Transcriptome Analysis of Ten-DPA Fiber in an Upland Cotton (<i>Gossypium hirsutum</i>) Line with Improved Fiber Traits from Phytochrome A1 RNAi Plants

Abstract

Silencing phytochrome A1 gene (PHYA1) by RNA interference in Upland cotton (Gossypium hirsutum L. cv. Coker 312) had generated PHYA1 RNAi lines with improved fiber quality (longer, stronger and finer fiber). To reveal molecular mechanisms that govern fiber development with positive fiber traits, a study of global gene expression profiling of 10-DPA fibers in a PHYA1 RNAi line and its parent Coker 312 was conducted by high-throughput RNA sequencing. A comparative analysis of transcriptomes between the two lines had identified 142 genes that were differentially expressed in the 10-DPA fiber of the RNAi line. Gene Ontology analysis showed that these differentially expressed genes were mainly involved in metabolic pathways, heterocyclic/organic cyclic compound binding and multiple enzyme activities, and cell structures which were reported to play important roles in fiber development. Twenty-eight KEGG pathways were mapped for the 142 genes, and the pathways related to glycolysis/gluconeogenesis and pyruvate metabolism were the most abundant and followed by cytochrome P450-involved pathways, suggesting that fiber improvement could be through the regulation of proteins involved in cytochrome P450 pathways. Genes encoding WRKY transcription factors, sucrose synthase, xyloglucan endotransglucosylase hydrolase, udp-glucuronate: xylan alpha-glucuronosyltransferase, and genes involved in lipid metabolism and

Deep Transcriptome Analysis Reveals Reactive Oxygen Species (ROS) Network Evolution, Response to Abiotic Stress, and Regulation of Fiber Development in Cotton

“…The expression levels of most of the SOD genes were higher at 10 DPA than at 20 DPA (Figure 4A,B). The result showed that the SOD genes are integral at 10 DPA, being a critical stage of fiber initiation and elongation, moreover, at the stage of 10 DPA, ABA inhibits fiber cell initiation and elongation [33]. Moreover, previous studies have shown that cotton annexin proteins; AnxGh1:AAR13288, AnxGh2:AAB67993, AnxGhFx:FJ415173, and AnxGhF:AAC33305 are present in higher amount in fibers of 10 DPA wild-type plants as compared to the fuzzless-lintless mutant [34].…”

Single Nucleotide Mutagenesis of the TaCHLI Gene Suppressed Chlorophyll and Fatty Acid Biosynthesis in Common Wheat Seedlings

“…PCR reaction and data collection were performed by using Applied Biosystems ® QuantStudio ® 3 (USA) with 2X SG Fast qPCR Master Mix (Low Rox) (Sangon Biotech, China). Relative gene expression levels were calculated by using the 2 -DDCT method with three replicates (Miao et al, 2017). All data were normalized against the expression level of the wheat actin gene.…”

Extensin arabinoside chain length is modulated in elongating cotton fibre

“…Predicted corresponding cotton genes are annotated on the basis of high similarity to the Arabidopsis orthologues. Transcripts of genes encoding extensin proteins have been identified in transcriptomics studies to be highly enriched both at 10 and 20 days post anthesis (DPA), further suggesting involvement in the fibre development ( Islam et al, 2016 , Miao et al, 2017 ). Also, in one of the three regression models a correlation between extensin content and fibre length and strength was indicated ( Rajasundaram et al, 2014 ).…”