Genome-scale analysis of the cotton KCS gene family revealed a binary mode of action for gibberellin A regulated fiber growth

Cotton GhMAX2 promotes single-celled fiber elongation by releasing the GhS1FA-mediated inhibition of fatty acid biosynthesis

KEY MESSAGE

Cotton GhMAX2 positively regulates fiber elongation by mediating the degradation of GhS1FA, which transcriptionally represses GhKCS9 expression. Strigolactones (SLs) are known to promote cotton fiber development. However, the precise molecular relationship between SL signaling and fiber cell elongation remains unclear. In this study, we investigate the role of F-box E3 ligase MORE AXILLARY GROWTH2 (MAX2) in upland cotton in relation to the regulation of fiber development. GhMAX2b and GhMAX2f act as key components for SL signal transduction, with their loss-of-function leading to a notable reduction in fiber length. Biochemical analysis showed that GhMAX2b/f trigger the ubiquitination and subsequent degradation of the transcription repressor strigolactone-1-factor-At (GhS1FA), which function as a substrate for these E3 ligases. Furthermore, GhS1FA inhibits fatty acids biosynthesis by directly binding to the W-box element within the promoter of 3-ketoacyl-CoA synthases 9 (GhKCS9) and repressing its expression. In summary, we propose that GhMAX2b/f promote fiber elongation, potentially operating partially independently of GhD53 degradation.

Regulatory networks of coresident subgenomes during rapid fiber cell elongation in upland cotton

Cotton, an intriguing plant species shaped by polyploidization, evolution, and domestication, holds particular interest due to the complex mechanisms governing fiber traits across its two subgenomes. However, the regulatory elements or transcriptional networks between subgenomes during fiber elongation remain to be fully clarified. Here, we analyzed 1462 cotton fiber samples to reconstruct the gene-expression regulatory networks that influence fiber cell elongation. Inter-subgenome expression quantitative trait loci (eQTLs) largely dictate gene transcription, with a notable tendency for the D subgenome to regulate A-subgenome eGenes. This regulation reveals synchronized homoeologous gene expression driven by co-localized eQTLs and divergent patterns that diminish genetic correlations, thus leading to preferential expression in the A and D subgenomes. Hotspot456 emerged as a key regulator of fiber initiation and elongation, and artificial selection of trans-eQTLs in hotspot456 that positively regulate KCS1 has facilitated cell elongation. Experiments designed to clarify the roles of trans-eQTLs in improved fiber breeding confirmed the inhibition of GhTOL9 by a specific trans-eQTL via GhWRKY28, which negatively affects fiber elongation. We propose a model in which the GhWRKY28-GhTOL9 module regulates this process through the ESCRT (endosomal sorting complex required for transport) pathway. This research significantly advances our understanding of cotton's evolutionary and domestication processes and the intricate regulatory mechanisms that underlie significant plant traits.

A β-ketoacyl-CoA synthase encoded by DDP1 controls rice anther dehiscence and pollen fertility by maintaining lipid homeostasis in the tapetum

KEY MESSAGE

DDP1, encoding a β-Ketoacyl-CoA Synthase, regulates rice anther dehiscence and pollen fertility by affecting the deposition of lipid on anther epidermis and pollen wall. Anther dehiscence and pollen fertility are crucial for male fertility in rice. Here, we studied the function of Defective in Dehiscence and Pollen1 (DDP1), a novel member of the KCS family in rice, in regulating anther dehiscence and pollen fertility. DDP1 encodes an endoplasmic reticulum (ER)-localized protein and is ubiquitously expressed in various organs, predominately in the microspores and tapetum. The ddp1 mutant exhibited partial male sterility attributed to defective anther dehiscence and pollen fertility, which was notably distinct from those observed in Arabidopsis thaliana and rice mutants associated with lipid metabolism. Mutations of DDP1 altered the content and composition of wax on anther epidermis and pollen wall, causing abnormalities in their morphology. Moreover, genes implicated in lipid metabolism, pollen development, and anther dehiscence exhibited significantly altered expression levels in the ddp1 mutant. These findings indicate that DDP1 controls anther dehiscence and pollen fertility to ensure normal male development by modulating lipid homeostasis in the tapetum, thereby enhancing our understanding of the mechanisms underlying rice anther dehiscence and pollen fertility.

Evolutionary comparison of lncRNAs in four cotton species and functional identification of LncR4682-PAS2-KCS19 module in fiber elongation

Long non-coding RNAs (lncRNAs) play an important role in various biological processes in plants. However, there have been few reports on the evolutionary signatures of lncRNAs in closely related cotton species. The lncRNA transcription patterns in two tetraploid cotton species and their putative diploid ancestors were compared in this paper. By performing deep RNA sequencing, we identified 280 429 lncRNAs from 21 tissues in four cotton species. lncRNA transcription evolves more rapidly than mRNAs, and exhibits more severe turnover phenomenon in diploid species compared to that in tetraploid species. Evolutionarily conserved lncRNAs exhibit higher expression levels, and lower tissue specificity compared with species-specific lncRNAs. Remarkably, tissue expression of homologous lncRNAs in Gossypium hirsutum and G. barbadense exhibited similar patterns, suggesting that these lncRNAs may be functionally conserved and selectively maintained during domestication. An orthologous lncRNA, lncR4682, was identified and validated in fibers of G. hirsutum and G. barbadense with the highest conservatism and expression abundance. Through virus-induced gene silencing in upland cotton, we found that lncR4682 and its target genes GHPAS2 and GHKCS19 positively regulated fiber elongation. In summary, the present study provides a systematic analysis of lncRNAs in four closely related cotton species, extending the understanding of transcriptional conservation of lncRNAs across cotton species. In addition, LncR4682-PAS2-KCS19 contributes to cotton fiber elongation by participating in the biosynthesis of very long-chain fatty acids.

