Gossypium
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA375965 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5512270_1.fastq.gz | Fastqsanger.gz | |||
| SRR5512270_2.fastq.gz | Fastqsanger.gz | |||
| SRR5512280_1.fastq.gz | Fastqsanger.gz | |||
| SRR5512280_2.fastq.gz | Fastqsanger.gz | |||
| SRR5512290_1.fastq.gz | Fastqsanger.gz |
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Project description:Genome resequencing provides insights into genetic variations during modern cotton breeding RNAseq data
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Project description:Cotton is the most important economic crop that provides natural fibre and by-products such as oil and protein. The global gene expression could provide insight into the biological processes underlying growth and development, which involving suites of genes expressed with temporal and spatial controls by regulatory networks. Improvement of cotton fiber in yield and quality is the main goal for molecular breeding, but many previous research have been largely focused on identifying genes only in fibres, so that we ignore seed which may play an important role in the development of fibers. In this study, we constructed and systematically analyzed twenty-one strand-specific RNA-Seq libraries on Gossypium hirsutum L. covering different tissues, organs and development stages, of which approximately 970 million reads were generated. In total, 5,6754 transcripts derived from 2,9541 unigenes were obtained to provide a global view of gene expression for cotton development. Hierarchical clustering of transcriptional profiles suggests that transcriptomes among tissues or organs corresponded well to their developmental relatedness. The organ (tissue)-specific gene expressions were investigated efficiently and provided further insight into the dynamic programming of the transcriptome, in particularly for coordinating development between fiber cell and seed (ovule). We identified series of transcription factors and seed-specific genes, which as the candidate genes should help elucidate key mechanisms and regulatory networks that underlie fiber and seed development. This report identified comprehensive transcriptome changes in different stage of cotton development and will serves as a valuable genome-wide transcriptome resource for cotton breeding. Examination of transcriptome of cotton
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Project description:Sea Island cotton (Gossypium barbadense) is the source of the world’s finest fiber-quality cotton, yet relatively little is understood about the genetic variation among diverse germplasm, the genes underlying important traits, and the effects of pedigree selection. Here, we resequenced 336 G. barbadense accessions and identified 16 million SNPs. Phylogenetic and population structure analyses revealed two major gene pools and a third admixed subgroup derived from geographical dissemination and interbreeding. We conducted a genome-wide association study (GWAS) of 15 traits including fiber quality, yield, disease resistance, maturity, and plant architecture. The highest number of associated loci was for fiber quality, followed by disease resistance and yield. Using gene expression analyses and VIGS transgenic experiments we confirmed the role of five candidate genes regulating four key traits, i.e., disease resistance, fiber length, fiber strength, and lint percentage. Geographical and temporal considerations demonstrate selection for the superior fiber quality (fiber length and fiber strength), and high lint-percentage in improving G. barbadense in China. Pedigree selection breeding wholly increased Fusarium wilt disease resistance, and separately improved fiber-quality and yield. Our work provides a foundation for understanding genomic variation in and selective breeding of Sea Island cotton.
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Project description:Cotton (Gossypium hirsutum) is widely distributed worldwide, and improving the quality of its fiber is one of the most important tasks in cotton breeding. Cotton fibers are primarily composed of cellulose, which is synthesized and regulated by cellulose synthase (CesAs). However, the molecular mechanism of CesA genes in cotton is unclear. In this study, the cotton transcriptome and metabolome were used to investigate the significant function of CesA genes in fiber development. Finally, 321 metabolites were obtained, 84 of which were associated with the corresponding genes. Interestingly, a target gene named Gh_A08G144300, one of the CesA gene family members, was closely correlated with the development of cotton fibers. Then, identification and functional analysis were conducted. The target CesA gene Gh_A08G144300 was selected and analysed to determine its specific function in cotton fiber development. High-level gene expression of Gh_A08G144300 was found at different fiber development stages by RNA-seq analysis, and the silencing of Gh_A08G144300 visibly inhibited the growth of cotton fibers, showing that it is critical for their growth. This study provides an important reference for research on the gene function of Gh_A08G144300 and the regulatory mechanism of fiber development in cotton.
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Project description:Insight into structure variations and evolution of allopolyploidy cotton genomes
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Project description: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.
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