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Cotton is a globally significant economic crop. Brassinosteroids (BRs) are crucial to cotton development. This study systematically analyzed the BR synthase gene family in four cotton species and identified 60 BR genes: 20 in Gossypium hirsutum (GhBRs), 20 in G. barbadense (GbBRs), 10 in G. arboreum (GaBRs), and 10 in G. raimondii (GrBRs). The analysis was extended to chromosomal localization, evolutionary relationships, domain features, and cis-regulatory elements in the promoter regions of BR synthase genes. The results showed that the BR synthase genes were evenly distributed across different subgenomes and chromosomes. Bioinformatics analyses revealed high conservation of amino acid sequences, secondary structures, and conserved domains among the subfamily members, which is closely linked to their pivotal roles in the BR biosynthesis pathway. Cis-element distribution analysis of the BR synthase genes further underscored the complexity of BR gene expression regulation, which is influenced by multiple factors, including plant hormones, abiotic stress, and transcription factors. Expression profiling of GhBRs genes in various cotton tissues and developmental stages highlighted the key roles of GhROT3-1 and GhDET2-1 in fiber elongation and initiation, respectively. Protein–protein interactions and transcription factor analyses further elucidated the regulatory mechanisms of GhROT3-1 and GhDET2-1 in cotton growth and development. This study lays a theoretical foundation for understanding the role of the BR signaling pathway in cotton development, facilitating molecular breeding.

Introduction: Cotton is an important economic crop to provide natural fibers as raw materials to textile industry, and is significantly affected by biotic and abiotic stress during the whole growth stage, in which Verticillium wilt (VW) caused by Verticillium dahliae is one of the most destructive disease to lead to a significant yield reduction. Heat shock proteins (Hsps) are important molecular chaperones, and play crucial roles in plant growth, development, resistance to biotic and abiotic stress. Hsp40 and Hsp70 are two key Hsps in cell chaperone network, however, the function and regulatory mechanism of Hsp40 and Hsp70 members in VW resistance and abiotic stress in cotton are largely unknown.Methods and Results: Herein, a systematic and comprehensive analysis of Hsp40s and Hsp70s in four cotton species of Gossypium arboretum, G. raimondii, G. hirsutum, and G. barbadense were performed. A total of 291 Hsp40s and 171 Hsp70s identified in four Gossypium species. Sequence analysis revealed that all Hsp40 proteins contained J domain that provides the binding sites to Hsp70. Protein-protein interaction prediction analysis displayed that GhHsp40-55 might interact with GhHsp70-2 and GhHsp70-13, suggesting their potential function as protein complex. Promoter cis-acting element analysis demonstrated that multiple cis-elements related to disease and stress response consists in GhHsp40 and GhHsp70 promoters. Further expression analysis showed that eight GhHsp40s (Hsp40-2,4,8,11,20,23,53,55) and seven GhHsp70s (Hsp70-2,3,6,8,13,19,22) were up-regulated after V. dahliae infection. In addition, five GhHsp40s (Hsp40-2,8,11,53,55) and four GhHsp70s (Hsp70-3,6,8,13) were up-regulated after salt treatment, six GhHsp40s (Hsp40-4,11,20,23) and three GhHsp70s (Hsp70-2,8,19) were up-regulated after drought treatment, four GhHsp40s (Hsp40-2,11,20,23) and four GhHsp70s (Hsp70-3,6,19,22) were up-regulated after temperature treatment, suggesting these Hsps have possible important function in the process of abiotic stress response.Discussion: Our results lay a foundation for understanding the function of Hsp40 and Hsp70 in the resistance against V. dahliae and abiotic stress, and elucidating the regulatory mechanism of the protein complex, evolution and molecular mechanism under stress.