Transcriptional regulation of phospholipid transport in cotton fiber elongation by GhMYB30D04-GhHD1 interaction complex

Cotton fiber length is basically determined by well-coordinated gene expression and phosphatidylinositol phosphates (PIPs) accumulation during fiber elongation but the regulatory mechanism governing PIPs transport remains unknown. Here, we report a MYB transcription factor GhMYB30D04 in Gossypium hirsutum that promotes fiber elongation through modulating the expression of PIP transporter gene GhLTPG1. Knockout of GhMYB30D04 gene in cotton (KO) results in a reduction of GhLTPG1 transcripts with lower accumulation of PIPs, leading to shorter fibers and lower fiber yield. Conversely, GhMYB30D04 overexpression (GhMYB30D04-OE) causes richer PIPs and longer cotton fibers, mimicking the effects of exogenously applying PIPs on the ovules of GhMYB30D04-KO and wild type. Furthermore, GhMYB30D04 interacts with GhHD1, the crucial transcription factor of fiber initiation, to form an activation complex stabilized by PIPs, both of which upregulate GhLTPG1 expression. Comparative omics-analysis revealed that higher and extended expressions of LTPG1 in fiber elongation mainly correlate with the variations of the GhMYB30D04 gene between two cotton allotetraploids, contributing to longer fiber in G. babardense. Our work clarifies a mechanism by which GhHD1-GhMYB30D04 form a regulatory module of fiber elongation to tightly control PIP accumulation. Our work still has an implication that GhMYB30D04-GhHD1 associates with development transition from fiber initiation to elongation.

Strigolactone-induced degradation of SMXL7 and SMXL8 contributes to gibberellin- and auxin-mediated fiber cell elongation in cotton

Cotton (Gossypium) fiber length, a key trait determining fiber yield and quality, is highly regulated by a class of recently identified phytohormones, strigolactones (SLs). However, the underlying molecular mechanisms of SL signaling involved in fiber cell development are largely unknown. Here, we show that the SL signaling repressors MORE AXILLARY GROWTH2-LIKE7 (GhSMXL7) and GhSMXL8 negatively regulate cotton fiber elongation. Specifically, GhSMXL7 and GhSMXL8 inhibit the polyubiquitination and degradation of the gibberellin (GA)-triggered DELLA protein (GhSLR1). Biochemical analysis revealed that GhSMXL7 and GhSMXL8 physically interact with GhSLR1, which interferes with the association of GhSLR1 with the E3 ligase GA INSENSITIVE2 (GhGID2), leading to the repression of GA signal transduction. GhSMXL7 also interacts with the transcription factor GhHOX3, preventing its binding to the promoters of essential fiber elongation regulatory genes. Moreover, both GhSMXL7 and GhSMXL8 directly bind to the promoter regions of the AUXIN RESPONSE FACTOR (ARF) genes GhARF18-10A, GhARF18-10D, and GhARF19-7D to suppress their expression. Cotton plants in which GhARF18-10A, GhARF18-10D, and GhARF19-7D transcript levels had been reduced by virus-induced gene silencing (VIGS) displayed reduced fiber length compared with control plants. Collectively, our findings reveal a mechanism illustrating how SL integrates GA and auxin signaling to coordinately regulate plant cell elongation at the single-cell level.

Exploring the regulatory role of non-coding RNAs in fiber development and direct regulation of GhKCR2 in the fatty acid metabolic pathway in upland cotton

Cotton fiber holds immense importance as the primary raw material for the textile industry. Consequently, comprehending the regulatory mechanisms governing fiber development is pivotal for enhancing fiber quality. Our study aimed to construct a regulatory network of competing endogenous RNAs (ceRNAs) and assess the impact of non-coding RNAs on gene expression throughout fiber development. Through whole transcriptome data analysis, we identified differentially expressed genes (DEGs) regulated by non-coding RNA (ncRNA) that were predominantly enriched in phenylpropanoid biosynthesis and the fatty acid elongation pathway. This analysis involved two contrasting phenotypic materials (J02-508 and ZRI015) at five stages of fiber development. Additionally, we conducted a detailed analysis of genes involved in fatty acid elongation, including KCS, KCR, HACD, ECR, and ACOT, to unveil the factors contributing to the variation in fatty acid elongation between J02-508 and ZRI015. Through the integration of histochemical GUS staining, dual luciferase assay experiments, and correlation analysis of expression levels during fiber development stages for lncRNA MSTRG.44818.23 (MST23) and GhKCR2, we elucidated that MST23 positively regulates GhKCR2 expression in the fatty acid elongation pathway. This identification provides valuable insights into the molecular mechanisms underlying fiber development, emphasizing the intricate interplay between non-coding RNAs and protein-coding genes.

Gibberellic acid promotes single-celled fiber elongation through the activation of two signaling cascades in cotton

The agricultural green revolution spectacularly enhanced crop yield through modification of gibberellin (GA) signaling. However, in cotton, the GA signaling cascades remain elusive, limiting our potential to cultivate new cotton varieties and improve yield and quality. Here, we identified that GA prominently stimulated fiber elongation through the degradation of DELLA protein GhSLR1, thereby disabling GhSLR1's physical interaction with two transcription factors, GhZFP8 and GhBLH1. Subsequently, the resultant free GhBLH1 binds to GhKCS12 promoter and activates its expression to enhance VLCFAs biosynthesis. With a similar mechanism, the free GhZFP8 binds to GhSDCP1 promoter and activates its expression. As a result, GhSDCP1 upregulates the expression of GhPIF3 gene associated with plant cell elongation. Ultimately, the two parallel signaling cascades synergistically promote cotton fiber elongation. Our findings outline the mechanistic framework that translates the GA signal into fiber cell elongation, thereby offering a roadmap to improve cotton fiber quality and yield.

Isolation and Functional Characterization of a Constitutive Promoter in Upland Cotton (Gossypium hirsutum L.)

Multiple cis-acting elements are present in promoter sequences that play critical regulatory roles in gene transcription and expression. In this study, we isolated the cotton FDH (Fiddlehead) gene promoter (pGhFDH) using a real-time reverse transcription-PCR (qRT-PCR) expression analysis and performed a cis-acting elements prediction analysis. The plant expression vector pGhFDH::GUS was constructed using the Gateway approach and was used for the genetic transformation of Arabidopsis and upland cotton plants to obtain transgenic lines. Histochemical staining and a β-glucuronidase (GUS) activity assay showed that the GUS protein was detected in the roots, stems, leaves, inflorescences, and pods of transgenic Arabidopsis thaliana lines. Notably, high GUS activity was observed in different tissues. In the transgenic lines, high GUS activity was detected in different tissues such as leaves, stalks, buds, petals, androecium, endosperm, and fibers, where the pGhFDH-driven GUS expression levels were 3-10-fold higher compared to those under the CaMV 35S promoter at 10-30 days post-anthesis (DPA) during fiber development. The results indicate that pGhFDH can be used as an endogenous constitutive promoter to drive the expression of target genes in various cotton tissues to facilitate functional genomic studies and accelerate cotton molecular breeding.

