Single-Cell RNA Sequencing of Developing Ears Facilitates Functional Analysis and Trait Candidate Gene Discovery in Maize

Xu, Xiaosa; Crow, Megan; Rice, Brian R.; Li, Forrest; Harris, Benjamin; Liu, Lei; Demesa-Arévalo, Edgar; Lu, Zefu; Wang, Liya; Drenkow, Jörg; Luo, Anding; Char, Si Nian; Yang, Bing; Sylvester, Anne W.; Gingeras, T; Schmitz, Robert J.; Ware, Doreen; Lipka, Alexander E.; Gillis, Jesse; Jackson, David

doi:10.2139/ssrn.3696748

Cited by 20 publications

(40 citation statements)

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“…Single-cell mRNA-seq (scRNA-seq) has been instrumental towards understanding developmental events at cellular resolution over the past decade (Chen et al, 2019; Hwang et al, 2018). Several studies have applied these approaches to plant tissues (Brennecke et al, 2013; Efroni and Birnbaum, 2016; Jean-Baptiste et al, 2019; Ryu et al, 2019; Satterlee et al, 2020; Shulse et al, 2019; Song et al, 2020; Xu et al, 2021; Zhang et al, 2019), but scRNA-seq has yet to be reported for individual cell types in plant embryos. This is primarily due to the presence of rigid cell walls that hold plant cells together.…”

Section: Introductionmentioning

confidence: 99%

Gene Expression Variation in Arabidopsis Embryos at Single-Nucleus Resolution

Kao

Schon

Mosiołek

et al. 2021

Preprint

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Soon after fertilization of egg and sperm, plant genomes become transcriptionally activated and drive a series of coordinated cell divisions to form the basic body plan during embryogenesis. Early embryonic cells rapidly diversify from each other, and investigation of the corresponding gene expression dynamics can help elucidate underlying cellular differentiation programs. However, current plant embryonic transcriptome datasets either lack cell-specific information or have RNA contamination from surrounding non-embryonic tissues. We have coupled fluorescence-activated nuclei sorting together with single-nucleus mRNA sequencing to construct a gene expression atlas of Arabidopsis thaliana early embryos at single-cell resolution. In addition to characterizing cell-specific transcriptomes, we found evidence that distinct epigenetic and transcriptional regulatory mechanisms operate across emerging embryonic cell types. These datasets and analyses, as well as the approach we devised, are expected to facilitate the discovery of molecular mechanisms underlying pattern formation in plant embryos.

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Section: Introductionmentioning

confidence: 99%

Gene Expression Variation in Arabidopsis Embryos at Single-Nucleus Resolution

Kao

Schon

Mosiołek

et al. 2021

Preprint

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“…Here, we reconstructed a transcriptomic atlas covering early rice inflorescence development at the single-cell resolution using scRNA-seq. Although we could not definitively exclude possible side-effects of protoplasting on our scRNA transcriptome, the removal of 61 rice orthologues of 332 protoplast-related genes collected from maize inflorescence (Table S2) (Xu et al, 2021) did not affect the original clustering, nor the spikelet, floret, and meristem subclustering. This result was consistent with previous reports from maize and Arabidopsis (Ma et al, 2020;Xu et al, 2021;Zhang et al, 2021a) and suggested that protoplasting did not strongly affect our results.…”

Section: Discussionmentioning

confidence: 98%

“…Although we could not definitively exclude possible side-effects of protoplasting on our scRNA transcriptome, the removal of 61 rice orthologues of 332 protoplast-related genes collected from maize inflorescence (Table S2) (Xu et al, 2021) did not affect the original clustering, nor the spikelet, floret, and meristem subclustering. This result was consistent with previous reports from maize and Arabidopsis (Ma et al, 2020;Xu et al, 2021;Zhang et al, 2021a) and suggested that protoplasting did not strongly affect our results. However, identification of protoplasting-responsive genes in rice inflorescence samples will further exclude the risk of batch effects caused by protoplasting.…”

Section: Discussionmentioning

confidence: 98%

A rice single cell transcriptomic atlas defines the developmental trajectories of rice floret and inflorescence meristems

et al. 2022

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Rice inflorescence development determines yield and relies on the activity of axillary meristems (AMs); however, high-resolution analysis of its early development is lacking.Here, we have used high-throughput single-cell RNA sequencing to profile 37 571 rice inflorescence cells and constructed a genome-scale gene expression resource covering the inflorescence-to-floret transition during early reproductive development. The differentiation trajectories of florets and AMs were reconstructed, and discrete cell types and groups of regulators in the highly heterogeneous young inflorescence were identified and then validated by in situ hybridization and with fluorescent marker lines.Our data demonstrate that a WOX transcription factor, DWARF TILLER1, regulates flower meristem activity, and provide evidence for the role of auxin in rice inflorescence branching by exploring the expression and biological role of the auxin importer OsAUX1.Our comprehensive transcriptomic atlas of early rice inflorescence development, supported by genetic evidence, provides single-cell-level insights into AM differentiation and floret development.

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“…Importantly, the availability of the sequenced genome and pan-genome resources creates new possibilities of gene identification and gene function analysis [ 150 , 151 , 152 , 153 ]. Further researches that take advantage of novel technologies, such as CRISPR/Cas9 and single-cell RNA sequencing [ 154 , 155 ], are promising to provide valuable insights into the genes that control meristem identity and inflorescence architecture in cereals. The accumulating knowledge on inflorescence development can be harnessed to boost the yield potential of crops.…”

Section: Conclusion and Future Perspectivesmentioning

confidence: 99%

Molecular Insights into Inflorescence Meristem Specification for Yield Potential in Cereal Crops

Wang

Yang

2021

IJMS

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Flowering plants develop new organs throughout their life cycle. The vegetative shoot apical meristem (SAM) generates leaf whorls, branches and stems, whereas the reproductive SAM, called the inflorescence meristem (IM), forms florets arranged on a stem or an axis. In cereal crops, the inflorescence producing grains from fertilized florets makes the major yield contribution, which is determined by the numbers and structures of branches, spikelets and florets within the inflorescence. The developmental progression largely depends on the activity of IM. The proper regulations of IM size, specification and termination are outcomes of complex interactions between promoting and restricting factors/signals. Here, we focus on recent advances in molecular mechanisms underlying potential pathways of IM identification, maintenance and differentiation in cereal crops, including rice (Oryza sativa), maize (Zea mays), wheat (Triticum aestivum), and barley (Hordeum vulgare), highlighting the researches that have facilitated grain yield by, for example, modifying the number of inflorescence branches. Combinatorial functions of key regulators and crosstalk in IM determinacy and specification are summarized. This review delivers the knowledge to crop breeding applications aiming to the improvements in yield performance and productivity.

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Single-Cell RNA Sequencing of Developing Ears Facilitates Functional Analysis and Trait Candidate Gene Discovery in Maize

Cited by 20 publications

References 0 publications

Gene Expression Variation in Arabidopsis Embryos at Single-Nucleus Resolution

Gene Expression Variation in Arabidopsis Embryos at Single-Nucleus Resolution

A rice single cell transcriptomic atlas defines the developmental trajectories of rice floret and inflorescence meristems

Molecular Insights into Inflorescence Meristem Specification for Yield Potential in Cereal Crops

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