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In this study, a total of 66 UDP-glucose pyrophosphorylase (UGP) (EC 2.7.7.9) genes were identified from the genomes of four cotton species, which are the members of Pfam glycosyltransferase family (PF01702) and catalyze the reaction between glucose-1-phosphate and UTP to produce UDPG. The analysis of evolutionary relationship, gene structure, and expression provides the basis for studies on function of UGP genes in cotton. The evolutionary tree and gene structure analysis revealed that the UGP gene family is evolutionarily conserved. Collinearity and Ka/Ks analysis indicated that amplification of UGP genes is due to repetitive crosstalk generating between new family genes, while being under strong selection pressure. The analysis of cis-acting elements exhibited that UGP genes play important role in cotton growth, development, abiotic and hormonal stresses. Six UGP genes that were highly expressed in cotton fiber at 15 DPA were screened by transcriptome data and qRT-PCR analysis. The addition of low concentrations of IAA and GA3 to ovule cultures revealed that energy efficiency promoted the development of ovules and fiber clusters, and qRT-PCR showed that expression of these six UGP genes was differentially increased. These results suggest that the UGP gene may play an important role in fiber development, and provides the opportunity to plant researchers to explore the mechanisms involve in fiber development in cotton.

Upland cotton is the most widely planted for natural fiber around the world, and either lint percentage (LP) or fiber length (FL) is the crucial component tremendously affecting cotton yield and fiber quality, respectively. In this study, two lines MBZ70-053 and MBZ70-236 derived from G. hirsutum CCRI70 recombinant inbred line (RIL) population presenting different phenotypes in LP and FL traits were chosen to conduct RNA sequencing on ovule and fiber samples, aiming at exploring the differences of molecular and genetic mechanisms during cotton fiber initiation and elongation stages. As a result, 249/128, 369/206, 4296/1198 and 3547/2129 up-/down- regulated differentially expressed genes (DGEs) in L2 were obtained at −3, 0, 5 and 10 days post-anthesis (DPA), respectively. Seven gene expression profiles were discriminated using Short Time-series Expression Miner (STEM) analysis; seven modules and hub genes were identified using weighted gene co-expression network analysis. The DEGs were mainly enriched into energetic metabolism and accumulating as well as auxin signaling pathway in initiation and elongation stages, respectively. Meanwhile, 29 hub genes were identified as 14-3-3ω, TBL35, GhACS, PME3, GAMMA-TIP, PUM-7, etc., where the DEGs and hub genes revealed the genetic and molecular mechanisms and differences during cotton fiber development.

Plant architecture, including branching pattern, is an important agronomic trait of cotton crops. In recent years, strigolactones (SLs) have been considered important plant hormones that regulate branch development. In some species such as Arabidopsis, DWARF14 is an unconventional receptor that plays an important role in the SL signaling pathway. However, studies on SL receptors in cotton are still lacking. Here, we cloned and analysed the structure of the GbD14 gene in Gossypium barbadense and found that it contains the domains necessary for a SL receptor. The GbD14 gene was expressed primarily in the roots, leaves and vascular bundles, and the GbD14 protein was determined via GFP to localize to the cytoplasm and nucleus. Gene expression analysis revealed that the GbD14 gene not only responded to SL signals but also was differentially expressed between cotton plants whose types of branching differed. In particular, GbD14 was expressed mainly in the axillary buds of normal-branching cotton, while it was expressed the most in the leaves of nulliplex-branch cotton. In cotton, the GbD14 gene can be induced by SL and other plant hormones, such as indoleacetic acid, abscisic acid, and jasmonic acid. Compared with wild-type Arabidopsis, GbD14-overexpressing Arabidopsis responded more rapidly to SL signals. Moreover, we also found that GbD14 can rescue the multi-branched phenotype of Arabidopsis Atd14 mutants. Our results indicate that the function of GbD14 is similar to that of AtD14, and GbD14 may be a receptor for SL in cotton and involved in regulating branch development. This research provides a theoretical basis for a profound understanding of the molecular mechanism of branch development and ideal plant architecture for cotton breeding improvements.

Cotton plant architecture, including fruit branch formation and flowering pattern, influences plant light exploitation, cotton yield and planting cost. DNA methylation has been widely observed at different developmental stages in both plants and animals and is associated with regulation of gene expression, chromatin remodelling, genome protection and other functions. Here, we investigated the global epigenetic reprogramming during the development of fruiting branches and floral buds at three developmental stages: the seedling stage, the pre-squaring stage and the squaring stage. We first identified 22 cotton genes which potentially encode DNA methyltransferases and demethylases. Among them, the homologous genes of CMT, DRM2 and MET1 were upregulated at pre-squaring and squaring stages, suggesting that DNA methylation is involved in the development of floral buds and fruit branches. Although the global methylation at all of three developmental stages was not changed, the CHG-type methylation of non-expressed genes was higher than those of expressed genes. In addition, we found that the expression of the homologous genes of the key circadian rhythm regulators, including CRY, LHY and CO, was associated with changes of DNA methylation at three developmental stages.

Circular RNAs (circRNAs), a class of recently discovered non-coding RNAs, play a role in biological and developmental processes. A recent study showed that circRNAs exist in plants and play a role in their environmental stress responses. However, cotton circRNAs and their role in Verticillium wilt response have not been identified up to now. In this study, two CSSLs (chromosome segment substitution lines) of G.barbadense introgressed into G. hirsutum, CSSL-1 and CSSL-4 (a resistant line and a susceptible line to Verticillium wilt, respectively), were inoculated with V. dahliae for RNA-seq library construction and circRNA analysis. A total of 686 novel circRNAs were identified. CSSL-1 and CSSL-4 had similar numbers of circRNAs and shared many circRNAs in common. However, CSSL-4 differentially expressed approximately twice as many circRNAs as CSSL-1, and the differential expression levels of the common circRNAs were generally higher in CSSL-1 than in CSSL-4. Moreover, two C-RRI comparisons, C-RRI-vs-C-RRM and C-RRI-vs-C-RSI, possessed a large proportion (approximately 50%) of the commonly and differentially expressed circRNAs. These results indicate that the differentially expressed circRNAs may play roles in the Verticillium wilt response in cotton. A total of 280 differentially expressed circRNAs were identified. A Gene Ontology analysis showed that most of the ‘stimulus response’ term source genes were NBS family genes, of which most were the source genes from the differentially expressed circRNAs, indicating that NBS genes may play a role in Verticillium wilt resistance and might be regulated by circRNAs in the disease-resistance process in cotton.