Genome-wide identification and expression analysis of the KCS gene family in soybean (Glycine max) reveal their potential roles in response to abiotic stress

Very long chain fatty acids (VLCFAs) are fatty acids with chain lengths of 20 or more carbon atoms, which are the building blocks of various lipids that regulate developmental processes and plant stress responses. 3-ketoacyl-CoA synthase encoded by the KCS gene is the key rate-limiting enzyme in VLCFA biosynthesis, but the KCS gene family in soybean (Glycine max) has not been adequately studied thus far. In this study, 31 KCS genes (namely GmKCS1 - GmKCS31) were identified in the soybean genome, which are unevenly distributed on 14 chromosomes. These GmKCS genes could be phylogenetically classified into seven groups. A total of 27 paralogous GmKCS gene pairs were identified with their Ka/Ks ratios indicating that they had undergone purifying selection during soybean genome expansion. Cis-acting element analysis revealed that GmKCS promoters contained multiple hormone- and stress-responsive elements, indicating that GmKCS gene expression levels may be regulated by various developmental and environmental stimuli. Expression profiles derived from RNA-seq data and qRT-PCR experiments indicated that GmKCS genes were diversely expressed in different organs/tissues, and many GmKCS genes were found to be differentially expressed in the leaves under cold, heat, salt, and drought stresses, suggesting their critical role in soybean resistance to abiotic stress. These results provide fundamental information about the soybean KCS genes and will aid in their further functional elucidation and exploitation.

DELLA-mediated gene repression is maintained by chromatin modification in rice

DELLA proteins are master regulators of gibberellic acid (GA) signaling through their effects on gene expression. Enhanced DELLA accumulation in rice and wheat varieties has greatly contributed to grain yield increases during the green revolution. However, the molecular basis of DELLA-mediated gene repression remains elusive. In this work, we show that the rice DELLA protein SLENDER RICE1 (SLR1) forms a tripartite complex with Polycomb-repressive complex 2 (PRC2) and the histone deacetylase HDA702 to repress downstream genes by establishing a silent chromatin state. The slr1 mutation and GA signaling resulted in dissociation of PRC2 and HDA702 from GA-inducible genes. Loss-of-function or downregulation of the chromatin regulators impaired SLR1-dependent histone modification and gene repression. Time-resolved analysis of GA signaling revealed that GA-induced transcriptional activation was associated with a rapid increase of H3K9ac followed by H3K27me3 removal. Collectively, these results establish a general epigenetic mechanism for DELLA-mediated gene repression and reveal details of the chromatin dynamics during transcriptional activation stimulated by GA signaling.

GhXB38D represses cotton fibre elongation through ubiquitination of ethylene biosynthesis enzymes GhACS4 and GhACO1

Ethylene plays an essential role in the development of cotton fibres. Ethylene biosynthesis in plants is elaborately regulated by the activities of key enzymes, 1-aminocyclopropane-1-carboxylate oxidase (ACO) and 1-aminocyclopropane-1-carboxylate synthase (ACS); however, the potential mechanism of post-translational modification of ACO and ACS to control ethylene synthesis in cotton fibres remains unclear. Here, we identify an E3 ubiquitin ligase, GhXB38D, that regulates ethylene biosynthesis during fibre elongation in cotton. GhXB38D gene is highly expressed in cotton fibres during the rapid elongation stage. Suppressing GhXB38D expression in cotton significantly enhanced fibre elongation and length, accompanied by the up-regulation of genes associated with ethylene signalling and fibre elongation. We demonstrated that GhXB38D interacts with the ethylene biosynthesis enzymes GhACS4 and GhACO1 in elongating fibres and specifically mediates their ubiquitination and degradation. The inhibition of GhXB38D gene expression increased the stability of GhACS4 and GhACO1 proteins in cotton fibres and ovules, resulting in an elevated concentration of ethylene. Our findings highlight the role of GhXB38D as a regulator of ethylene synthesis by ubiquitinating ACS4 and ACO1 proteins and modulating their stability. GhXB38D acts as a negative regulator of fibre elongation and serves as a potential target for enhancing cotton fibre yield and quality through gene editing strategy.

A comprehensive overview of cotton genomics, biotechnology and molecular biological studies

Cotton is an irreplaceable economic crop currently domesticated in the human world for its extremely elongated fiber cells specialized in seed epidermis, which makes it of high research and application value. To date, numerous research on cotton has navigated various aspects, from multi-genome assembly, genome editing, mechanism of fiber development, metabolite biosynthesis, and analysis to genetic breeding. Genomic and 3D genomic studies reveal the origin of cotton species and the spatiotemporal asymmetric chromatin structure in fibers. Mature multiple genome editing systems, such as CRISPR/Cas9, Cas12 (Cpf1) and cytidine base editing (CBE), have been widely used in the study of candidate genes affecting fiber development. Based on this, the cotton fiber cell development network has been preliminarily drawn. Among them, the MYB-bHLH-WDR (MBW) transcription factor complex and IAA and BR signaling pathway regulate the initiation; various plant hormones, including ethylene, mediated regulatory network and membrane protein overlap fine-regulate elongation. Multistage transcription factors targeting CesA 4, 7, and 8 specifically dominate the whole process of secondary cell wall thickening. And fluorescently labeled cytoskeletal proteins can observe real-time dynamic changes in fiber development. Furthermore, research on the synthesis of cotton secondary metabolite gossypol, resistance to diseases and insect pests, plant architecture regulation, and seed oil utilization are all conducive to finding more high-quality breeding-related genes and subsequently facilitating the cultivation of better cotton varieties. This review summarizes the paramount research achievements in cotton molecular biology over the last few decades from the above aspects, thereby enabling us to conduct a status review on the current studies of cotton and provide strong theoretical support for the future direction.

Genome-wide identification and expression analysis of 3-ketoacyl-CoA synthase gene family in rice (Oryza sativa L.) under cadmium stress

3-Ketoacyl-CoA synthase (KCS) is the key rate-limiting enzyme for the synthesis of very long-chain fatty acids (VLCFAs) in plants, which determines the carbon chain length of VLCFAs. However, a comprehensive study of KCSs in Oryza sativa has not been reported yet. In this study, we identified 22 OsKCS genes in rice, which are unevenly distributed on nine chromosomes. The OsKCS gene family is divided into six subclasses. Many cis-acting elements related to plant growth, light, hormone, and stress response were enriched in the promoters of OsKCS genes. Gene duplication played a crucial role in the expansion of the OsKCS gene family and underwent a strong purifying selection. Quantitative Real-time polymerase chain reaction (qRT-PCR) results revealed that most KCS genes are constitutively expressed. We also revealed that KCS genes responded differently to exogenous cadmium stress in japonica and indica background, and the KCS genes with higher expression in leaves and seeds may have functions under cadmium stress. This study provides a basis for further understanding the functions of KCS genes and the biosynthesis of VLCFA in rice.

