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Single-cell transcriptomic analysis reveals the developmental trajectory and transcriptional regulatory networks of pigment glands in Gossypium bickii [bulk RNA-seq]

ABSTRACT: Comprehensive utilization of cottonseeds is limited by the presence of pigment gland and its inclusion gossypol. The ideal cotton is glandless-seeds and glanded-plant, a trait found in only few Australian wild cotton species, including Gossypium bickii. Introgressing the trait to cultivated species is proved to be difficult. Understanding the biological processes towards pigment gland morphogenesis and the associated underlying molecular mechanisms will facilitate breeding cultivated cotton varieties with the trait of glandless-seeds and glanded-plant. Single-cell RNA sequencing (scRNA-seq) was performed on 12,222 protoplasts isolated from cotyledons of germinating G. bickii seeds 48-hours after imbibition. Clustered into 14 distinct clusters unsupervisedly, these cells could be grouped into eight cell populations with the assistance of known cell marker genes. The pigment gland cells were well separated from others, and could be separated into pigment gland parenchyma cells, secretory cells, and apoptotic cells. In this study, integrating pigment gland cells developmental trajectory, transcription factors regulatory networks, and core transcription factors functional validation, a relatively complete model was proposed for pigment gland formation. Light and gibberellin were verified to promote the formation of pigment glands. Besides, three novel genes, GbiERF114 (ETHYLENE RESPONSE FACTOR 114), GbiZAT11 (ZINC FINGER OF ARABIDOPSIS THALIANA 11) and GbiNTL9 (NAC TRANSCRIPTION FACTOR-LIKE 9), were found to affect pigment gland formation. These findings shed new insights into pigment gland morphogenesis and lay the cornerstone for future cotton scRNA-seq investigations.

ORGANISM(S): Gossypium bickii

PROVIDER: GSE224574 | GEO | 2023/04/21

REPOSITORIES: GEO

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Project description:Gossypium barbadense is widely cultivated because of its extra-long staple cotton with superior luster, silkiness and high yield. These economically important traits were selected during initial domestication of an agronomically inferior wild ancestor, followed by millennia of human- mediated selection. To reveal the effects of this history on the cotton fiber transcriptome, we conducted comparative expression profiling on mechanically isolated fiber cells at three different stages encompassing early, mid, and late fiber elongation in wild (K101) and domesticated (Pima S-7) accessions, using a microarray platform that interrogates 42,429 unigenes. The distribution of differentially expressed genes across developmental stages was different in the two accessions, with a shift toward greater change earlier in cultivated than in wild G. barbadense. Approximately 4200 genes were differentially expressed between wild and domesticated accessions at one or more of the stages studied. Domestication appears to have led to enhanced modulation of cellular redox levels and the avoidance or delay of stress-like processes. Prolonged fiber growth in cultivated relative to wild G. barbadense is associated with upregulation of signal transduction and hormone signaling genes and down-regulation of cell wall maturation genes. Clues are provided into the processes and genes that may unwittingly have been selected by humans during domestication and development of modern elite lines. Several of the transcriptomic differences between wild and domesticated G. barbadense described here appear to have parallels in a second domesticated cotton species, Gossypium hirsutum, suggesting that replicated domestication of two different species has resulted in overlapping, parallel, metabolic transformations. Two accessions of G. barbadense were studied, the elite cultivar, Pima S-7, and a wild accession from Bolivia, K101. Seeds of both accessions were sown in sterilized potting mix in the Pohl Conservatory at Iowa State University, Ames, IA, and three biological replicates were grown for 3-5 months. Flowers were tagged at anthesis and harvested at three time points, 2, 10, and 20 days postanthesis. For each of three biological replicates, ovules were excised, frozen in liquid nitrogen, and stored at -80C.

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Single-cell transcriptomic analysis reveals the developmental trajectory and transcriptional regulatory networks of pigment glands in Gossypium bickii [bulk RNA-seq]

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