Abstract Background Cotton is the world’s largest and most important source of renewable natural fiber. BEL1-like homeodomain (BLH) genes are ubiquitous in plants and have been reported to contribute to plant development. However, there is no comprehensive characterization of this gene family in cotton. In this study, 32, 16, and 18 BLH genes were identified from the G. hirsutum, G. arboreum, and G. raimondii genome, respectively. In addition, we also studied the phylogenetic relationships, chromosomal location, gene structure, and gene expression patterns of the BLH genes. Results The results indicated that these BLH proteins were divided into seven distinct groups by phylogenetic analysis. Among them, 25 members were assigned to 15 chromosomes. Furthermore, gene structure, chromosomal location, conserved motifs, and expression level of BLH genes were investigated in G. hirsutum. Expression profiles analysis showed that four genes (GhBLH1_3, GhBLH1_4, GhBLH1_5, and GhBLH1_6) from BLH1 subfamily were highly expressed during the fiber cell elongation period. The expression levels of these genes were significantly induced by gibberellic acid and brassinosteroid, but not auxin. Exogenous application of gibberellic acid significantly enhanced GhBLH1_3, GhBLH1_4, and GhBLH1_5 transcripts. Expression levels of GhBLH1_3 and GhBLH1_4 genes were significantly increased under brassinosteroid treatment. Conclusions The BLH gene family plays a very important role in many biological processes during plant growth and development. This study deepens our understanding of the role of the GhBLH1 gene involved in fiber development and will help us in breeding better cotton varieties in the future.

Abstract Background The pentatricopeptide repeat (PPR) gene family, which contains multiple 35-amino acid repeats, constitutes one of the largest gene families in plants. PPR proteins function in organelles to target specific transcripts and are involved in plant development and growth. However, the function of PPR proteins in cotton is still unknown. Results In this study, we characterized a PPR gene YELLOW-GREEN LEAF (GhYGL1d) that is required for cotton plastid development. The GhYGL1d gene has a DYW domain in C-terminal and is highly express in leaves, localized to the chloroplast fractions. GhYGL1d share high amino acid-sequence homology with AtECB2. In atecb2 mutant, overexpression of GhYGL1d rescued the seedling lethal phenotype and restored the editing of accD and ndhF transcripts. Silencing of GhYGL1d led to the reduction of chlorophyll and phenotypically yellow-green leaves in cotton. Compared with wild type, GhYGL1d-silenced cotton showed significant deformations of thylakoid structures. Furthermore, the transcription levels of plastid-encoded polymerase (PEP) and nuclear-encoded polymerase (NEP) dependent genes were decreased in GhYGL1d-silenced cotton. Conclusions Our data indicate that GhYGL1d not only contributes to the editing of accD and ndhF genes, but also affects the expression of NEP- and PEP-dependent genes to regulate the development of thylakoids, and therefore regulates leaf variegation in cotton.

Abstract Background Zinc finger proteins (ZFPs) containing only a single zinc finger domain play important roles in the regulation of plant growth and development, as well as in biotic and abiotic stress responses. To date, the evolutionary history and functions of the ZFP gene family have not been identified in cotton. Results In this paper, we identified 29 ZFP genes in Gossypium hirsutum. This gene family was divided into seven subfamilies, 22 of which were distributed over 17 chromosomes. Bioinformatic analysis revealed that 20 GhZFP genes originated from whole genome duplications and two originated from dispersed duplication events, indicating that whole genome duplication is the main force in the expansion of the GhZFP gene family. Most GhZFP8 subfamily genes, except for GhZFP8–3, were highly expressed during fiber cell growth, and were induced by brassinosteroids in vitro. Furthermore, we found that a large number of GhZFP genes contained gibberellic acid responsive elements, auxin responsive elements, and E-box elements in their promoter regions. Exogenous application of these hormones significantly stimulated the expression of these genes. Conclusions Our findings reveal that GhZFP8 genes are involved in cotton fiber development and widely induced by auxin, gibberellin and BR, which provides a foundation for the identification of more downstream genes with potential roles in phytohormone stimuli, and a basis for breeding better cotton varieties in the future.