Two major chromosome evolution events with unrivaled conserved gene content in pomegranate

Pomegranate has a unique evolutionary history given that different cultivars have eight or nine bivalent chromosomes with possible crossability between the two classes. Therefore, it is important to study chromosome evolution in pomegranate to understand the dynamics of its population. Here, we de novo assembled the Azerbaijani cultivar "Azerbaijan guloyshasi" (AG2017; 2n = 16) and re-sequenced six cultivars to track the evolution of pomegranate and to compare it with previously published de novo assembled and re-sequenced cultivars. High synteny was observed between AG2017, Bhagawa (2n = 16), Tunisia (2n = 16), and Dabenzi (2n = 18), but these four cultivars diverged from the cultivar Taishanhong (2n = 18) with several rearrangements indicating the presence of two major chromosome evolution events. Major presence/absence variations were not observed as >99% of the five genomes aligned across the cultivars, while >99% of the pan-genic content was represented by Tunisia and Taishanhong only. We also revisited the divergence between soft- and hard-seeded cultivars with less structured population genomic data, compared to previous studies, to refine the selected genomic regions and detect global migration routes for pomegranate. We reported a unique admixture between soft- and hard-seeded cultivars that can be exploited to improve the diversity, quality, and adaptability of local pomegranate varieties around the world. Our study adds body knowledge to understanding the evolution of the pomegranate genome and its implications for the population structure of global pomegranate diversity, as well as planning breeding programs aiming to develop improved cultivars.

Comparative phylogenomic insights of KCS and ELO gene families in Brassica species indicate their role in seed development and stress responsiveness

Very long-chain fatty acids (VLCFAs) possess more than twenty carbon atoms and are the major components of seed storage oil, wax, and lipids. FAE (Fatty Acid Elongation) like genes take part in the biosynthesis of VLCFAs, growth regulation, and stress responses, and are further comprised of KCS (Ketoacyl-CoA synthase) and ELO (Elongation Defective Elongase) sub-gene families. The comparative genome-wide analysis and mode of evolution of KCS and ELO gene families have not been investigated in tetraploid Brassica carinata and its diploid progenitors. In this study, 53 KCS genes were identified in B. carinata compared to 32 and 33 KCS genes in B. nigra and B. oleracea respectively, which suggests that polyploidization might has impacted the fatty acid elongation process during Brassica evolution. Polyploidization has also increased the number of ELO genes in B. carinata (17) over its progenitors B. nigra (7) and B. oleracea (6). Based on comparative phylogenetics, KCS, and ELO proteins can be classified into eight and four major groups, respectively. The approximate date of divergence for duplicated KCS and ELO genes varied from 0.03 to 3.20 million years ago (MYA). Gene structure analysis indicated that the maximum number of genes were intron-less and remained conserved during evolution. The neutral type of selection seemed to be predominant in both KCS and ELO genes evolution. String-based protein-protein interaction analysis suggested that bZIP53, a transcription factor might be involved in the activation of transcription of ELO/KCS genes. The presence of biotic and abiotic stress-related cis-regulatory elements in the promoter region suggests that both KCS and ELO genes might also play their role in stress tolerance. The expression analysis of both gene family members reflect their preferential seed-specific expression, especially during the mature embryo development stage. Furthermore, some KCS and ELO genes were found to be specifically expressed under heat stress, phosphorus starvation, and Xanthomonas campestris infection. The current study provides a basis to understand the evolution of both KCS and ELO genes in fatty acid elongation and their role in stress tolerance.

Tackling functional redundancy of Arabidopsis fatty acid elongase complexes

Very-long-chain fatty acids (VLCFA) are precursors for various lipids playing important physiological and structural roles in plants. Throughout plant tissues, VLCFA are present in multiple lipid classes essential for membrane homeostasis, and also stored in triacylglycerols. VLCFA and their derivatives are also highly abundant in lipid barriers, such as cuticular waxes in aerial epidermal cells and suberin monomers in roots. VLCFA are produced by the fatty acid elongase (FAE), which is an integral endoplasmic reticulum membrane multi-enzymatic complex consisting of four core enzymes. The 3-ketoacyl-CoA synthase (KCS) catalyzes the first reaction of the elongation and determines the chain-length substrate specificity of each elongation cycle, whereas the other three enzymes have broad substrate specificities and are shared by all FAE complexes. Consistent with the co-existence of multiple FAE complexes, performing sequential and/or parallel reactions to produce the broad chain-length-range of VLCFA found in plants, twenty-one KCS genes have been identified in the genome of Arabidopsis thaliana. Using CRISPR-Cas9 technology, we established an expression platform to reconstitute the different Arabidopsis FAE complexes in yeast. The VLCFA produced in these yeast strains were analyzed in detail to characterize the substrate specificity of all KCS candidates. Additionally, Arabidopsis candidate proteins were transiently expressed in Nicotiana benthamiana leaves to explore their activity and localization in planta. This work sheds light on the genetic and biochemical redundancy of fatty acid elongation in plants.

Strigolactones act downstream of gibberellins to regulate fiber cell elongation and cell wall thickness in cotton (Gossypium hirsutum)

Strigolactones (SLs) are a class of phytohormones that regulate plant shoot branching and adventitious root development. However, little is known regarding the role of SLs in controlling the behavior of the smallest unit of the organism, the single cell. Here, taking advantage of a classic single-cell model offered by the cotton (Gossypium hirsutum) fiber cell, we show that SLs, whose biosynthesis is fine-tuned by gibberellins (GAs), positively regulate cell elongation and cell wall thickness by promoting the biosynthesis of very long-chain fatty acids (VLCFAs) and cellulose, respectively. Furthermore, we identified two layers of transcription factors (TFs) involved in the hierarchical regulation of this GA-SL crosstalk. The top-layer TF GROWTH-REGULATING FACTOR 4 (GhGRF4) directly activates expression of the SL biosynthetic gene DWARF27 (D27) to increase SL accumulation in fiber cells and GAs induce GhGRF4 expression. SLs induce the expression of four second-layer TF genes (GhNAC100-2, GhBLH51, GhGT2, and GhB9SHZ1), which transmit SL signals downstream to two ketoacyl-CoA synthase genes (KCS) and three cellulose synthase (CesA) genes by directly activating their transcription. Finally, the KCS and CesA enzymes catalyze the biosynthesis of VLCFAs and cellulose, respectively, to regulate development of high-grade cotton fibers. In addition to providing a theoretical basis for cotton fiber improvement, our results shed light on SL signaling in plant development at the single-cell level.

