Single‐cell <scp>RNA</scp>‐seq reveals fate determination control of an individual fibre cell initiation in cotton (<i>Gossypium hirsutum</i>)

Qin, Yuan; Sun, Miaomiao; Li, Weiwen; Xu, Mingqi; Shao, Lei; Liu, Yuqi; Zhao, Guannan; Liu, Zhenping; Xu, Zhongping; You, Jiaqi; Ye, Zhengxiu; Xu, Jie; Yang, Xiyan; Wang, Maojun; Lindsey, Keith; Zhang, Xianlong; Tu, Lili

doi:10.1111/pbi.13918

Cited by 57 publications

(47 citation statements)

References 107 publications

(225 reference statements)

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“…Many cotton genes homologous to the Arabidopsis leaf trichome initiation complex were identified as highly expressed in fiber cell initials, and some of these genes rescued the trichome phenotype by ectopic expression in Arabidopsis null mutants (Guan et al., 2008; Qin et al., 2022; Suo et al., 2003; Wang et al., 2004). Table S1 provides functionally characterized cotton genes involved in early fiber development.…”

Section: Recent Advances In Understanding Of Cotton Fiber Developmentmentioning

confidence: 99%

“…The model was proposed that the combined expression of both GhMML3_A12 and GhMML3_D12 was associated with lint development, whereas fuzz development is mainly determined by the expression level of GhMML3_D12 at 3 DPA (Zhu et al., 2018). The recent study evaluated gene expression in cells differentiating from the cotton ovule outer integument during fiber initiation by using a single‐cell RNAseq technique (Qin et al., 2022). High expression of GhMML3 was detected from −1 to 3 DPA, suggesting a role in promoting lint and fuzz fiber differentiation (Qin et al., 2022).…”

Section: Recent Advances In Understanding Of Cotton Fiber Developmentmentioning

confidence: 99%

“…The recent study evaluated gene expression in cells differentiating from the cotton ovule outer integument during fiber initiation by using a single‐cell RNAseq technique (Qin et al., 2022). High expression of GhMML3 was detected from −1 to 3 DPA, suggesting a role in promoting lint and fuzz fiber differentiation (Qin et al., 2022). Clustered regularly interspaced short palindromic repeats (CRISPR) knock‐out lines of both, GhMML3_A12 and GhMML3_D12 homeologs, showed a fiberless phenotype, which confirmed their function (Qin et al., 2022).…”

Section: Recent Advances In Understanding Of Cotton Fiber Developmentmentioning

confidence: 99%

“…High expression of GhMML3 was detected from −1 to 3 DPA, suggesting a role in promoting lint and fuzz fiber differentiation (Qin et al., 2022). Clustered regularly interspaced short palindromic repeats (CRISPR) knock‐out lines of both, GhMML3_A12 and GhMML3_D12 homeologs, showed a fiberless phenotype, which confirmed their function (Qin et al., 2022).…”

Section: Recent Advances In Understanding Of Cotton Fiber Developmentmentioning

confidence: 99%

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Bridging molecular genetics and genomics for cotton fiber quality improvement

Naoumkina

Kim

2023

Crop Science

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Upland cotton (Gossypium hirsutum L.) is the main source of natural fiber for the textile industry. Cotton fibers are unicellular trichomes that emerge from the epidermal cells of the seed. In cultivated cotton species, seed trichomes differentiate into two distinct types, spinnable lint, and short fuzz. The main priority for cotton growers is fiber yield, whereas the textile industry also demands better fiber quality characteristics, such as length, uniformity, strength, maturity, and optimal fineness. However, it is a major challenge for breeders to improve fiber quality while maintaining yield, because of the observed negative correlation between yield and fiber quality traits. Recent technical advances in sequencing and bioinformatics have facilitated the assembly of reference quality genomes of multiple cotton species, bringing a new era for cotton genomics. Available genomic resources will help genetically dissect the agronomic and fiber quality traits of cotton and identify gene variants that can be used for cotton improvement through breeding or biotechnology. Here, we review recent progress in the sequencing of genomes of cotton species and approaches in molecular genetics and genomics for the improvement of cotton fiber quality traits.We discuss progress in the understanding of each stage of cotton fiber development and the remaining challenges.

