Abstract:
:In the wake of recent progress of high throughput transcriptome profiling technologies, extensive housekeeping gene mining has been conducted in humans. However, very few studies have been reported in maize (Zea mays L.), an important crop plant, and none were conducted on a genome -wide level. In this study, we surveyed housekeeping genes throughout the maize transcriptome using RNA-seq and microarray techniques, and validated the housekeeping profile with quantitative polymerase chain reaction (qPCR) under a series of conditions including different genotypes and nitrogen supplies. Seven microarray datasets and two RNA-seq libraries representing 40 genotypes at more than 20 developmental stages were selected to screen for commonly expressed genes. A total of 1,661 genes showed constitutive expression in both microarray and RNA-seq datasets, serving as our starting housekeeping gene candidates. To determine for stably expressed housekeeping genes, NormFinder was used to select the top 20 % invariable genes to be the more likely candidates, which resulted in 48 and 489 entries from microarray and RNA-seq data, respectively. Among them, nine genes (2OG-Fe, CDK, DPP9, DUF, NAC, RPN, SGT1, UPF1 and a hypothetical protein coding gene) were expressed in all 40 maize diverse genotypes tested covering 16 tissues at more than 20 developmental stages under normal and stress conditions, implying these as being the most reliable reference genes. qPCR analysis confirmed the stable expression of selected reference gene candidates compared to two widely used housekeeping genes. All the reference gene candidates showed higher invariability than ACT and GAPDH. The hypothetical protein coding gene exhibited the most stable expression across 26 maize lines with different nitrogen treatments with qPCR, followed by CDK encoding the cyclin-dependent kinase. As the first study to systematically screen for housekeeping genes in maize, we identified candidates by examining the transcriptome atlas generated from RNA-seq and microarray technologies. The nine top-ranked qPCR-validated novel housekeeping genes provide a valuable resource of reference genes for maize gene expression analysis.
journal_name
Plant Mol Bioljournal_title
Plant molecular biologyauthors
Lin F,Jiang L,Liu Y,Lv Y,Dai H,Zhao Hdoi
10.1007/s11103-014-0246-1subject
Has Abstractpub_date
2014-11-01 00:00:00pages
543-54issue
4-5eissn
0167-4412issn
1573-5028journal_volume
86pub_type
杂志文章abstract::The plant senescence syndrome resembles, in many molecular and phenotypic aspects, plant responses to abiotic stresses. Both processes have an enormous negative global agro-economic impact and endanger food security worldwide. Premature plant senescence is the main cause of losses in grain filling and biomass yield du...
journal_title:Plant molecular biology
pub_type: 杂志文章,评审
doi:10.1007/s11103-013-0038-z
更新日期:2013-08-01 00:00:00
abstract::A combined chemical, biochemical and molecular study was conducted to understand the differential accumulation of volatile sesquiterpenes in melon fruits. Sesquiterpenes were present mainly in the rinds of climacteric varieties, and a great diversity in their composition was found among varieties. Sesquiterpenes were ...