Abstract Background Cell elongation and expansion are significant contributors to plant growth and morphogenesis, and are often regulated by environmental cues and endogenous hormones. Auxin is one of the most important phytohormones involved in the regulation of plant growth and development and plays key roles in plant cell expansion and elongation. Cotton fiber cells are a model system for studying cell elongation due to their large size. Cotton is also the world’s most utilized crop for the production of natural fibers for textile and garment industries, and targeted expression of the IAA biosynthetic gene iaaM increased cotton fiber initiation. Polar auxin transport, mediated by PIN and AUX/LAX proteins, plays a central role in the control of auxin distribution. However, very limited information about PIN-FORMED (PIN) efflux carriers in cotton is known. Results In this study, 17 PIN-FORMED (PIN) efflux carrier family members were identified in the Gossypium hirsutum (G. hirsutum) genome. We found that PIN1–3 and PIN2 genes originated from the At subgenome were highly expressed in roots. Additionally, evaluation of gene expression patterns indicated that PIN genes are differentially induced by various abiotic stresses. Furthermore, we found that the majority of cotton PIN genes contained auxin (AuxREs) and salicylic acid (SA) responsive elements in their promoter regions were significantly up-regulated by exogenous hormone treatment. Conclusions Our results provide a comprehensive analysis of the PIN gene family in G. hirsutum, including phylogenetic relationships, chromosomal locations, and gene expression and gene duplication analyses. This study sheds light on the precise roles of PIN genes in cotton root development and in adaption to stress responses.

Cotton is the main source of renewable fiber in the world and is primarily used for textile production. Cotton fibers are single cells differentiated from the ovule epidermis and are an excellent model system for studying cell elongation, polyploidization, and cell wall biosynthesis. Plant hormones, which are present in relatively low concentrations, play important roles in various developmental processes, and recently, multiple reports have revealed the pivotal roles of hormones in regulating cotton fiber development. For example, exogenous application of hormones has been shown to promote the initiation and growth of fiber cells. However, a comprehensive understanding about phytohormone regulating fiber development is still unknown. Here, we focus on recent advances in elucidating the roles of multiple phytohormones in the control of fiber development, namely auxin, gibberellin, brassinosteroid, ethylene, cytokinin, abscisic acid, and strigolactones. We not only review the identification of genes involved in hormone biosynthetic and signaling pathways but also discuss the mechanisms of these phytohormones in regulating the initiation and elongation of fiber cells in cotton. Auxin, gibberellin, brassinosteroid, ethylene, jasmonic acid, and strigolactones play positive roles in fiber development, whereas cytokinin and abscisic acid inhibit fiber growth. Our aim is to provide a comprehensive review of the role of phytohormones in cotton fiber development that will serve as the basis for further elucidation of the mechanisms by which plant hormones regulate fiber growth.

CCRI63, with the largest cultivated area among hybrids in China, is a successful promotion of elite upland cotton (Gossypium hirsutum L.) hybrid cultivar. We have constructed a detailed genomic variation map of CCRI63 by aligning whole-genome shotgun sequencing reads from CCRI63 to the TM-1 reference genome. Genomic single nucleotide polymorphism (SNP) and insertion-deletion (Indel) mutational hotspots were identified, most of which were located on chromosome D02, and associated with disease resistance and lipid glycosylation and modification. The density of heterozygous SNP sites showed 73 quantitative trait loci overlapped with peak intervals of high-density heterozygous SNPs, suggesting that the heterozygous sites in the peak are important for improvement of CCRI63 yield and fibre quality. To avoid loss of genetic components, unmapped reads were used for de novo assembly of the missing regions in the reference genome, and 153 novel functional genes were obtained. The large-scale genetic variation and novel functional genes identified in the CCRI63 genome can facilitate future gene-phenotype studies and provide an additional resource for the improvement of cotton. [ABSTRACT FROM AUTHOR]