A very-long-chain fatty acid synthesis gene, SD38, influences plant height by activating ethylene biosynthesis in rice

As an important trait in crop breeding, plant height is associated with lodging resistance and yield. With the identification and cloning of several semi-dwarfing genes, increasing numbers of semi-dwarf cultivars have emerged, which has led to a 'green revolution' in rice (Oryza sativa) production. In this study, we identified a rice semi-dwarf mutant, semi-dwarf 38 (sd38), which showed significantly reduced cell length. SD38 encodes a fatty acid elongase, β-ketoacyl-CoA synthase, which is involved in the synthesis of very-long-chain fatty acids (VLCFAs). Expression analysis showed that SD38 was localized on the membrane of the endoplasmic reticulum, and was expressed in all analyzed tissues with differential abundance. The mutation of SD38 affected lipid metabolism in the sd38 mutant. A functional complementarity test in Saccharomyces cerevisiae indicated that SD38 was capable of complementing the deficiency of ELO3p activity in BY4741-elo3 knockout yeast cells by participating in the synthesis of C24:0 VLCFA. Significant changes were observed in the expression of genes involved in ethylene synthesis, which resulted in reduced content of the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) in the sd38 mutant. Exogenously supplied VLCFA (C24:0) increased the expression levels of OsACS3, OsACS4, and OsACO7 and the plant height of sd38 mutant seedlings, similar to the effect of exogenous application of ACC and ethephon. These results reveal a relationship among VLCFAs, ethylene biosynthesis, and plant height and improve our understanding of plant height development in crops.

Genome-wide identification and characterization of the KCS gene family in sorghum (Sorghum bicolor (L.) Moench)

The aboveground parts of plants are covered with cuticle, a hydrophobic layer composed of cutin polyester and cuticular wax that can protect plants from various environmental stresses. β-Ketoacyl-CoA synthase (KCS) is the key rate-limiting enzyme in plant wax synthesis. Although the properties of KCS family genes have been investigated in many plant species, the understanding of this gene family in sorghum is still limited. Here, a total of 25 SbKCS genes were identified in the sorghum genome, which were named from SbKCS1 to SbKCS25. Evolutionary analysis among different species divided the KCS family into five subfamilies and the SbKCSs were more closely related to maize, implying a closer evolutionary relationship between sorghum and maize. All SbKCS genes were located on chromosomes 1, 2, 3, 4, 5, 6, 9 and 10, respectively, while Chr 1 and Chr 10 contained more KCS genes than other chromosomes. The prediction results of subcellular localization showed that SbKCSs were mainly expressed in the plasma membrane and mitochondria. Gene structure analysis revealed that there was 0-1 intron in the sorghum KCS family and SbKCSs within the same subgroup were similar. Multiple cis-acting elements related to abiotic stress, light and hormone response were enriched in the promoters of SbKCS genes, which indicated the functional diversity among these genes. The three-dimensional structure analysis showed that a compact spherical space structure was formed by various secondary bonds to maintain the stability of SbKCS proteins, which was necessary for their biological activity. qRT-PCR results revealed that nine randomly selected SbKCS genes expressed differently under drought and salt treatments, among which SbKCS8 showed the greatest fold of expression difference at 12 h after drought and salt stresses, which suggested that the SbKCS genes played a potential role in abiotic stress responses. Taken together, these results provided an insight into investigating the functions of KCS family in sorghum and in response to abiotic stress.

Expressed genes and their new alleles identification during fibre elongation reveal the genetic factors underlying improvements of fibre length in cotton

Interspecific breeding in cotton takes advantage of genetic recombination among desirable genes from different parental lines. However, the expression new alleles (ENAs) from crossovers within genic regions and their significance in fibre length (FL) improvement are currently not understood. Here, we generated resequencing genomes of 191 interspecific backcross inbred lines derived from CRI36 (Gossypium hirsutum) × Hai7124 (Gossypium barbadense) and 277 dynamic fibre transcriptomes to identify the ENAs and extremely expressed genes (eGenes) potentially influencing FL, and uncovered the dynamic regulatory network of fibre elongation. Of 35 420 eGenes in developing fibres, 10 366 ENAs were identified and preferentially distributed in chromosomes subtelomeric regions. In total, 1056-1255 ENAs showed transgressive expression in fibres at 5-15 dpa (days post-anthesis) of some BILs, 520 of which were located in FL-quantitative trait locus (QTLs) and GhFLA9 (recombination allele) was identified with a larger effect for FL than GhFLA9 of CRI36 allele. Using ENAs as a type of markers, we identified three novel FL-QTLs. Additionally, 456 extremely eGenes were identified that were preferentially distributed in recombination hotspots. Importantly, 34 of them were significantly associated with FL. Gene expression quantitative trait locus analysis identified 1286, 1089 and 1059 eGenes that were colocalized with the FL trait at 5, 10 and 15 dpa, respectively. Finally, we verified the Ghir_D10G011050 gene linked to fibre elongation by the CRISPR-cas9 system. This study provides the first glimpse into the occurrence, distribution and expression of the developing fibres genes (especially ENAs) in an introgression population, and their possible biological significance in FL.

Modifying the yeast very long chain fatty acid biosynthetic machinery by the expression of plant 3-ketoacyl CoA synthase isozymes

Eukaryotes express a multi-component fatty acid elongase to produce very long chain fatty acids (VLCFAs), which are building blocks of diverse lipids. Elongation is achieved by cyclical iteration of four reactions, the first of which generates a new carbon-carbon bond, elongating the acyl-chain. This reaction is catalyzed by either ELONGATION DEFECTIVE LIKE (ELO) or 3-ketoacyl-CoA synthase (KCS) enzymes. Whereas plants express both ELO and KCS enzymes, other eukaryotes express only ELOs. We explored the Zea mays KCS enzymatic redundancies by expressing each of the 26 isozymes in yeast strains that lacked endogenous ELO isozymes. Expression of the 26 maize KCS isozymes in wild-type, scelo2 or scelo3 single mutants did not affect VLCFA profiles. However, a complementation screen of each of the 26 KCS isozymes revealed five that were capable of complementing the synthetically lethal scelo2; scelo3 double mutant. These rescued strains express novel VLCFA profiles reflecting the different catalytic capabilities of the KCS isozymes. These novel strains offer a platform to explore the relationship between VLCFA profiles and cellular physiology.