journal_title:Plant molecular biology
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doi:10.1007/s11103-008-9296-6
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abstract::The rice blast resistance gene Pib is a member of the nucleotide binding site (NBS) and leucine-rich repeat (LRR) class of plant disease resistance (R) genes and belongs to a small gene family. We describe here the isolation and characterization of a Pib homologue (PibH8), and extensive investigation of the expression...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1023/a:1012457113700
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abstract::Plants produce ethylene in response to many biotic and abiotic stresses. In response to ozone the foliage of potato plants sequentially expressed two ACC synthase genes (ST-ACS4, ST-ACS5). The same expression pattern of the two genes also occurred in response to Cu2+ and infection with Alternaria solani. ST-ACS5 expre...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1023/a:1005857717196
更新日期:1997-12-01 00:00:00
abstract::Transfer RNA genes have been mapped to at least nine different loci on the physical map of the Euglena gracilis chloroplast genome. One of these loci in the ribosomal RNA operons is present three times per genome. The DNA sequences of six of the nine different loci, containing 21 different tRNA genes, have been determ...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/BF00016064
更新日期:1984-05-01 00:00:00
abstract::Plants cope with pathogens with distinct mechanisms. One example is a gene-for-gene system, in which plants recognize the pathogen molecule by specified protein(s), this being called the R factor. However, mechanisms of interaction between proteins from the host and the pathogen are not completely understood. Here, we...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/s11103-005-5817-8
更新日期:2006-05-01 00:00:00
abstract::Tomato protoplasts have been transformed with plasmid DNA's, containing a chimeric kanamycin resistance gene and putative tomato origins of replication. A calcium phosphate-DNA mediated transformation procedure was employed in combination with either polyethylene glycol or polyvinyl alcohol. There were no indications ...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/BF00015816
更新日期:1987-09-01 00:00:00
abstract::The auxin-binding protein isolated from maize coleoptiles and characterized in detail describes an auxin recognition protein at the outer surface of the plasmalemma which mediates the auxin effect on cell elongation in maize coleoptiles. Its homologue in tobacco mesophyll protoplasts mediates the auxin effect on secre...
journal_title:Plant molecular biology
pub_type: 杂志文章,评审
doi:10.1007/BF00019401
更新日期:1990-06-01 00:00:00
abstract::A chimeric gene consisting of a bean (Phaseolus vulgaris L.) chalcone synthase (CHS) promoter fused to a bacterial chloramphenicol acetyltransferase (CAT) reporter gene was strongly expressed, and further induced by fungal elicitor, when electroporated into alfalfa (Medicago sativa L.) suspension cell protoplasts. Fun...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/BF00015079
更新日期:1991-05-01 00:00:00
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journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/s11103-016-0430-6
更新日期:2016-04-01 00:00:00
abstract::We have sequenced and analysed the transaldolase (tal) genes from two cyanobacteria, Anabaena variabilis (ATCC 29413) and Synechocystis sp. PCC 6803, which are filamentous heterocyst-forming and unicellular organisms, respectively. The deduced amino acid sequences of the two cyanobacterial tal genes are 78% identical ...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/BF00017817
更新日期:1996-01-01 00:00:00
abstract:KEY MESSAGE:In this manuscript, we disclosed the influence of light on the accumulation of storage reserves in B. napus embryos.1.Light induced the gene expression in the developing embryos of B. napus.2.Light promoted the starch synthesis in chloroplasts of B. napus embryos.3.Light enhanced the metabolic activity of s...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/s11103-020-01003-0
更新日期:2020-07-01 00:00:00
abstract::The PR-like proteins, class I beta-1,3-glucanase (GLU I) and chitinase (CHN I), are induced as part of a stereotypic response that can provide protection against viral, bacterial, and fungal pathogens. We have identified two Nicotiana plumbaginifolia ankyrin-repeat proteins, designated Glucanohydrolase Binding Protein...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/s11103-004-4679-9
更新日期:2004-11-01 00:00:00
abstract::We have cloned, sequenced, and examined the expression of genes from pine trees that appear to encode extracellular class II chitinase. Nucleotide sequence analysis indicates a coding sequence composed of three exons interrupted by two introns at locations identical to those found in other chitinase genes that possess...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1023/a:1005708611020
更新日期:1997-04-01 00:00:00
abstract::Exocarp color of sand pear is an important trait for the fruit production and has caused our concern for a long time. Our previous study explored the different expression genes between the two genotypes contrasting for exocarp color, which indicated the different suberin, cutin, wax and lignin biosynthesis between the...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/s11103-014-0173-1
