‘Boju’ is a traditional Chinese herbal tea known for its unique flavor. To distinguish the flavor characteristics of its two main commercial cultivars, Chrysanthemum morifolium Hemsl. cv. 'Da Boju' (DBJ) and Chrysanthemum morifolium Hemsl cv. 'Xiao Boju' (XBJ), an integrated analytical platform combining electronic nose, electronic tongue, and gas chromatography-ion mobility spectrometry (GC - IMS) was employed. Results showed that the electronic nose effectively differentiated the two cultivars, with the W2W sensor being the most responsive. Taste analysis indicated that both cultivars shared a profile characterized by saltiness, umami, and a lingering bitter aftertaste. GC - IMS detected 125 volatile signals, annotating 66 compounds. Further multivariate analysis screened 28 characteristic volatile markers, mainly classified as terpenoids, which elucidated the chemical basis for the observed sensory differences. This study provides a reliable strategy for the quality assessment of commercial chrysanthemum teas.

This study combined electronic nose, electronic tongue, and gas chromatography - ion mobility spectrometry (GC - IMS) to comprehensively evaluate the flavor characteristics of commercially available 'Boju' from both sensory attributes and chemical composition. In the electronic nose and electronic tongue analyses, the W2W sensor was identified as the key discriminator for the odor difference between Chrysanthemum morifolium Hemsl. cv. 'Da Boju' (DBJ) and Chrysanthemum morifolium Hemsl cv. 'Xiao Boju' (XBJ). A slight salty taste was detected in DBJ, while umami and lingering bitterness were the characteristic tastes distinguishing DBJ from XBJ. The utilisation of GC - IMS facilitated the identification of 125 volatile chemical components, of which 66 compounds were definitively identified. Orthogonal partial least squares discriminant analysis (OPLS - DA) was subsequently implemented in order to identify 28 characteristic volatile elements.

Cotton is susceptible to waterlogging stress. Under hypoxic conditions, cellular energy production declined, shifting pyruvate metabolism from aerobic respiration to anaerobic fermentation. In this pathway, Pyruvate decarboxylase 2 (PDC2) catalyzes the conversion of pyruvate to acetaldehyde and subsequently ethanol, activating glycolysis to sustain ATP production, which is crucial for basal respiration and stress tolerance. However, the functional role of PDC2 in mediating cotton’s tolerance response to waterlogging stress remains largely unexplored. In this study, we present preliminary evidence that GhPDC2 functions as a positive regulator of waterlogging tolerance in cotton. Transcriptomic profiling revealed significant upregulation of GhPDC2 in roots subjected to waterlogging, implying its involvement in stress adaptation. Further functional validation demonstrated that overexpression of GhPDC2 enhanced waterlogging tolerance compared to the WT and mutant lines, as evidenced by improved growth metrics including chlorophyll content, fresh/dry weight, and root length, alongside elevated ethanol accumulation, and increased ADH and PDC2 enzymatic activity. Additionally, GhPDC2 overexpression enhanced ROS scavenging capacity. Conversely, silencing GhPDC2 in cotton significantly compromised the development of adaptive morphological traits under waterlogging. Collectively, these findings demonstrate that GhPDC2 modulates anaerobic metabolism during waterlogging by alleviating energy crises through ethanol accumulation, mitigating ROS production, and ultimately confers oxidative protection.

To adapt to low-oxygen environments, plants develop aerated tissues and hydrophobic barriers that facilitate internal respiration while protecting against radial oxygen loss (ROL). In plants exhibiting lenticel structures, reduced oxygen levels induce hypertrophy as a compensatory mechanism for oxygen deficiency and enhanced hydrophobic tolerance. However, the physiological mechanisms underlying the aeration and hydrophobic tolerance of inducible hypertrophied lenticels (Hpls) in cotton remain poorly understood. In this study, cotton lenticels were examined following exposure to continuous waterlogging for 10 and 20 days. Tolerant genotypes demonstrated an increase in Hpl formation and adventitious root development (AR), together with improved tolerance to 20 days of waterlogging stress. The Hpl regions exhibited induced thickening of cell wall and xylem tissue. Within the endodermal cells of Hpl, there was notable accumulation of extracellular vesicular tubular structures (EVBs), lignin, suberin, and casparian bands. Furthermore, the Hpl regions facilitated the formation of adventitious roots as well as internal aerated tissues characterized by cortical and arenchymatous phellem (AP). The development of secondary aerated tissues combined with the accumulation of hydrophobic polymers indicates that inducible Hpl plays a dual role in improving waterlogging tolerance.

