A high-resolution gene expression atlas links dedicated meristem genes to key architectural traits

Knauer, Steffen; Javelle, Marie; Lin, Li; Li, Xianran; Ma, Xiaoli; Wimalanathan, Kokulapalan; Kumari, Sunita; Johnston, Robyn; Leiboff, Samuel; Meeley, Robert B.; Schnable, Patrick S.; Ware, Doreen; Lawrence‐Dill, Carolyn J.; Yu, Jianming; Muehlbauer, Gary J.; Scanlon, Michael J.; Timmermans, Marja C.P.

doi:10.1101/gr.250878.119

Cited by 45 publications

(70 citation statements)

References 67 publications

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“…In agreement with previous transcriptomic analyses showing widespread expression of ARF10 and ARF25 during maize ontogeny ( Harper et al, 2011 ), in situ hybridization analyses reveal that ARF10/ARF25 transcripts accumulate throughout the maize seedling shoot ( Fig. 3 ; Knauer et al, 2019 ). ARF10/ARF25 transcripts are found throughout young leaf primordia, including the husk leaves of axillary meristems, and are enriched in the epidermis and margins of later primordia ( Fig.…”

Section: Resultssupporting

confidence: 92%

Plant homeodomain proteins provide a mechanism for how leaves grow wide

et al. 2020

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The mechanisms whereby leaf anlagen undergo proliferative growth and expansion to form wide, flat leaves are unclear. The maize gene NARROWSHEATH1 (NS1) is a WUSCHEL-related homeobox3 (WOX3) homolog expressed at the margins of leaf primordia, and is required for mediolateral outgrowth. To investigate the mechanisms of NS1 function, we used chromatin immunoprecipitation and laser-microdissection RNAseq of leaf primordial margins to identify gene targets bound and modulated by NS1. Microscopic analyses of cell division and gene expression in expanding leaves, and reverse genetic analyses of homologous NS1 target genes in Arabidopsis, reveal that NS1 controls mediolateral outgrowth by repression of a growth inhibitor and promotion of cell division at primordial leaf margins. Intriguingly, homologous WOX gene products are expressed in stem-cell organizing centers and traffic to adjoining cells to activate stem-cell identity non-autonomously. In contrast, WOX3/NS1 does not traffic, and stimulates cell divisions in the same cells where it is transcribed.

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Section: Resultssupporting

confidence: 92%

Plant homeodomain proteins provide a mechanism for how leaves grow wide

et al. 2020

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“…The tip of the maize SAM is thought to house the stem-cells (4,8), which are essential for the generating the above-ground somatic tissue of the maize plant as well as cells that give rise to the germline. Our cell clustering analysis independently identified a transcriptionally distinct cell population in which DYNAMIN (DYN), a previously-identified marker of tip cells in the maize SAM, was upregulated (4).…”

Section: Characterization Of the Maize Stem-cell Nichementioning

confidence: 99%

“…To further investigate the organization of the maize SAM we examined gene expression patterns among cells derived from a recently-reported domain situated in the center, or 'core' region, of the SAM, which is marked by the expression of GRMZM2G049151, a gene of unknown function (4). We identified cells within the core region by transcript accumulation of GRMZM2G049151, and used differential expression (DE) analysis to characterize their expression profiles ( Fig.…”

Section: Characterization Of a Sam Core Regionmentioning

confidence: 99%

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Plant stem cell organization and differentiation at single-cell resolution

Satterlee

Strable

Scanlon

2020

Preprint

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Plants maintain populations of pluripotent stem cells in shoot apical meristems (SAMs), which continuously produce new aboveground organs. We used single-cell RNA sequencing to achieve an unbiased characterization of the transcriptional landscape of the maize shoot stem-cell niche and its differentiating cellular descendants. Stem cells housed in the SAM tip are engaged in genome integrity maintenance and exhibit a low rate of cell division, consistent with their contributions to germline and somatic cell fates. Surprisingly, we find no evidence for a canonical stem cell organizing center subtending these cells. In addition, we use trajectory inference to trace the gene expression changes that accompany cell differentiation. These data provide a valuable scaffold on which to better dissect the genetic control of plant shoot morphogenesis.

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“…Transcriptome analysis is a powerful method for exploring gene expression dynamics at both the genome-wide and single-gene levels. To date, transcriptome analysis of leaf development has been performed in species including Arabidopsis [13,14], maize [15,16,17,18,19,20,21,22], and rice [23,24,25]. In particular, transcriptome changes accompanied by tissue differentiation have been intensively studied in the developing leaf blade in maize.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Analysis of Spatiotemporal Expression Patterns During Rice Leaf Development

Miya

Yoshikawa

Satō

et al. 2020

Preprint

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Background: Rice leaves consist of three distinct regions along a proximal-distal axis, namely the leaf blade, sheath, and blade-sheath boundary region. Each region has a unique morphology and function, but the genetic programs underlying the development of each region are poorly understood. To fully elucidate rice leaf development and discover genes with unique functions in rice and grasses, it is crucial to explore genome-wide transcriptional profiles during the development of the three regions.Results: In this study, we performed microarray analysis to profile the spatial and temporal patterns of gene expression in the rice leaf using dissected parts of leaves sampled in broad developmental stages. The dynamics in each region revealed that the transcriptomes changed dramatically throughout the progress of tissue differentiation, and those of the leaf blade and sheath differed greatly at the mature stage. Cluster analysis of expression patterns among leaf parts revealed groups of genes that may be involved in specific biological processes related to rice leaf development. Moreover, we found novel genes potentially involved in rice leaf development using a combination of transcriptome data and in situ hybridization, and analyzed their spatial expression patterns at high resolution. We successfully identified multiple genes that exhibit localized expression in tissues characteristic of rice or grass leaves.Conclusions: Although the genetic mechanisms of leaf development have been elucidated in several eudicots, direct application of that information to rice and grasses is not appropriate due to the morphological and developmental differences between them. Our analysis provides not only insights into the development of rice leaves but also expression profiles that serve as a valuable resource for gene discovery. The genes and gene clusters identified in this study may facilitate future research on the unique developmental mechanisms of rice leaves.

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A high-resolution gene expression atlas links dedicated meristem genes to key architectural traits

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Cited by 45 publications

References 67 publications

Plant homeodomain proteins provide a mechanism for how leaves grow wide

Plant homeodomain proteins provide a mechanism for how leaves grow wide

Plant stem cell organization and differentiation at single-cell resolution

Genome-Wide Analysis of Spatiotemporal Expression Patterns During Rice Leaf Development

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