Proteomic Analysis of Differences in Fiber Development between Wild and Cultivated Gossypium hirsutum L

Transcriptome and proteome profiling revealed the key genes and pathways involved in the fiber quality formation in brown cotton

Colored cotton is also called eco-cotton because of its natural color fiber. It is inferior in yield and quality than white cotton. The underlying regulatory genes involved in fiber quality and pigment synthesis are not well understood. This study aimed to investigate the transcriptomic and proteomic changes during fiber development in a brown cotton cultivar (Z161) and a white cotton cultivar. The differential proteins with the same expression trend as genes were significantly and positively correlated with corresponding fold changes in expression. Enrichment analysis revealed that Z161, enriched in fiber elongation genes related to flavonoid biosynthesis, phenylalanine metabolism, glutathione metabolism, and many more genes (proteins) are up-regulated. Moreover, 164 glycosyltransferases genes, 15 MYB-bHLH-WD40 genes, and other transcription factors such as C2H2 (12), ERF (11), and NAC (7) were preferentially expressed in Z161. Weighted correlation network analysis identified fatty acid synthesis and energy metabolism as the principal metabolic pathways in both cotton genotypes during fiber development. Identified 15 hub genes will provide important insights for genetic manipulation of fiber quality and pigment deposition balance in brown cotton fibers.

GWAS Mediated Elucidation of Heterosis for Metric Traits in Cotton (Gossypium hirsutum L.) Across Multiple Environments

For about a century, plant breeding has widely exploited the heterosis phenomenon-often considered as hybrid vigor-to increase agricultural productivity. The ensuing F₁ hybrids can substantially outperform their progenitors due to heterozygous combinations that mitigate deleterious mutations occurring in each genome. However, only fragmented knowledge is available concerning the underlying genes and processes that foster heterosis. Although cotton is among the highly valued crops, its improvement programs that involve the exploitation of heterosis are still limited in terms of significant accomplishments to make it broadly applicable in different agro-ecological zones. Here, F₁ hybrids were derived from mating a diverse Upland Cotton germplasm with commercially valuable cultivars in the Line × Tester fashion and evaluated across multiple environments for 10 measurable traits. These traits were dissected into five different heterosis types and specific combining ability (SCA). Subsequent genome-wide predictions along-with association analyses uncovered a set of 298 highly significant key single nucleotide polymorphisms (SNPs)/Quantitative Trait Nucleotides (QTNs) and 271 heterotic Quantitative Trait Nucleotides (hQTNs) related to agronomic and fiber quality traits. The integration of a genome wide association study with RNA-sequence analysis yielded 275 candidate genes in the vicinity of key SNPs/QTNs. Fiber micronaire (MIC) and lint percentage (LP) had the maximum number of associated genes, i.e., each with 45 related to QTNs/hQTNs. A total of 54 putative candidate genes were identified in association with HETEROSIS of quoted traits. The novel players in the heterosis mechanism highlighted in this study may prove to be scientifically and biologically important for cotton biologists, and for those breeders engaged in cotton fiber and yield improvement programs.

Fumonisin B1-Induced Changes in Cotton Fiber Elongation Revealed by Sphingolipidomics and Proteomics

Sphingolipids are essential biomolecules and membrane components, but their regulatory role in cotton fiber development is poorly understood. Here, we found that fumonisin B1 (FB1)—a sphingolipid synthesis inhibitor—could block fiber elongation severely. Using liquid chromatography tandem mass spectrometry (LC-MS/MS), we detected 95 sphingolipids that were altered by FB1 treatment; of these, 29 (mainly simple sphingolipids) were significantly increased, while 33 (mostly complex sphingolipids) were significantly decreased. A quantitative analysis of the global proteome, using an integrated quantitative approach with tandem mass tag (TMT) labeling and LC-MS/MS, indicated the upregulation of 633 and the downregulation of 672 proteins after FB1 treatment. Most differentially expressed proteins (DEPs) were involved in processes related to phenylpropanoid and flavonoid biosynthesis. In addition, up to 20 peroxidases (POD) were found to be upregulated, and POD activity was also increased by the inhibitor. To our knowledge, this is the first report on the effects of FB1 treatment on cotton fiber and ovule sphingolipidomics and proteomics. Our findings provide target metabolites and biological pathways for cotton fiber improvement.