更新日期:2014-05-01 00:00:00
abstract::The funiculus provides the sole channel of communication between the seed and the parent plant; however, little is known about its role in nutrient supply during seed maturation. Here, we investigated the dynamic metabolite profiles of the funiculus during seed maturation in Brassica napus. The funiculus was fully dev...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/s11103-016-0530-3
更新日期:2016-11-01 00:00:00
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journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/BF00040693
更新日期:1994-11-01 00:00:00
abstract::Transcriptional activator-like effectors (TALEs) are proteins secreted by Xanthomonas bacteria when they infect plants. TALEs contain a modular DNA binding domain that can be easily engineered to bind any sequence of interest, and have been used to provide user-selected DNA-binding modules to generate chimeric nucleas...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/s11103-011-9866-x
更新日期:2012-02-01 00:00:00
abstract::Plants that utilize the highly efficient C4 photosynthetic pathway possess two types of specialized leaf cells, the mesophyll and bundle sheath. In mature leaves of amaranth, a dicotyledonous C4 plant, ribulose 1,5-bisphosphate carboxylase (Rubisco) is localized specifically to the chloroplasts of bundle sheath cells,...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/BF00015971
更新日期:1993-06-01 00:00:00
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journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/BF00040606
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journal_title:Plant molecular biology
pub_type: 杂志文章,评审
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更新日期:2002-12-01 00:00:00
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journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/BF00020881
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abstract::Evidence is emerging that the E2F family of transcription factors plays an important role in the regulation of gene expression at the G1/S transition in plants. Here, we show that in the tobacco proliferating cell nuclear antigen (PCNA), whose transcript is specifically expressed at G1/S phase, the two E2F binding sit...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/s11103-004-6601-x
更新日期:2005-01-01 00:00:00
abstract:KEY MESSAGE:TaPSK5 is a less conserved target of miR164 in wheat encoding a positive regulator of root growth and yield traits that could be used for crop improvement. MicroRNAs (miRNAs) play key roles in regulating plant growth and development by targeting the mRNAs of conserved genes. However, little is known about t...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/s11103-020-01064-1
更新日期:2020-12-01 00:00:00
abstract::Salicylic acid (SA) is a stress-induced hormone involved in the activation of defense genes. Here we analyzed the early genetic responses to SA of wild type and npr1-1 mutant Arabidopsis seedlings, using Complete Arabidopsis Transcriptome MicroArray (CATMAv2) chip. We identified 217 genes rapidly induced by SA (early ...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/s11103-009-9458-1
更新日期:2009-05-01 00:00:00
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journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/s11103-020-01037-4
更新日期:2020-09-01 00:00:00
abstract::Heat shock protein 90 (Hsp90) is an abundant and highly conserved molecular chaperone. In Arabidopsis, the Hsp90 gene family consists of seven members. Here, we report that the AtHsp90-6 gene gives rise to two mRNA populations, termed AtHsp90-6L and AtHsp90-6S due to alternative initiation of transcription. The AtHsp9...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/s11103-008-9322-8
更新日期:2008-07-01 00:00:00
abstract::DNA amplification fingerprinting (DAF) using a high primer-to-template ratio and single, very short arbitrary primers, was used to generate amplified fragment length polymorphic markers (AFLP) in soybean (Glycine max (L.) Merr.). The inheritance of AFLPs was studied using a cross between the ancestral Glycine soja PI4...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/BF00039524
更新日期:1994-10-01 00:00:00
abstract::Tobacco and tomato plants were generated exhibiting insect resistance due to the introduction of modified cryIA(b) and cryIC genes of Bacillus thuringiensis. Limited modifications at selected regions of the coding sequences of both genes are sufficient to obtain resistance against Spodoptera exigua, Heliothis virescen...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/BF00039519
更新日期:1994-10-01 00:00:00
abstract::Co-suppression of host genes and 35S transgenes encoding nitrate reductase was previously reported in transgenic tobacco plants (Nicotiana tabacum cv. Paraguay or Burley) using either a full-length cDNA or fragments devoid of the 3' and/or 5' UTR. Co-suppression was previously shown to affect a limited fraction of the...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/BF00019126
更新日期:1995-10-01 00:00:00