Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Tissue-specific transcriptomic profiling of Sorghum propinquum using a rice genome array

ABSTRACT: Sorghum (Sorghum bicolor) is one of the world's most important cereal crops. S. propinquum is a perennial wild relative of S. bicolor with well-developed rhizomes. Functional genomics analysis of S. propinquum, especially with respect to molecular mechanisms related to rhizome growth and development, can contribute to the development of more sustainable grain, forage, and bioenergy cropping systems. In this study, we used a whole rice genome oligonucleotide microarray to obtain tissue-specific gene expression profiles of S. propinquum with special emphasis on rhizome development. A total of 548 tissue-enriched genes were detected, including 31 and 114 unique genes that were predominantly expressed in the rhizome tips (RT) and internodes (RI), respectively. Further GO analysis indicated that the functions of these tissue-enriched genes corresponded to their characteristic biological processes. A few distinct cis-elements, including ABA-responsive RY repeat CATGCA, sugar-repressive TTATCC, and GA-responsive TAACAA, were found to be prevalent in RT-enriched genes, implying an important role in rhizome growth and development. Comprehensive comparative analysis of these rhizome-enriched genes and rhizome-specific genes previously identified in S. propinquum indicated that phytohormones, including ABA, GA, and SA, are key regulators of gene expression during rhizome development. Co-localization of rhizome-enriched genes with rhizome-related QTLs in rice and sorghum generated functional candidates for future cloning of genes associated with rhizome growth and development. In conclusion, a whole rice genome oligonucleotide microarray was used to profile gene expression across five tissues of the perennial wild sorghum S. propinquum. Expression patterns of the five tissues were consistent with the different functions of each organ, and RT- and RI-enriched genes revealed clues regarding molecular mechanisms of rhizome development. Plant hormones, including ABA, GA, and SA, function as key regulators of rhizome gene expression and development. To shed further light on the identities of rhizome-specific genes, rhizome-enriched candidates were identified using QTL co-localization and comparative analysis. In this study, the specific gene expression patterns across five tissues, including rhizome tip (RT, distal 1 cm of the young rhizome), rhizome internodes (RI), shoot tip (ST, distal 5 mm of the tiller after removing all leaves), shoot internodes (SI) and young leaf (YL) in Sorghum propinquum, especially in the rhizome, were characterized by using a rice genome array. Three independent biological replicates for each tissue from individual plants were performed. The reference was equivalent to a mix of the 5 tissues.

ORGANISM(S): Sorghum propinquum

SUBMITTER: ting zhang

PROVIDER: E-GEOD-40380 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Sorghum (Sorghum bicolor) is one of the world's most important cereal crops. S. propinquum is a perennial wild relative of S. bicolor with well-developed rhizomes. Functional genomics analysis of S. propinquum, especially with respect to molecular mechanisms related to rhizome growth and development, can contribute to the development of more sustainable grain, forage, and bioenergy cropping systems. In this study, we used a whole rice genome oligonucleotide microarray to obtain tissue-specific gene expression profiles of S. propinquum with special emphasis on rhizome development. A total of 548 tissue-enriched genes were detected, including 31 and 114 unique genes that were predominantly expressed in the rhizome tips (RT) and internodes (RI), respectively. Further GO analysis indicated that the functions of these tissue-enriched genes corresponded to their characteristic biological processes. A few distinct cis-elements, including ABA-responsive RY repeat CATGCA, sugar-repressive TTATCC, and GA-responsive TAACAA, were found to be prevalent in RT-enriched genes, implying an important role in rhizome growth and development. Comprehensive comparative analysis of these rhizome-enriched genes and rhizome-specific genes previously identified in S. propinquum indicated that phytohormones, including ABA, GA, and SA, are key regulators of gene expression during rhizome development. Co-localization of rhizome-enriched genes with rhizome-related QTLs in rice and sorghum generated functional candidates for future cloning of genes associated with rhizome growth and development. In conclusion, a whole rice genome oligonucleotide microarray was used to profile gene expression across five tissues of the perennial wild sorghum S. propinquum. Expression patterns of the five tissues were consistent with the different functions of each organ, and RT- and RI-enriched genes revealed clues regarding molecular mechanisms of rhizome development. Plant hormones, including ABA, GA, and SA, function as key regulators of rhizome gene expression and development. To shed further light on the identities of rhizome-specific genes, rhizome-enriched candidates were identified using QTL co-localization and comparative analysis.