BACKGROUND:Cotton (Gossypium spp.) serves as a vital global crop for textile production, with naturally pigmented brown cotton has gained industrial interest due to its eco-friendly coloration. However, the molecular mechanisms underlying variation in color intensity in brown cotton fibers remain poorly characterized. In this study, we investigated the genetic and biochemical basis of fiber color differentiation in hybrid-derived cotton lines spanning white, light-brown, middle-brown, and deep-brown phenotypes. RESULTS:Biochemical quantification revealed significantly elevated proanthocyanidin levels in brown cotton fibers compared to those in white counterparts, with their content positively correlating with color intensity. Transcriptomic profiling identified significant activation of flavonoid biosynthesis pathway genes in pigmented fibers. Among differentially expressed transcription factors, GhMYB5 (Ghir_D07G002110), an R2R3-type MYB regulator, exhibited gradual upregulation corresponding to color deepening. Functional characterization through qRT-PCR demonstrated GhMYB5's potential regulation of key flavonoid pathway genes GhCHS1 (Ghir_A10G012390), GhCHI3 (Ghir_A05G041560), and GhF3H (Ghir_D11G018670). Protein-DNA interaction assays (DAP-seq), yeast one-hybrid validation and LUC analysis confirmed direct binding of GhMYB5 to the promoter region of GhCHS1, establishing a regulatory node in proanthocyanidin biosynthesis. CONCLUSIONS:Our findings reveal that GhMYB5-mediated transcriptional activation of GhCHS1 promotes proanthocyanidin accumulation in brown cotton fibers, providing a molecular explanation for color intensification. The identified MYB-CHS regulatory module offers potential targets for molecular breeding of naturally colored cotton varieties with enhanced pigmentation properties. This study advances our understanding of plant pigment biosynthesis and supports sustainable textile production through engineering of natural fiber coloration.

Brown cotton and white cotton are two important raw materials used in the cotton fiber industry. Clarifying the differences in morphology, agronomic traits, and fiber pigments between these varieties can facilitate the implementation of corresponding cultivation and breeding techniques. Therefore, we obtained F2 generation brown cotton plants through hybridization and compared them with their parents. In terms of agronomic traits, plant morphology and leaf shape were similar, but brown cotton presented more villi on the main stem. The first fruiting branch node was within the range of 4–6 cm, and the first fruiting branch node height was greater than that of TM-1, i.e., between 13.25 cm and 22.79 cm, with no difference compared with that of P26. The plant height was greater than that of the parents, and the number of bolls was essentially the same as that in TM-1 and greater than that in P26. The lint percentage and average fiber length were lower in TM-1 than in P26, and the seed index was greater than that in TM-1 and P26. Pigment measurements revealed that the chlorophyll a content in brown cotton during the boll stage was lower than that in white cotton, and the content of proanthocyanidin in the cotton fibers was greater in brown cotton than in white cotton. At 15 days after pollination, the highest content was 159.8 mg/g. To determine the differences in gene expression levels, we conducted transcriptome sequencing. Gene Ontology (GO) analysis revealed that the differentially expressed genes (DEGs) were enriched in pathways related to the cell wall and enzyme activity, whereas Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the DEGs were enriched in flavonoid synthesis pathways. Transcription factor analysis revealed that the expression of the MYB3 transcription factor (Ghir_D07G002110) was higher in brown cotton, and bioinformatics analysis revealed that this gene has regulatory effects on the CHS, CHI1, and F3H genes.

