Global gene expression analysis of the shoot apical meristem of maize (<i>Zea mays</i> L.)

Ohtsu, Kazuhiro; Smith, Brian J.; Emrich, Scott J.; Borsuk, Lisa A.; Zhou, Rongyan; Chen, Tianle; Zhang, Xiaolan; Timmermans, Marja C.P.; Beck, Jon; Buckner, Brent; Janick-Buckner, Diane; Nettleton, Dan; Scanlon, Michael J.; Schnable, Patrick S.

doi:10.1111/j.1365-313x.2007.03244.x

Cited by 125 publications

(109 citation statements)

References 74 publications

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“…2F), indicating the presence of substantially active TEs or TE fragments in maize seed development. Although it remains to be determined whether these NTRs have any biological function, some evidence has shown that TE-related regions are widely active and have acquired specific cell functions during their evolution (Vicient et al, 2001;de Araujo et al, 2005;Ohtsu et al, 2007;Lopes et al, 2008;Picault et al, 2009), and we did observe 46 TE-associated NTRs with EST evidence in addition to the support of our RNA-seq data (Fig. 2F).…”

Section: Discovery Of Ntrssupporting

confidence: 74%

The Differential Transcription Network between Embryo and Endosperm in the Early Developing Maize Seed

Chen

Shu

et al. 2013

Plant Physiology

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Transcriptome analysis of early-developing maize (Zea mays) seed was conducted using Illumina sequencing. We mapped 11,074,508 and 11,495,788 paired-end reads from endosperm and embryo, respectively, at 9 d after pollination to define gene structure and alternative splicing events as well as transcriptional regulators of gene expression to quantify transcript abundance in both embryo and endosperm. We identified a large number of novel transcribed regions that did not fall within maize annotated regions, and many of the novel transcribed regions were tissue-specifically expressed. We found that 50.7% (8,556 of 16,878) of multiexonic genes were alternatively spliced, and some transcript isoforms were specifically expressed either in endosperm or in embryo. In addition, a total of 46 trans-splicing events, with nine intrachromosomal events and 37 interchromosomal events, were found in our data set. Many metabolic activities were specifically assigned to endosperm and embryo, such as starch biosynthesis in endosperm and lipid biosynthesis in embryo. Finally, a number of transcription factors and imprinting genes were found to be specifically expressed in embryo or endosperm. This data set will aid in understanding how embryo/endosperm development in maize is differentially regulated.Maize (Zea mays) seeds are one of the most important crop materials that provide resources for food, feed, biofuel, and raw material for processing. Maize seed development initiates from double fertilization, in which two of the pollen sperms fuse with an egg cell and a central cell to produce embryo and endosperm, respectively (Randolph, 1936;Chaudhury et al., 2001). The main function of endosperm is to provide nutrient for the developing embryo and germinating embryo.After fertilization, the zygote undergoes an asymmetric division into a small apical cell and a large basal cell, giving rise to the embryo proper and the suspensor, respectively. The radial symmetry of the proembryo is shifted to a bilateral symmetry at the transition stage, which is characterized by protoderm formation. The shoot apical meristem and the root apical meristem can be distinguished at the onset of the coleoptile stage, and then the position of the future coleoptile is marked by a small protuberance. The mature embryo is composed of the embryo axis, which is formed by the plumule with five or six short internodes, and leaf primordia and primary root surrounded by the coleoptile and the coleorhiza, respectively, and the scutellum (Randolph, 1936;Abbe and Stein, 1954;Diboll, 1968;Lammeren, 1986;Vernoud et al., 2005).Maize endosperm follows the nucleus-type endosperm development, where the fertilized central cell undergoes several rounds of synchronous division in the absence of cell wall formation and cytokinesis to produce a syncytium (Lopes and Larkins, 1993;Olsen, 2004). Cellularization allows the formation of the internuclear radial microtubule systems and open-ended alveolation from the periphery of the endosperm toward the central vacuole (Olsen et al., ...