Network Pharmacology Identifies the Mechanisms of Action of TaohongSiwu Decoction Against Essential Hypertension

BACKGROUND TaohongSiwu decoction (THSWT), a traditional herbal formula, has been used to treat cardiovascular and cerebrovascular diseases such as essential hypertension (EH) in China. However, the pharmacological mechanism is not clear. To investigate the mechanisms of THSWT in the treatment of EH, we performed compounds, targets prediction and network analysis using a network pharmacology method. MATERIAL AND METHODS We selected chemical constituents and targets of THSWT according to TCMSP and UniProtKB databases and collected therapeutic targets on EH from Online Mendelian Inheritance in Man (OMIM), Drugbank and DisGeNET databases. The protein-protein interaction (PPI) was analyzed by using String database. Then network was constructed by using Cytoscape_v3.7.1, and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment was performed by using Database for Annotation, Visualization and Integrated Discovery (DAVID) software. RESULTS The results of our network pharmacology research showed that the THSWT, composed of 6 Chinese herbs, contained 15 compounds, and 23 genes regulated the main signaling pathways related to EH. Moreover, the PPI network based on targets of THSWT on EH revealed the interaction relationship between targets. These core compounds were 6 of the 15 disease-related compounds in the network, kaempferol, quercetin, luteolin, Myricanone, beta-sitosterol, baicalein, and the core genes contained ADRB2, CALM1, HMOX1, JUN, PPARG, and VEGFA, which were regulated by more than 3 compounds and significantly associated with Calcium signaling pathway, cGMP-PKG signaling pathway, cAMP signaling pathway, PI3K-Akt signaling pathway, Rap1 signaling pathway, and Ras signaling pathway. CONCLUSIONS This network pharmacological study can reveal potential mechanisms of multi-target and multi-component THSWT in the treatment of EH, provide a scientific basis for studying the mechanism.

Transcriptome analysis reveals differences in the mechanisms of fiber initiation and elongation between long- and short-fiber cotton (Gossypium hirsutum L.) lines

Background

Improving the yield and fiber quality of upland cotton is a goal of plant breeders. However, increasing the yield and quality of cotton fibers is becoming more urgent. While the growing human population needs more cotton fiber, climate change is reducing the amount of land on which cotton can be planted, or making it difficult to ensure that water and other resources will be available in optimal quantities. The most logical means of improving yield and quality is understanding and manipulating the genes involved. Here, we used comparative transcriptomics to explore differences in gene expression between long- and short-fiber cotton lines to identify candidate genes useful for cotton improvement.

Results

Light and electron microscopy revealed that the initial fiber density was significantly greater in our short-fiber group (SFG) than in our long-fiber group (LFG). Compared with the SFG fibers, the LFG fibers were longer at all developmental stages. Comparison of the LFG and SFG transcriptomes revealed a total of 3538 differentially expressed genes (DEGs). Notably, at all three developmental stages examined, two expression patterns, consistently downregulated (profile 0) and consistently upregulated (profile 7), were identified, and both were significantly enriched in the SFG and LFG. Twenty-two DEGs known to be involved in fiber initiation were detected in profile 0, while 31 DEGs involved in fiber elongation were detected in profile 7. Functional annotation suggested that these DEGs, which included ERF1, TUA2, TUB1, and PER64, affect fiber elongation by participating in the ethylene response, microtubule synthesis, and/or the peroxidase (POD) catalytic pathway. qRT-PCR was used to confirm the RNA sequencing results for select genes.

Conclusions

A comparison of SFG and LFG transcription profiles revealed modest but important differences in gene expression between the groups. Notably, our results confirm those of previous studies suggesting that genes involved in ethylene, tubulin, and POD pathways play important roles in fiber development. The 22 consistently downregulated DEGs involved in fiber initiation and the 31 consistently upregulated genes involved in fiber elongation are seemingly good candidate genes for improving fiber initiation and elongation in cotton.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5986-5) contains supplementary material, which is available to authorized users.

Cotton functional genomics reveals global insight into genome evolution and fiber development

Due to the economic value of natural textile fiber, cotton has attracted much research attention, which has led to the publication of two diploid genomes and two tetraploid genomes. These big data facilitate functional genomic study in cotton, and allow researchers to investigate cotton genome structure, gene expression, and protein function on the global scale using high-throughput methods. In this review, we summarized recent studies of cotton genomes. Population genomic analyses revealed the domestication history of cultivated upland cotton and the roles of transposable elements in cotton genome evolution. Alternative splicing of cotton transcriptomes was evaluated genome-widely. Several important gene families like MYC, NAC, Sus and GhPLDα1 were systematically identified and classified based on genetic structure and biological function. High-throughput proteomics also unraveled the key functional proteins correlated with fiber development. Functional genomic studies have provided unprecedented insights into global-scale methods for cotton research.