ETHYLENE-INSENSITIVE3 (EIN3) or EIN3-Like (EIL) proteins, play critical roles in integrating ethylene signaling and physiological regulation in plants by modulating the expression of various downstream genes, such as ethylene-response factors (ERFs). However, little is known about the characteristics of EIN3/EILs in the gymnosperm Ginkgo biloba. In the present study, a genome-wide comparative analysis of Ginkgo EIN3/EIL gene family was performed with those from an array of species, including bryophytes (Physcomitrella patens), gymnosperms (Cycas panzhihuaensis), and angiosperms (Arabidopsis thaliana, Gossypium raimondii, Gossypium hirsutum, Oryza sativa, and Brachypodium distachyon). Within the constructed phylogenetic tree for the 53 EIN3/EILs identified, 5 GbEILs from G. biloba, 2 PpEILs from P. patens, and 3 CpEILs from C. panzhihuaensis were assigned to one cluster, suggesting that their derivation occurred after the split of their ancestors and angiosperms. Although considerable divergence accumulated in amino acid sequences along with the evolutionary process, the specific EIN3_DNA-binding domains were evolutionarily conserved among the 53 EIN3/EILs. Collinearity analysis indicated that whole-genome or segmental duplication and subsequent purifying selection might have prompted the generation and evolution of EIN3/EIL multigene families. Based on the expression patterns of five GbEILs at the four developmental stages of Ginkgo ovules, one GbEIL gene (Gb_03292) was further investigated for its role in mediating ethylene signaling. The functional activity of Gb_03292 was closely related to ethylene signaling, as it complemented the triple response via ectopic expression in ein3eil1 double mutant Arabidopsis. Additionally, GbEIL likely modulates the expression of a Ginkgo ERF (Gb_15517) by directly binding to its promoter. These results demonstrated that the GbEIL gene could have participated in mediating ethylene signal transduction during ovule development in G. biloba. The present study also provides insights into the conservation of ethylene signaling across the gymnosperm G. biloba and angiosperm species.

BACKGROUND:Calcium-dependent protein kinase (CDPK) plays a key role in cotton tolerance to abiotic stress. However, its role in cotton heat stress tolerance is not well understood. Here, we characterize the GhCDPK gene family and their expression profiles with the aim of identifying CDPK genes associated with heat stress tolerance. RESULTS:This study revealed 48 GhCDPK members in the cotton genome, distributed on 18 chromosomes. Tree phylogenetic analysis showed three main clustering groups of the GhCDPKs. Cis-elements revealed many abiotic stress and phytohormone pathways conserved promoter regions. Similarly, analysis of the transcription factor binding sites (TFBDS) in the GhCDPK genes showed many stress and hormone related sites. The expression analysis based on qRT-PCR showed that GhCDPK16 was highly responsive to high-temperature stress. Subsequent protein-protein interactions of GhCDPK16 revealed predictable interaction with ROS generating, calcium binding, and ABA signaling proteins. Overexpression of GhCDPK16 in cotton and Arabidopsis improved thermotolerance by lowering ROS compound buildup. Under heat stress, GhCDPK16 transgenic lines upregulated heat-inducible genes GhHSP70, GHSP17.3, and GhGR1, as demonstrated by qRT-PCR analysis. Contrarily, GhCDPK16 knockout lines in cotton exhibited an increase in ROS accumulation. Furthermore, antioxidant enzyme activity was dramatically boosted in the GhCDPK16-ox transgenic lines. CONCLUSIONS:The collective findings demonstrated that GhCDPK16 could be a viable gene to enhance thermotolerance in cotton and, therefore, a potential candidate gene for improving heat tolerance in cotton.

Fertilizer application is a decisive measure for the productivity of medicinal chrysanthemum plants. Therefore, determining the optimal doses of nutrients required for the growth and yield is crucial. In this study, we set out to investigate the effect of various nutrients on the growth, yield, and functional components of chrysanthemum under eight different fertilization levels at seedling, branching, and flowering growth periods. The results show that plant height, stem diameter, and leaf area under the balance fertilization treatment were the highest (82 cm, 0.78 cm, and 38.50 cm2, respectively), while the flower size and yield under the high potassium treatment were significantly increased compared to using balance fertilization. Chlorophyll content was also highest under the high potassium treatment. Moreover, plant defensive antioxidant peroxidase (POD) was responsive to low nitrogen treatment and low phosphorus treatment, while high potassium treatment enhanced the phenylalanine aminolase (PAL) activity and increased the content of flavonoids and chlorogenic acid in Chrysanthemum morifolium. In addition, low phosphorus treatment promoted the accumulation of flavonoids and chlorogenic acid content. Convincingly, the results show that growth, flowering, and functional indicators of chrysanthemum may thrive best under high potassium and balanced fertilization dosages, which will contribute to the development of a new economical chrysanthemum fertilizer ratio.