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Section: Recent Advances In Understanding Of Cotton Fiber Developmentmentioning

confidence: 99%

Section: Recent Advances In Understanding Of Cotton Fiber Developmentmentioning

confidence: 99%

Section: Recent Advances In Understanding Of Cotton Fiber Developmentmentioning

confidence: 99%

Section: Recent Advances In Understanding Of Cotton Fiber Developmentmentioning

confidence: 99%

See 2 more Smart Citations

Bridging molecular genetics and genomics for cotton fiber quality improvement

Naoumkina

Kim

2023

Crop Science

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“…Recently, application of single-cell RNA sequencing (scRNA-seq) in plants improved the understanding of cell heterogeneity in various plant species, such as Arabidopsis , rice, maize, cotton, peanut, and poplar [ 13 – 29 ]. In Arabidopsis , rice and maize, the root cell types, have been well profiled [ 14 , 17 , 18 , 20 – 22 ].…”

Section: Introductionmentioning

confidence: 99%

Asymmetric gene expression and cell-type-specific regulatory networks in the root of bread wheat revealed by single-cell multiomics analysis

Zhang

Lai

et al. 2023

Genome Biol

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Background Homoeologs are defined as homologous genes resulting from allopolyploidy. Bread wheat, Triticum aestivum, is an allohexaploid species with many homoeologs. Homoeolog expression bias, referring to the relative contribution of homoeologs to the transcriptome, is critical for determining the traits that influence wheat growth and development. Asymmetric transcription of homoeologs has been so far investigated in a tissue or organ-specific manner, which could be misleading due to a mixture of cell types. Results Here, we perform single nuclei RNA sequencing and ATAC sequencing of wheat root to study the asymmetric gene transcription, reconstruct cell differentiation trajectories and cell-type-specific gene regulatory networks. We identify 22 cell types. We then reconstruct cell differentiation trajectories that suggest different origins between epidermis/cortex and endodermis, distinguishing bread wheat from Arabidopsis. We show that the ratio of asymmetrically transcribed triads varies greatly when analyzing at the single-cell level. Hub transcription factors determining cell type identity are also identified. In particular, we demonstrate that TaSPL14 participates in vasculature development by regulating the expression of BAM1. Combining single-cell transcription and chromatin accessibility data, we construct the pseudo-time regulatory network driving root hair differentiation. We find MYB3R4, REF6, HDG1, and GATAs as key regulators in this process. Conclusions Our findings reveal the transcriptional landscape of root organization and asymmetric gene transcription at single-cell resolution in polyploid wheat.

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Single‐Cell Transcriptome Atlas and Regulatory Dynamics in Developing Cotton Anthers

Li,

Ma,

et al. 2023

Advanced Science

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Plant anthers are composed of different specialized cell types with distinct roles in plant reproduction. High temperature (HT) stress causes male sterility, resulting in crop yield reduction. However, the spatial expression atlas and regulatory dynamics during anther development and in response to HT remain largely unknown. Here, the first single‐cell transcriptome atlas and chromatin accessibility survey in cotton anther are established, depicting the specific expression and epigenetic landscape of each type of cell in anthers. The reconstruction of meiotic cells, tapetal cells, and middle layer cell developmental trajectories not only identifies novel expressed genes, but also elucidates the precise degradation period of middle layer and reveals a rapid function transition of tapetal cells during the tetrad stage. By applying HT, heterogeneity in HT response is shown among cells of anthers, with tapetal cells responsible for pollen wall synthesis are most sensitive to HT. Specifically, HT shuts down the chromatin accessibility of genes specifically expressed in the tapetal cells responsible for pollen wall synthesis, such as QUARTET 3 (QRT3) and CYTOCHROME P450 703A2 (CYP703A2), resulting in a silent expression of these genes, ultimately leading to abnormal pollen wall and male sterility. Collectively, this study provides substantial information on anthers and provides clues for heat‐tolerant crop creation.

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Single‐cell RNA‐seq reveals fate determination control of an individual fibre cell initiation in cotton (Gossypium hirsutum)

Abstract: This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process which may lead to differences between this version and the Version of Record. Please cite this article as

Cited by 57 publications

References 107 publications

Bridging molecular genetics and genomics for cotton fiber quality improvement

Bridging molecular genetics and genomics for cotton fiber quality improvement

Asymmetric gene expression and cell-type-specific regulatory networks in the root of bread wheat revealed by single-cell multiomics analysis

Single‐Cell Transcriptome Atlas and Regulatory Dynamics in Developing Cotton Anthers

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