Transcriptional and Metabolic Analysis of Senescence Induced by Preventing Pollination in Maize

Sekhon, Rajandeep S.; Childs, Kevin L.; Santoro, Nicholas; Foster, Cliff E.; Buell, C. Robin; León, Natalia de; Kaeppler, Shawn M.

doi:10.1104/pp.112.199224

Cited by 76 publications

(87 citation statements)

References 81 publications

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“…The microarray data, from genome-wide gene expression analysis of the maize inbred line B73 (GSE27004) and transcriptomic analysis of induced maize senescence, was provided by Dr. Shawn Kaeppler of the University of Wisconsin (Sekhon et al 2011(Sekhon et al , 2012. The Affymetrix GeneChip array data of gene expression during infection with three fungi and drought treatment were downloaded from GEO with the accession numbers GSE31188, GSE19501, GSE29747, and GSE16567 (Zheng et al 2010;Ghareeb et al 2011;Voll et al 2011).…”

Section: Microarray Data Collection and Analyses Of Expression Profilesmentioning

confidence: 99%

Isolation, structural analysis, and expression characteristics of the maize TIFY gene family

Zhang

et al. 2015

Mol Genet Genomics

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TIFY, previously known as ZIM, comprises a plant-specific family annotated as transcription factors that might play important roles in stress response. Despite TIFY proteins have been reported in Arabidopsis and rice, a comprehensive and systematic survey of ZmTIFY genes has not yet been conducted. To investigate the functions of ZmTIFY genes in this family, we isolated and characterized 30 ZmTIFY (1 TIFY, 3 ZML, and 26 JAZ) genes in an analysis of the maize (Zea mays L.) genome in this study. The 30 ZmTIFY genes were distributed over eight chromosomes. Multiple alignment and motif display results indicated that all ZmTIFY proteins share two conserved TIFY and Jas domains. Phylogenetic analysis revealed that the ZmTIFY family could be divided into two groups. Putative cis-elements, involved in abiotic stress response, phytohormones, pollen grain, and seed development, were detected in the promoters of maize TIFY genes. Microarray data showed that the ZmTIFY genes had tissue-specific expression patterns in various maize developmental stages and in response to biotic and abiotic stresses. The results indicated that ZmTIFY4, 5, 8, 26, and 28 were induced, while ZmTIFY16, 13, 24, 27, 18, and 30 were suppressed, by drought stress in the maize inbred lines Han21 and Ye478. ZmTIFY1, 19, and 28 were upregulated after infection by three pathogens, whereas ZmTIFY4, 13, 21, 23, 24, and 26 were suppressed. These results indicate that the ZmTIFY family may have vital roles in response to abiotic and biotic stresses. The data presented in this work provide vital clues for further investigating the functions of the genes in the ZmTIFY family.

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Section: Microarray Data Collection and Analyses Of Expression Profilesmentioning

confidence: 99%

Isolation, structural analysis, and expression characteristics of the maize TIFY gene family

Zhang

et al. 2015

Mol Genet Genomics

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“…Mapping of sequences, creation of bins, and other relevant details are as described earlier (Sekhon et al, 2012). For the MapMan analysis, the log 2 ratio of fold change in expression (KLS30/KSS30) was calculated for each stage of sampling.…”

Section: Microarray and Rna-seq Analysesmentioning

confidence: 99%

Phenotypic and Transcriptional Analysis of Divergently Selected Maize Populations Reveals the Role of Developmental Timing in Seed Size Determination

et al. 2014

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Seed size is a component of grain yield and an important trait in crop domestication. To understand the mechanisms governing seed size in maize (Zea mays), we examined transcriptional and developmental changes during seed development in populations divergently selected for large and small seed size from Krug, a yellow dent maize cultivar. After 30 cycles of selection, seeds of the large seed population (KLS30) have a 4.7-fold greater weight and a 2.6-fold larger size compared with the small seed population (KSS30). Patterns of seed weight accumulation from the time of pollination through 30 d of grain filling showed an earlier onset, slower rate, and earlier termination of grain filling in KSS30 relative to KLS30. This was further supported by transcriptome patterns in seeds from the populations and derived inbreds. Although the onset of key genes was earlier in small seeds, similar maximum transcription levels were observed in large seeds at later stages, suggesting that functionally weaker alleles, rather than transcript abundance, may be the basis of the slow rate of seed filling in KSS30. Gene coexpression networks identified several known genes controlling cellularization and proliferation as well as novel genes that will be useful candidates for biotechnological approaches aimed at altering seed size in maize and other cereals.

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“…At the transcriptional level, the regulation of senescence has been well studied in model species such as A. thaliana (Gepstein et al, 2003;Lim et al, 2003;Lin and Wu, 2004). Furthermore, this process has been partially assessed in other species such as rice (Lee et al, 2001), tobacco (Pageau et al, 2006), pea (Pic et al, 2002), wheat (Uauy et al, 2006), cotton (Kong et al, 2013), maize (Sekhon et al, 2012;Zhang et al, 2014), turnip (Gombert et al, 2006), barley (Hollmann et al, 2014;Jukanti et al, 2008) and sunflower (Cabello et al, 2006;Fernandez et al, 2012a;Moschen et al, 2014). Transcription factors (TFs) are key proteins in the regulation of gene expression and signal transduction networks regulating different biological processes.…”

Section: Introductionmentioning

confidence: 99%

Integrating transcriptomic and metabolomic analysis to understand natural leaf senescence in sunflower

Moschen

Luoni

Rienzo

et al. 2015

Plant Biotechnology Journal

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SummaryLeaf senescence is a complex process, which has dramatic consequences on crop yield. In sunflower, gap between potential and actual yields reveals the economic impact of senescence. Indeed, sunflower plants are incapable of maintaining their green leaf area over sustained periods. This study characterizes the leaf senescence process in sunflower through a systems biology approach integrating transcriptomic and metabolomic analyses: plants being grown under both glasshouse and field conditions. Our results revealed a correspondence between profile changes detected at the molecular, biochemical and physiological level throughout the progression of leaf senescence measured at different plant developmental stages. Early metabolic changes were detected prior to anthesis and before the onset of the first senescence symptoms, with more pronounced changes observed when physiological and molecular variables were assessed under field conditions. During leaf development, photosynthetic activity and cell growth processes decreased, whereas sucrose, fatty acid, nucleotide and amino acid metabolisms increased. Pathways related to nutrient recycling processes were also up-regulated. Members of the NAC, AP2-EREBP, HB, bZIP and MYB transcription factor families showed high expression levels, and their expression level was highly correlated, suggesting their involvement in sunflower senescence. The results of this study thus contribute to the elucidation of the molecular mechanisms involved in the onset and progression of leaf senescence in sunflower leaves as well as to the identification of candidate genes involved in this process.

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Transcriptional and Metabolic Analysis of Senescence Induced by Preventing Pollination in Maize

Cited by 76 publications

References 81 publications

Isolation, structural analysis, and expression characteristics of the maize TIFY gene family

Isolation, structural analysis, and expression characteristics of the maize TIFY gene family

Phenotypic and Transcriptional Analysis of Divergently Selected Maize Populations Reveals the Role of Developmental Timing in Seed Size Determination

Integrating transcriptomic and metabolomic analysis to understand natural leaf senescence in sunflower

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