IntroductionCotton (Gossypium hirsutum L.) is susceptible to long-term waterlogging stress; however, genomic information of cotton response mechanisms toward long days of waterlogging is quite elusive.MethodsHere, we combined the transcriptome and metabolome expression level changes in cotton roots after 10 and 20 days of waterlogging stress treatment pertaining to potential resistance mechanisms in two cotton genotypes.Results and discussionNumerous adventitious roots and hypertrophic lenticels were induced in CJ1831056 and CJ1831072. Transcriptome analysis revealed 101,599 differentially expressed genes in cotton roots with higher gene expression after 20 days of stress. Reactive oxygen species (ROS) generating genes, antioxidant enzyme genes, and transcription factor genes (AP2, MYB, WRKY, and bZIP) were highly responsive to waterlogging stress among the two genotypes. Metabolomics results showed higher expressions of stress-resistant metabolites sinapyl alcohol, L-glutamic acid, galactaric acid, glucose 1-phosphate, L-valine, L-asparagine, and melibiose in CJ1831056 than CJ1831072. Differentially expressed metabolites (adenosine, galactaric acid, sinapyl alcohol, L-valine, L-asparagine, and melibiose) significantly correlated with the differentially expressed PRX52, PER1, PER64, and BGLU11 transcripts. This investigation reveals genes for targeted genetic engineering to improve waterlogging stress resistance to enhance abiotic stress regulatory mechanisms in cotton at the transcript and metabolic levels of study.

Fig. 6 (corrected). 1H-NMR spectra of acetylated MWL in cotton stalks. (B) The ratio of G/S showed in the histogram. CK, no fungus control. Each sample had two duplications. Student’s t-test was used in this study. **P<0.01, *P<0.05. Fig. 6 (original). 1H-NMR spectra of acetylated MWL in cotton stalks. (B) The ratio of G/S showed in the histogram. CK, no fungus control. Each sample had two duplications. Student’s t-test was used in this study. **P<0.01, *P<0.05.

Vacuolar processing enzymes (VPEs) play important roles in plant development, programmed cell death, and the responsiveness to biotic and abiotic stresses. To characterize the VPEs in upland cotton (Gossypium hirsutum), the VPE gene family within four Gossypium species, consisting of G. hirsutum, G. barbadense, G. arboreum, and G. raimondii, together with Arabidopsis thaliana, was comparatively analyzed at the genome-wide level. As a result, a total of 43 VPEs were identified, including 13 GhVPEs, 12 GbVPEs, 7 GaVPEs, and 7 GrVPEs, which are evenly distributed with one gene on a chromosome from four Gossypium species, respectively. The phylogenetic tree showed that the identified VPEs within the four Gossypium species could be categorized into β-type, δ-type, and γ-type VPE clades. Collinearity analysis presented 36 of intraspecies VPE-pairs and 152 of interspecies VPE-pairs, respectively, which are included in synteny blocks on chromosome. These results indicate that VPE duplication events have accorded well with the whole genome duplication. And expression profiles of GhVPEs in G. hirsutum seedlings demonstrated that the GhVPEs from the same clade are not necessarily identical in the pattern of transcriptional expression. Upon abiotic stresses (i.e., waterlogging and salt treatments), three GhVPEs (i.e., Ghir_A05G004610, Ghir_A09G011870, and Ghir_D09G011410) were significantly upregulated in their expression amounts, respectively. The GhVPE genes that presented inducible expression under some abiotic stresses may be applied to the improvement of resilience to abiotic stresses for the cultivated cottons.

Calmodulins (CAMs) and calmodulin-like proteins (CMLs) can participate in the regulation of various physiological processes via sensing and decoding Ca2+ signals. To reveal the characteristics of the CAM/CML family in Ginkgo biloba, a comprehensive analysis was performed at the genome-wide level. A total of 26 CAMs/CMLs, consisting of 5 GbCAMs and 21 GbCMLs, was identified on 11 out of 12 chromosomes in G. biloba. They displayed a certain degree of multiplicity in their sequences, albeit with conserved EF hands. Collinearity analysis suggested that tandem rather than segmental or whole-genome duplications were likely to play roles in the evolution of the Ginkgo CAM/CML family. Furthermore, GbCAMs/GbCMLs were grouped into higher, lower, and moderate expression in magnitude. The cis-acting regulatory elements involved in phytohormone-responsiveness within GbCAM/GbCML promotors may explain their varied expression profiles. The ectopic expression of a GbCML gene (Gb_30819) in transgenic Arabidopsis led to phenotypes with significantly shortened root length and seedling height, and decreased yields of both pods and seeds. Moreover, an electrophoresis mobility shift assay demonstrated the Ca2+-binding activity of Gb_30819 in vitro. Altogether, these results contribute to insights into the characteristics of the evolution and expression of GbCAMs/GbCMLs, as well as evidence for Ca2+-CAM/CML pathways functioning within the ancient gymnosperm G. biloba.