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Section: Discovery Of Ntrssupporting

confidence: 74%

The Differential Transcription Network between Embryo and Endosperm in the Early Developing Maize Seed

Chen

Shu

et al. 2013

Plant Physiology

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“…Several improvements were made in tissue fixation and handling (Supplemental Fig. S7), including the adoption of acetone fixation (Ohtsu et al, 2007), the minimization of section ribbon expansion time (in water) on slides, and the use of only freshly dewaxed slides for laser capture.…”

Section: Optimization Of the Lcm Procedures And The Data Analysesmentioning

confidence: 99%

“…S1B). Before LCM, tissues were fixed in ice-cold 100% (v/v) acetone (Ohtsu et al, 2007), exchanged for acetone:Hemo-De (50:50; Scientific Safety Solvents), and then exchanged for 100% (v/v) Hemo-De. Fixation vials were placed at 60°C, and paraplast Plus chips (Leica Microsystems) were added gradually to the Hemo-De to slowly infiltrate the tissue with wax.…”

Section: Floral Tissue Isolationmentioning

confidence: 99%

Floral Transcriptomes in Woodland Strawberry Uncover Developing Receptacle and Anther Gene Networks

et al. 2014

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ORCID IDs: 0000-0002-6902-740X (C.K.); 0000-0001-9969-9381 (Z.L.).Flowers are reproductive organs and precursors to fruits and seeds. While the basic tenets of the ABCE model of flower development are conserved in angiosperms, different flowering plants exhibit different and sometimes unique characteristics. A distinct feature of strawberry (Fragaria spp.) flowers is the development of several hundreds of individual apocarpous (unfused) carpels. These individual carpels are arranged in a spiral pattern on the subtending stem tip, the receptacle. Therefore, the receptacle is an integral part of the strawberry flower and is of significant agronomic importance, being the precursor to strawberry fruit. Taking advantage of next-generation sequencing and laser capture microdissection, we generated different tissue-and stage-transcriptomic profiling of woodland strawberry (Fragaria vesca) flower development. Using pairwise comparisons and weighted gene coexpression network analysis, we identified modules of coexpressed genes and hub genes of tissue-specific networks. Of particular importance is the discovery of a developing receptacle-specific module exhibiting similar molecular features to those of young floral meristems. The strawberry homologs of a number of meristem regulators, including LOST MERISTEM and WUSCHEL, are identified as hub genes operating in the developing receptacle network. Furthermore, almost 25% of the F-box genes in the genome are transiently induced in developing anthers at the meiosis stage, indicating active protein degradation. Together, this work provides important insights into the molecular networks underlying strawberry's unique reproductive developmental processes. This extensive floral transcriptome data set is publicly available and can be readily queried at the project Web site, serving as an important genomic resource for the plant biology research community.

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“…Similar to the SAM, lateral shoot meristems undergo vegetative growth, first initiating a bikeeled prophyll followed by foliar husk leaves before transitioning into an inflorescence meristem or undergoing senescence ( Figures 1F and 1L) (Kiesselbach, 1949). Previous studies have analyzed transcripts encoded in various hand-dissected and laser-microdissected shoot apices from 14-d-old seedlings using microarray analysis, as well as 454-based and Illumina-based RNA sequencing (RNA-seq) (Emrich et al, 2007;Ohtsu et al, 2007;Brooks et al, 2009;Jia et al, 2009;Nogueira et al, 2009). However, as yet, no transcriptomic analyses of maize SAM ontogeny during embryogenesis have been described.…”

Section: Introductionmentioning

confidence: 99%

Ontogeny of the Maize Shoot Apical Meristem

Takacs

et al. 2012

Plant Cell

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The maize (Zea mays) shoot apical meristem (SAM) arises early in embryogenesis and functions during stem cell maintenance and organogenesis to generate all the aboveground organs of the plant. Despite its integral role in maize shoot development, little is known about the molecular mechanisms of SAM initiation. Laser microdissection of apical domains from developing maize embryos and seedlings was combined with RNA sequencing for transcriptomic analyses of SAM ontogeny. Molecular markers of key events during maize embryogenesis are described, and comprehensive transcriptional data from six stages in maize shoot development are generated. Transcriptomic profiling before and after SAM initiation indicates that organogenesis precedes stem cell maintenance in maize; analyses of the first three lateral organs elaborated from maize embryos provides insight into their homology and to the identity of the single maize cotyledon. Compared with the newly initiated SAM, the mature SAM is enriched for transcripts that function in transcriptional regulation, hormonal signaling, and transport. Comparisons of shoot meristems initiating juvenile leaves, adult leaves, and husk leaves illustrate differences in phase-specific (juvenile versus adult) and meristem-specific (SAM versus lateral meristem) transcript accumulation during maize shoot development. This study provides insight into the molecular genetics of SAM initiation and function in maize.

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Global gene expression analysis of the shoot apical meristem of maize (Zea mays L.)

Cited by 125 publications

References 74 publications

The Differential Transcription Network between Embryo and Endosperm in the Early Developing Maize Seed

The Differential Transcription Network between Embryo and Endosperm in the Early Developing Maize Seed

Floral Transcriptomes in Woodland Strawberry Uncover Developing Receptacle and Anther Gene Networks

Ontogeny of the Maize Shoot Apical Meristem

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