Project description:The Oryza longistaminata is a perennial wild rice species with AA genome, which characterized by the presence of rhizomatous stem. The rhizomatousness trait in rice was previously identified quantitatively controlled by many genes, but the molecular mechanism related to the rhizome initiation and elongation is still unknown. In this study, the specific gene expression patterns across five tissues in O. longistaminata, especially in the rhizome were characterized by using the Affymetrix rice microarray platform, the rhizome-specific expressed genes and its corresponding regulatory were further analyzed. The different gene sets were determined exclusively expressed in five tissues; strikingly 58 genes with functions related to transcription regulation and cell proliferation were identified as prevalent sets in rhizome tip, of them, several genes were functionally involved in tiller initiation and elongation. And a set of genes were differentially regulated in the rhizome tip relative to shoot tip, the predominant repressed genes are involved in photosynthesis, while genes related to phytohormone and the gene families with redundancy function were obviously differentially regulated. Several cis-regulatory elements, including CGACG, GCCCORE, GAGAC and a Myb Core, were highly enriched in rhizome tip or internode, and two cis-elements such as RY repeat and TAAAG, which implicated in the ABA signaling pathway, were found overrepresented in the rhizome tip in comparison with shoot tip. A few rhizome-specific expressed genes were co-localized on the rhizome-related QTLs regions, indicating these genes may be good functional candidates for the rhizome related gene cloning. The whole genome profiling of oryza longistaminata indicated that a very complex gene regulatory network underlies rhizome development and growth, and there might be an overlapping regulatory mechanism in the establishment of rhizome and tiller. Phytohormone such as IAA and GA are involved in the signaling pathway in determining rhizome. Several cis-elements enriched in rhizome and the identified rhizome-specific genes co-localized on the rhizome-related QTL intervals provide a base for further dissection of the molecular mechanism of rhizomatousness In this study, the specific gene expression patterns across five tissues including rhizome tip (RT, distal 1 cm of the young rhizome), rhizome internodes (RI), shoot tip (ST, distal 5 mm of the tiller after removing all leaves), shoot internodes (SI) and young leaf (YL) in O. longistaminata, especially in the rhizome were characterized by using the Affymetrix rice microarray platform.

Project description:Nelumbo, a perennial aquatic herbage that belongs to the family of Nelumbonaceae, comprises two extant species: N. nucifera Gaertn. and N. lutea (Wild.) Pers. Based on a previous study, N. nucifera is distributed in over Asia and Northern Australia while N. lutea is found in North America and northern of South America (1). N. nucifera can be divided into two cultivars including temperate lotus and tropical lotus based on its rhizome phenotype. The temperate lotus rhizome is expanded at the end of growth while tropical lotus root is of no significant enlargement during development (2). Normally, the temperate lotus root buds germinate in April, thereafter it takes several days from sowing to long roots and leaves. In mid-to-late may, vertical leaves rise out of the water, following July and August are the blooming period. Secondarily the first half of September is the final flowering period. The fruit ripening period is from late July to mid September, which is also the period of stem expansion and enrichment. After mid-October, it’s the dormant period, which is the lotus storage organ’s substance accumulation period. Thus the storage organ, mainly lotus rhizome, provides the energy for the lifecycle (Fig.1). Lotus rhizome, which is called metamorphic storage organ, is a kind of modified subterraneous stem, like potato (Solanum tuberosum) tuber and onion (Allium cepa L.) bulb (3). Most parts of lotus like rhizome, leaf, lotus seed and germ are used for traditional medicine (4). Rhizome especially is a kind of popular vegetable in Asia for its richness in nutrients including starch, proteins, vitamins (5). Nowadays it is a worldwide product in the form of the processed and semi-finished form like tea and vegetables. In general, the development of lotus rhizome can be classified into four stages: stolon stage, initial swelling, middle swelling, and later swelling stage (6, 7). The first three stages mainly focus on cell division and synthesis of some important carbohydrates, like starch, which play a critical part in the quantity and quality of rhizome, while accumulation of starch greatly increases at the last stage. Numerous studies have done in lotus to shed light on the environmental factors and morphometric indexes relevant to rhizome formation (8, 9). Short day light and low temperature promote tuber formation (10, 11). Also genes and proteins related to hormone, photoperiod (12, 13), starch synthesis (14, 15) and flowering time locus family genes were involved in the lotus rhizome formation (16). Previous studies include transcriptomics (6), genomics (17) and certain physiological researches, revealing numerous genes involved in photoperiod pathway, starch metabolism and hormone signal transduction, trying to make lotus a model plant of rhizome growth, while there is a lack of protein-level dynamic analysis and protein phosphorylation information, which is a strong proof for the dynamic processes in lotus rhizome. Proteomics is an indispensable method in storage organs research findings (18, 19), 2-DE and MALDI-TOF-TOF was employed to find some different protein profiles in fresh-cut lotus tuber before and after browning (20). And comparative proteomic was employed to analyze the Horsetail (Equisetum hyemale) underground stem to throw light upon the related proteins of developing rhizomes in ancient vascular plant Equisetum hyemale and different monocot species (21). Proteomics can also assist us in getting the changes of proteins in differently treated samples of potato tuber by using a LC-MS spectral-counting proteomics strategy (1), and shed light on the molecular basis of tuberization in potato to monitor differentially expressed proteins at different development stages (22). But the proteomic study of lotus rhizome enlargement hasn’t been reported now. Here, we employed comparative proteomics and phosphoproteomics to get proteins and its phosphorylation changes in the course of different rhizome development stages. Our data highlights some pathways, proteins and phosphorylated proteins during the development, and the difference between proteome and phosphoproteome in rhizome formation process.

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Tissue-specific transcriptomic profiling of Sorghum propinquum using a rice genome array

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