Cotton (Gossypium hirsutum L.) is a major crop worldwide. Although its raw material is largely valuable in the textile sector and as a source of edible oil, it is susceptible to waterlogging stress circumstances. As a result, increasing plant stress tolerance requires an understanding of the mechanisms by which the plant adapts to waterlogging stress. In this study, 17 of 30 cotton genotypes increased germination after 10 days of waterlogging, but 28 of 30 cotton genotypes decreased germination after 20 days of stress. Plant height, taproot length, and fresh weight decreased significantly in many plants after 10 and 20 days of stress as compared to controls. Furthermore, leaf area dropped at 10 days but dramatically increased as stress time increased up to 20 days of waterlogging. Chlorophyll content increased in numerous cotton genotypes. However, sensitive cultivars, on the other hand, dropped considerably, with a loss rate of 0.5734–3.4485 mg⸳g-1 compared to 0.6799–1.2619 mg⸳g-1 in the control group. Likewise, as the stress period increased from 10 to 20 days, antioxidant activity peroxidase (POD), superoxide dismutase (SOD), and catalase (CAT) increased at a decreasing rate. This article clarifies the physio-biochemical processes that support cotton's waterlogging stress response, which will be valuable for future waterlogging stress research as well as cotton genetic research and breeding. However, it is critical to test the selected varieties in the field in order to determine their optimum resistance to waterlogging situations.

With the continuous growth of the human population, the demand for fiber is also rising sharply. As one of the main fiber plants available globally, cotton fiber yield (Gossypium hirsutum) is affected by boll abscission, which is related to the formation of the abscission layer. Therefore, we explored the formation of the abscission layer in cotton. The formation of the abscission layer in the cotton boll stalk was promoted by exogenous ethylene. It was found that both the number of the Golgi apparatus and the number of stacking layers increased in the dissociated cells. The GhArfGAP gene family in cotton was screened by the bioinformatics method, and the species and evolutionary relationship of the GhArfGAP gene family were analyzed. qRT-PCR showed that GhArfGAP13, GhArfGAP15, GhArfGAP25, and GhArfGAP34 in cotton had spatiotemporal-specific expression patterns. Subcellular localization suggested that GhArfGAP25 played a role in the Golgi apparatus. The expression of GhArfGAP25 in transgenic Arabidopsis thaliana is increased in the roots, stems, and leaves. Finally, we found that ethylene could induce the formation of the abscission layer in cotton. GhArfGAP13, GhArfGAP15, GhArfGAP25, and GhArfGAP34 might regulate the changes in the Golgi apparatus in the abscission layer. Taken together, the findings provide new ideas for the study of the formation of cotton abscission.

Background: Calcium-dependent protein kinases (CDPKs) play important roles both in developments and response to stresses, via mediating Ca 2+ signal transduction in plants. To characterize the CDPKs in apple ( Malus domestica ), the apple CDPK gene family, together with those from pear ( Pyrus bretschneideri ), peach ( Prunus persica ), strawberry ( Fragaria vesca ), and and Arabidopsis thaliana , were analyzed at the genome-wide level in the present study. Results: A total of 116 CDPK s, consisting of 24 MdCDPK s, 28 PbCDPK s, 16 PpCDPK s, 14 FvCDPK s, and 34 AtCDPK s, was identified from apple, pear, peach, strawberry, and Arabidopsis, respectively. An integrated analysis of these CDPK s was performed on their chromosomal distribution, phylogenetic and collinearity relationships, characteristics of gene structures and conserved motifs. As a result, the CDPK gene family members were showed to be highly conserved both at their kinase and EF-hand domains. Among 209 gene-pairs with interspecies collinearity, there existed 22, 36, 21, and 25 ones between MdCDPK s and other CDPK s in Arabidopsis, pear, strawberry, and peach, respectively. And the evaluated Ka / Ks ratios were less than 1 between the CDPK gene pairs with collinearity relationships. Transcriptomic analysis demonstrated that among 24 members of the apple CDPK gene family, two up-regulatory ones ( HF05266 and HF09216 ) and two down-regulatory ones ( HF05471 and HF15429 ), were differentially expressed with significance between the apple fruit developmental stage S4 (mature) and other stages (early growing-S1, mid growing-S2, and late growing-S3), respectively. Conclusions: The whole genome duplication and subsequent purifying selection, might have played an important role in the CDPK gene expansion, leading to structural and functional novelty during evolution of the species lineages. In many cases, the MdCDPK genes within a phylogenetic group could show the different expression patterns at the transcriptional level, suggesting that these MdCDPK s have undergone genetic variant events and potential functional diversification. Some of MdCDPK s with significantly differential expression, were indicated their particular functions at the specific stages of apple fruit development.