GhBZR3 suppresses cotton fiber elongation by inhibiting very-long-chain fatty acid biosynthesis

The BRASSINAZOLE-RESISTANT (BZR) transcription factor is a core component of brassinosteroid (BR) signaling and is involved in the development of many plant species. BR is essential for the initiation and elongation of cotton fibers. However, the mechanism of BR-regulating fiber development and the function of BZR is poorly understood in Gossypium hirsutum L. (cotton). Here, we identified a BZR family transcription factor protein referred to as GhBZR3 in cotton. Overexpression of GhBZR3 in Arabidopsis caused shorter root hair length, hypocotyl length, and hypocotyl cell length, indicating that GhBZR3 negatively regulates cell elongation. Pathway enrichment analysis from VIGS-GhBZR3 cotton plants found that fatty acid metabolism and degradation might be the regulatory pathway that is primarily controlled by GhBZR3. Silencing GhBZR3 expression in cotton resulted in taller plant height as well as longer fibers. The very-long-chain fatty acid (VLCFA) content was also significantly increased in silenced GhBZR3 plants compared with the wild type. The GhKCS13 promoter, a key gene for VLCFA biosynthesis, contains two GhBZR3 binding sites. The results of yeast one-hybrid, electrophoretic mobility shift, and luciferase assays revealed that GhBZR3 directly interacted with the GhKCS13 promoter to suppress gene expression. Taken together, these results indicate that GhBZR3 negatively regulates cotton fiber development by reducing VLCFA biosynthesis. This study not only deepens our understanding of GhBZR3 function in cotton fiber development, but also highlights the potential of improving cotton fiber length and plant growth using GhBZR3 and its related genes in future cotton breeding programs.

Revealing Genetic Differences in Fiber Elongation between the Offspring of Sea Island Cotton and Upland Cotton Backcross Populations Based on Transcriptome and Weighted Gene Coexpression Networks

Fiber length is an important indicator of cotton fiber quality, and the time and rate of cotton fiber cell elongation are key factors in determining the fiber length of mature cotton. To gain insight into the differences in fiber elongation mechanisms in the offspring of backcross populations of Sea Island cotton Xinhai 16 and land cotton Line 9, we selected two groups with significant differences in fiber length (long-fiber group L and short-fiber group S) at different fiber development stages 0, 5, 10 and 15 days post-anthesis (DPA) for transcriptome comparison. A total of 171.74 Gb of clean data was obtained by RNA-seq, and eight genes were randomly selected for qPCR validation. Data analysis identified 6055 differentially expressed genes (DEGs) between two groups of fibers, L and S, in four developmental periods, and gene ontology (GO) term analysis revealed that these DEGs were associated mainly with microtubule driving, reactive oxygen species, plant cell wall biosynthesis, and glycosyl compound hydrolase activity. Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis indicated that plant hormone signaling, mitogen-activated protein kinase (MAPK) signaling, and starch and sucrose metabolism pathways were associated with fiber elongation. Subsequently, a sustained upregulation expression pattern, profile 19, was identified and analyzed using short time-series expression miner (STEM). An analysis of the weighted gene coexpression network module uncovered 21 genes closely related to fiber development, mainly involved in functions such as cell wall relaxation, microtubule formation, and cytoskeletal structure of the cell wall. This study helps to enhance the understanding of the Sea Island–Upland backcross population and identifies key genes for cotton fiber development, and these findings will provide a basis for future research on the molecular mechanisms of fiber length formation in cotton populations.

Identification of key proteins related to high-quality fiber in Upland cotton via proteomics analysis

The dynamics of cotton fiber elongation and microfibirl deposition orientation were delineated; advanced ethylene synthesis and redox reaction homeostasis may be crucial for high-quality fiber formation. Fiber length, strength, and fineness determine the use and commercial value of cotton fiber, but their underlying molecular mechanisms remain obscure. We compared the dynamic change trajectories of length, diameter and microfibril orientation angle of the fibers produced by an introgression line SY6167 which generates high-quality fibers even better than Sea island cotton with those of the common-quality fibers from TM-1 across 5 to 30 days post anthesis (DPA). The proteomes were profiled and compared at six representative time points using 2-DE and MS/MS. 14 proteins differentially expressed inside each of cotton line temporally and significantly different tween the two lines were identified. The dynamic change trajectories of fiber length and microfibril angle are close to "s" and reverse "s" growth curves, respectively. SY6167 and TM-1 fibers entered the logarithmic elongation phase simultaneously at 10 DPA, and SY6167 kept elongating logarithmically for 2 more days than TM-1. In parallel to logarithmic elongation, microfibril orientation angles dived sharply, and SY6167 declined faster for a shorter duration than TM-1. 53% of the identified proteins are related to redox homeostasis, and most of them are expressed at higher levels in SY6167 during logarithmic elongation. 1-Aminocyclopropane-1-Carboxylic Acid Oxidase (ACO) started to accumulate at 16 DPA in SY6167, and its encoding genes were highly expressed at this stage, with a much higher level than TM-1. These findings suggest high-quality fibers are associated with high expression of the proteins related to stress and redox homeostasis, the continuously elevated expression of ethylene synthesis ACO gene may play an essential role.

Identification and Structure Analysis of KCS Family Genes Suggest Their Reponding to Regulate Fiber Development in Long-Staple Cotton Under Salt-Alkaline Stress

Plant 3-ketoacyl-CoA synthase (KCS) gene family catalyzed a β ketoacyl-CoA synthase, which was the rate-limiting enzyme for the synthesis of very long chain fatty acids (VLCFAs). Gossypium barbadense was well-known not only for high-quality fiber, which was perceived as a cultivated species of Gossypium. In this study, a total of 131 KCS genes were identified in four cotton species, there were 38, 44, 26, 23 KCS genes in the G. barbadense, the G. hirsutum, the G. arboreum and G. raimondii, respectively. The gene structure and expression pattern were analyzed. GBKCS genes were divided into six subgroups, the chromosome distribution of members of the family were mapped. The prediction of cis-acting elements of the GBKCS gene promoters suggested that the GBKCS genes may be involved in hormone signaling, defense and the stress response. Collinearity analysis on the KCS genes of the four cotton species were formulated. Tandem duplication played an indispensable role in the evolution of the KCS gene family. Specific expression analysis of 20 GBKCS genes indicated that GBKCS gene were widely expressed in the first 25 days of fiber development. Among them, GBKCS3, GBKCS8, GBKCS20, GBKCS34 were expressed at a high level in the initial long-term level of the G. barbadense fiber. This study established a foundation to further understanding of the evolution of KCS genes and analyze the function of GBKCS genes.

