function in mechanical support, transport, and, in some species, are a major sink organ for carbon in the form of cell wall polymers. This study reports cell wall composition, proteomic, and metabolite analyses of the rice elongating internode. Cellulose, lignin, and xylose increase as a percentage of cell wall material along eight segments of the second rice internode (internode II) at booting stage, from the younger to the older internode segments, indicating active cell wall synthesis. Liquid-chromatography tandem mass spectrometry (LC-MS/MS) of trypsin-digested proteins from this internode at booting reveals 2,547 proteins with at least two unique peptides in two biological replicates. The dataset includes many glycosyltransferases, acyltransferases, glycosyl hydrolases, cell wall-localized proteins, and protein kinases that have or may have functions in cell wall biosynthesis or remodeling. Phospho-enrichment of internode II peptides identified 21 unique phosphopeptides belonging to 20 phosphoproteins including a leucine rich repeat-III family receptor like kinase. GO over-representation and KEGG pathway analyses highlight the abundances of proteins involved in biosynthetic processes, especially the synthesis of secondary metabolites such as phenylpropanoids and flavonoids. LC-MS/MS of hot methanol-extracted secondary metabolites from internode II at four stages (booting/elongation, early mature, mature, and post mature) indicates that internode secondary metabolites are distinct from those of roots and leaves, and differ across stem maturation. This work fills a void of in-depth proteomics and metabolomics data for grass stems, specifically for rice, and provides baseline knowledge for more detailed studies of cell wall synthesis and other biological processes characteristic of internode development, toward improving grass agronomic properties.

Drought is a major constraint to the productivity of many crops affecting various physiological and biochemical processes. Seventy percent of the peanuts are grown in semiarid tropics that are frequently prone to drought stress. So, we analyzed its effect in 4 cultivars of peanut, with different degrees of drought tolerance, under 10 and 20 days of water stress using two-dimensional gel electrophoresis and mass spectrometry. A total of 189 differentially expressed protein spots were identified in the leaf proteome of all the 4 cultivars using PD Quest Basic software; 74 in ICGV 91114, 41 in ICGS 76, 44 in J 11 and 30 in JL 24. Of these, 30 protein spots were subjected to in-gel trypsin digestion followed by MALDI-TOF that are functionally categorized into 5 groups: molecular chaperones, signal transducers, photosynthetic proteins, defense proteins and detoxification proteins. Of these, 12 proteins were sequenced. Late embryogenesis abundant protein, calcium ion binding protein, sucrose synthase isoform-1, 17.3 kDa heat shock protein and structural maintenance of chromosome proteins were overexpressed only in the 15 and 20 days stressed plants of ICGV 91114 cultivar while cytosolic ascorbate peroxidase was expressed with varying levels in the 10 and 20 days stressed plants of all the 4 cultivars. Signaling protein like 14-3-3 and defense proteins like alpha-methyl-mannoside-specific lectin and mannose/glucose-binding lectins were differentially expressed in the 4 cultivars. Photosynthetic protein like Rubisco was down-regulated in the stressed plants of all 4 cultivars while Photosystem-I reaction center subunit-II of chloroplast precursor protein was overexpressed in only 20 days stressed plants of ICGV 91114, ICGS 76 and J11 cultivars. These differentially expressed proteins could potentially be used as protein markers for screening the peanut germplasm and further crop improvement.

Deciphering the transcriptomic insight during organogenesis in castor (Ricinus communis L.), jatropha 1 (Jatropha curcas L.) and sunflower (Helianthus annuus L.) 2 3 Abstract 21 Background: Castor is a non-edible oilseed crop with a multitude of pharmaceutical and industrial uses. 22Profitable cultivation of the crop is hindered by various factors and one of the approaches for genetic 23 improvement of the crop belonging to a monotypic genus is to exploit biotechnological tools. The major 24 limitation for successful exploitation of biotechnological tools is the in vitro recalcitrance of castor tissues. 25Response of castor tissues to in vitro culture is poor which necessitated study on understanding the molecular 26 basis of organogenesis in cultured tissues of castor, through de novo transcriptome analysis, by comparing with 27 two other crops (jatropha and sunflower) with good regeneration ability. 29Results: RNA-seq analysis was carried out with hypocotyl explants from castor, jatropha and cotyledons from 30 sunflower cultured on MS media supplemented with different concentrations of hormones. Genes that showed 31 strong differential expression analysis during dedifferentiation and organogenic differentiation stages of callus 32 included components of auxin and cytokinin signaling, secondary metabolite synthesis, genes encoding 33 transcription factors, receptor kinases and protein kinases. In castor, many genes involved in auxin biosynthesis 34 and homeostasis like WAT1 (Wall associated thinness), vacuolar transporter genes, transcription factors like 35 short root like protein were down-regulated while genes like DELLA were upregulated accounting for 36 regeneration recalcitrance. Validation of 62 differentially expressed genes through qRT-PCR showed a consensus 37 of 77.4% with the RNA-Seq analysis. 39Conclusion: This study provides information on the set of genes involved in the process of organogenesis in 40 three oilseed crops which forms a basis for understanding and improving the efficiency of plant regeneration and 41 genetic transformation in castor. 42 43 44 45 46 3 Background 47Castor (Ricinus communis L.) is a tropical plant that belongs to Euphorbiaceae family and grown mainly for its non-48 edible oil. Despite the premier position India holds with 85% of world's total castor production dominating 49 international castor oil trade, profitable cultivation of this crop is hampered by the vulnerability of the released 50 cultivars to several biotic threats at various stages of crop growth and the presence of the toxic protein, ricin in the 51 seeds limiting the use of seed cake as cattle feed. The genetic variability to biotic stresses and seed quality traits is 52 limited in the cultivar germplasm [1, 2]. Conventional breeding techniques have limited scope in improvement of 53 resistance to biotic stresses and oil quality necessitating the exploitation of biotechnological and genetic engineering 54 tools [3, 4, 5]. The main prerequisites for genetic improvement are reliable and reproducible protoc...

Deciphering the transcriptomic insight during organogenesis in castor (Ricinus communis L.), jatropha (Jatropha curcas L.) and sunflower (Helianthus annuus L.