ABC (ATP-binding cassette) transporters are a class of superfamily transmembrane proteins that are commonly observed in natural organisms. The ABCC (ATP-binding cassette C subfamily) protein belongs to a subfamily of the ABC protein family and is a multidrug resistance-associated transporter that localizes to the tonoplast and plays a significant role in pathogenic microbial responses, heavy metal regulation, secondary metabolite transport, and plant growth. Recent studies have shown that the ABCC protein is also involved in the transport of anthocyanins/proanthocyanidins (PAs). To clarify the types and numbers of ABCC genes involved in PA transport in Gossypium hirsutum, the phylogenetic evolution, physical location, and structure of ABCC genes were classified by bioinformatic methods in the upland cotton genome, and the expression levels of these genes were analyzed at different developmental stages of the cotton fiber. The results showed that 42 ABCC genes were initially identified in the whole genome of upland cotton; they were designated GhABCC1-42. The gene structure and phylogenetic analysis showed that the closely related ABCC genes were structurally identical. The analysis of chromosomal localization demonstrated that there were no ABCC genes on the chromosomes of AD/At2, AD/At5, AD/At6, AD/At10, AD/At12, AD/At13, AD/Dt2, AD/Dt6, AD/Dt10, and AD/Dt13. Outside the genes, there were ABCC genes on other chromosomes, and gene clusters appeared on the two chromosomes AD/At11 and AD/Dt8. Phylogenetic tree analysis showed that some ABCC proteins in G. hirsutum were clustered with those of Arabidopsis thaliana, Vitis vinifera and Zea mays, which are known to function in anthocyanin/PA transport. The protein structure prediction indicated that the GhABCC protein structure is similar to the AtABCC protein in A. thaliana, and most of these proteins have a transmembrane domain. At the same time, a quantitative RT-PCR analysis of 42 ABCC genes at different developmental stages of brown cotton fiber showed that the relative expression levels of GhABCC24, GhABCC27, GhABCC28, GhABCC29 and GhABCC33 were consistent with the trend of PA accumulation, which may play a role in PA transport. These results provide a theoretical basis for further analysis of the function of the cotton ABCC genes and their role in the transport of PA.

Abstract Background: With the continuous growth of population, the demand for fiber is also rising sharply. As one of the main fiber plants in the world, cotton fiber yield of upland cotton is affected by boll abscission, which is related to the formation of abscission zone. Therefore, we explored the formation of the abscission zone of upland cotton.Result: The formation of abscission layer of cotton boll stalk was promoted by exogenous ethylene. It was found that both the number of Golgi apparatus and the number of stacking layers increased in the dissociated cells. The GhArfGAP gene family in upland cotton was screened by bioinformatics method, and the species and evolutionary relationship of GhArfGAP gene family were analyzed. qRT-PCR showed that the expression patterns of GhArfGAP13,GhArfGAP15, GhArfGAP25 and GhArfGAP34 in cotton were spatiotemporal specific. Subcellular localization suggested that GhArfGAP25 played a role in Golgi apparatus . The expression of GhArfGAP25 in transgenic Arabidopsis increased in the root, stem and leaf.Conclusions: Ethylene could induce the formation of abscission zone in upland cotton. GhArfGAP13,GhArfGAP15,GhArfGAP25,GhArfGAP34 might regulate the changes of Golgi apparatus in abscisson zone.Taken together the findings provide new ideas for the study of cotton abscission formation.

Background : The B-BOX (BBX) proteins have important functions in the regulation of photomorphogenesis. The BBX gene family has been identified in several plants, such as rice, Arabidopsis and tomato. However, there still lack a genome-wide survey of BBX genes in cotton. Results : In our present study, 63 GhBBX genes were identified in cotton. The analyses of phylogenetic evolution and gene structure showed that the GhBBX genes were divided into five subfamilies, and contained B-box conserved domains. qRT-PCR analysis releaved that both GhBBX27 and GhBBX33 had potential roles in proanthocyanidin synthesis of brown cotton fibers. Conclusions : This study provides a genome-wide survey of the BBX gene family in cotton and highlights its role in proanthocyanidin synthesis. This result will help us to further understand the complexity of the BBX gene family and the functional characteristics of its members.