Genome-Wide Identification and Expression Profiling of KCS Gene Family in Passion Fruit (Passiflora edulis) Under Fusarium kyushuense and Drought Stress Conditions

Plant and fruit surfaces are covered with cuticle wax and provide a protective barrier against biotic and abiotic stresses. Cuticle wax consists of very-long-chain fatty acids (VLCFAs) and their derivatives. β-Ketoacyl-CoA synthase (KCS) is a key enzyme in the synthesis of VLCFAs and provides a precursor for the synthesis of cuticle wax, but the KCS gene family was yet to be reported in the passion fruit (Passiflora edulis). In this study, thirty-two KCS genes were identified in the passion fruit genome and phylogenetically grouped as KCS1-like, FAE1-like, FDH-like, and CER6-like. Furthermore, thirty-one PeKCS genes were positioned on seven chromosomes, while one PeKCS was localized to the unassembled genomic scaffold. The cis-element analysis provides insight into the possible role of PeKCS genes in phytohormones and stress responses. Syntenic analysis revealed that gene duplication played a crucial role in the expansion of the PeKCS gene family and underwent a strong purifying selection. All PeKCS proteins shared similar 3D structures, and a protein-protein interaction network was predicted with known Arabidopsis proteins. There were twenty putative ped-miRNAs which were also predicted that belong to nine families targeting thirteen PeKCS genes. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation results were highly associated with fatty acid synthase and elongase activity, lipid metabolism, stress responses, and plant-pathogen interaction. The highly enriched transcription factors (TFs) including ERF, MYB, Dof, C2H2, TCP, LBD, NAC, and bHLH were predicted in PeKCS genes. qRT-PCR expression analysis revealed that most PeKCS genes were highly upregulated in leaves including PeKCS2, PeKCS4, PeKCS8, PeKCS13, and PeKCS9 but not in stem and roots tissues under drought stress conditions compared with controls. Notably, most PeKCS genes were upregulated at 9th dpi under Fusarium kyushuense biotic stress condition compared to controls. This study provides a basis for further understanding the functions of KCS genes, improving wax and VLCFA biosynthesis, and improvement of passion fruit resistance.

The hexokinase Gene Family in Cotton: Genome-Wide Characterization and Bioinformatics Analysis

Hexokinase (HXK) is involved in hexose phosphorylation, sugar sensing, and signal transduction, all of which regulate plant growth and adaptation to stresses. Gossypium hirsutum L. is one of the most important fiber crops in the world, however, little is known about the HXKs gene family in G. hirsutum L. We identified 17 GhHXKs from the allotetraploid G. hirsutum L. genome (AADD). G. raimondii (DD) and G. arboreum (AA) are the diploid progenitors of G. hirsutum L. and contributed equally to the At_genome and Dt_genome GhHXKs genes. The chromosomal locations and exon-intron structures of GhHXK genes among cotton species are conservative. Phylogenetic analysis grouped the HXK proteins into four and three groups based on whether they were monocotyledons and dicotyledons, respectively. Duplication event analysis demonstrated that HXKs in G. hirsutum L. primarily originated from segmental duplication, which prior to diploid hybridization. Experiments of qRT-PCR, transcriptome and promoter cis-elements demonstrated that GhHXKs' promoters have auxin and GA responsive elements that are highly expressed in the fiber initiation and elongation stages, while the promoters contain ABA-, MeJA-, and SA-responsive elements that are highly expressed during the synthesis of the secondary cell wall. We performed a comprehensive analysis of the GhHXK gene family is a vital fiber crop, which lays the foundation for future studies assessing its role in fiber development.

Comparative transcriptome analysis of fiber and nonfiber tissues to identify the genes preferentially expressed in fiber development in Gossypium hirsutum

Cotton is an important natural fiber crop and economic crop worldwide. The quality of cotton fiber directly determines the quality of cotton textiles. Identifying cotton fiber development-related genes and exploring their biological functions will not only help to better understand the elongation and development mechanisms of cotton fibers but also provide a theoretical basis for the cultivation of new cotton varieties with excellent fiber quality. In this study, RNA sequencing technology was used to construct transcriptome databases for different nonfiber tissues (root, leaf, anther and stigma) and fiber developmental stages (7 days post-anthesis (DPA), 14 DPA, and 26 DPA) of upland cotton Coker 312. The sizes of the seven transcriptome databases constructed ranged from 4.43 to 5.20 Gb, corresponding to approximately twice the genome size of Gossypium hirsutum (2.5 Gb). Among the obtained clean reads, 83.32% to 88.22% could be compared to the upland cotton TM-1 reference genome. By analyzing the differential gene expression profiles of the transcriptome libraries of fiber and nonfiber tissues, we obtained 1205, 1135 and 937 genes with significantly upregulated expression at 7 DPA, 14 DPA and 26 DPA, respectively, and 124, 179 and 213 genes with significantly downregulated expression. Subsequently, Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analyses were performed, which revealed that these genes were mainly involved in catalytic activity, carbohydrate metabolism, the cell membrane and organelles, signal transduction and other functions and metabolic pathways. Through gene annotation analysis, many transcription factors and genes related to fiber development were screened. Thirty-six genes were randomly selected from the significantly upregulated genes in fiber, and expression profile analysis was performed using qRT-PCR. The results were highly consistent with the gene expression profile analyzed by RNA-seq, and all of the genes were specifically or predominantly expressed in fiber. Therefore, our RNA sequencing-based comparative transcriptome analysis will lay a foundation for future research to provide new genetic resources for the genetic engineering of improved cotton fiber quality and for cultivating new transgenic cotton germplasms for fiber quality improvement.

Comprehensive analysis of KCS gene family in Citrinae reveals the involvement of CsKCS2 and CsKCS11 in fruit cuticular wax synthesis at ripening

Cuticular wax covers the surface of fleshy fruit and plays a protective role in fruit development and postharvest storage, including reducing fruit water loss, resisting biotic and abiotic stress and affecting fruit glossiness. The β-ketoacyl-CoA synthase (KCS) is the rate-limiting enzyme of very long chain fatty acids (VLCFAs) synthesis, which provides precursors for the synthesis of cuticular wax. In this study, a total of 96 KCS genes were identified in six Citrinae species, including 13, 16, 21, 14, 16 and 16 KCS genes in the primitive species (Atalantia buxifolia), the wild species (Citrus ichangensis), and four cultivated species (Citrus medica, Citrus grandis, Citrus sinensis and Citrus clementina), respectively. Compared with primitive species, wild and cultivated species showed expansion of KCS gene family. Evolutionary analysis of KCS gene family indicated that uneven gain and loss of genes resulted in variable numbers of KCS genes in Citrinae, and KCS genes have undergone purifying selection. Expression profiles in C. sinensis revealed that the KCS genes had diverse expression patterns among various tissues. Furthermore, CsKCS2 and CsKCS11 were predominantly expressed in the flavedo and their expression increased sharply with ripening. Subcellular localization analysis indicated that CsKCS2 and CsKCS11 were located in the endoplasmic reticulum. Further, heterologous expression of CsKCS2 and CsKCS11 in Arabidopsis significantly increased the content of cuticular wax in leaves. Thus, CsKCS2 and CsKCS11 are involved in the accumulation of fruit cuticular wax at ripening. This work will facilitate further functional verification and understanding of the evolution of KCS genes in Citrinae.

The application of ammonium sulphate and amino acid on cotton: effects on can improve growth, yield, quality and nitrogen absorption

A field study was carried out to determine the influence of foliage applied plant growth promoter and retardant in improving soil applied sulphur fertilizer use efficiency in cotton during two consecutive summers 2014 and 2015. Experimental trial comprised of three different sources of sulphur (ammonium sulphate, potassium sulphate and elemental sulphur) and foliar spray of plant growth promoter and growth retardant including tap water was taken as control. Among treatments soil applied ammonium sulphate with foliage applied amino acid produced maximum plant height, sympodial branches, pods per plant, seed cotton yield, fiber yield, biological yield, protein contents, oil contents and leaf nitrogen uptake as compared to the other treatments. Whereas, soil applied potassium sulphate with foliar spray of mepiquat chloride on cotton significantly improved the boll weight and leaf potassium uptake. We conclude that soil applied ammonium sulphate and foliage spray of amino acid was more effective in improving the productivity and quality attributes of cotton.

Recent Advances and Future Perspectives in Cotton Research

Cotton is not only the world's most important natural fiber crop, but it is also an ideal system in which to study genome evolution, polyploidization, and cell elongation. With the assembly of five different cotton genomes, a cotton-specific whole-genome duplication with an allopolyploidization process that combined the A- and D-genomes became evident. All existing A-genomes seemed to originate from the A₀-genome as a common ancestor, and several transposable element bursts contributed to A-genome size expansion and speciation. The ethylene production pathway is shown to regulate fiber elongation. A tip-biased diffuse growth mode and several regulatory mechanisms, including plant hormones, transcription factors, and epigenetic modifications, are involved in fiber development. Finally, we describe the involvement of the gossypol biosynthetic pathway in the manipulation of herbivorous insects, the role of GoPGF in gland formation, and host-induced gene silencing for pest and disease control. These new genes, modules, and pathways will accelerate the genetic improvement of cotton.

Cotton pan-genome retrieves the lost sequences and genes during domestication and selection

BACKGROUND

Millennia of directional human selection has reshaped the genomic architecture of cultivated cotton relative to wild counterparts, but we have limited understanding of the selective retention and fractionation of genomic components.

RESULTS

We construct a comprehensive genomic variome based on 1961 cottons and identify 456 Mb and 357 Mb of sequence with domestication and improvement selection signals and 162 loci, 84 of which are novel, including 47 loci associated with 16 agronomic traits. Using pan-genome analyses, we identify 32,569 and 8851 non-reference genes lost from Gossypium hirsutum and Gossypium barbadense reference genomes respectively, of which 38.2% (39,278) and 14.2% (11,359) of genes exhibit presence/absence variation (PAV). We document the landscape of PAV selection accompanied by asymmetric gene gain and loss and identify 124 PAVs linked to favorable fiber quality and yield loci.

CONCLUSIONS

This variation repertoire points to genomic divergence during cotton domestication and improvement, which informs the characterization of favorable gene alleles for improved breeding practice using a pan-genome-based approach.

GhPIPLC2D promotes cotton fiber elongation by enhancing ethylene biosynthesis

Inositol-1,4,5-trisphosphate (IP₃) is an important second messenger and one of the products of phosphoinositide-specific phospholipase C (PIPLC)-mediated phosphatidylinositol (4,5) bisphosphate (PIP₂) hydrolysis. However, the function of IP₃ in cotton is unknown. Here, we characterized the function of GhPIPLC2D in cotton fiber elongation. GhPIPLC2D was preferentially expressed in elongating fibers. Suppression of GhPIPLC2D transcripts resulted in shorter fibers and decreased IP₃ accumulation and ethylene biosynthesis. Exogenous application of linolenic acid (C18:3) and phosphatidylinositol (PI), the precursor of IP₃, improved IP₃ and myo-inositol-1,2,3,4,5,6-hexakisphosphate (IP₆) accumulation, as well as ethylene biosynthesis. Moreover, fiber length in GhPIPLC2D-silenced plant was reduced after exogenous application of IP₆ and ethylene. These results indicate that GhPIPLC2D positively regulates fiber elongation and IP₃ promotes fiber elongation by enhancing ethylene biosynthesis. Our study broadens our understanding of the function of IP₃ in cotton fiber elongation and highlights the possibility of cultivating better cotton varieties by manipulating GhPIPLC2D in the future.

•

GhPIPLC2D positively regulates cotton fiber elongation

•

GhPIPLC2D cleaves PIP₂ into IP₃, which could be phosphorylated to IP₆

•

IP₆ enhances fiber elongation via improving ethylene biosynthesis

Gibberellin induced transcription factor bZIP53 regulates CesA1 expression in maize kernels

Proper development of the maize kernel is of great significance for high and stable maize yield to ensure national food security. Gibberellin (GA), one of the hormones regulating plant growth, is involved in modulating the development of maize kernels. Cellulose, one of the main components of plant cells, is also regulated by gibberellin. The mechanism of hormone regulation during maize grain development is highly complicated, and reports on GA-mediated modulation of cellulose synthesis during maize grain development are rare. Our study revealed that during grain growth and development, the grain length and bulk density of GA-treated corn kernels improved significantly, and the cellulose content of grains increased, while seed coat thickness decreased. The transcription factor basic region/leucine zipper motif 53 (bZIP53), which is strongly correlated with cellulose synthase gene 1 (CesA1) expression, was screened by transcriptome sequencing and the expression of the cellulose synthase gene in maize grain development after GA treatment was determined. It was found that bZIP53 expression significantly promoted the expression of CesA1. Further, analysis of the transcription factor bZIP53 determined that the gene-encoded protein was localized in the cell and nuclear membranes, but the transcription factor bZIP53 itself showed no transcriptional activation. Further studies are required to explore the interaction of bZIP53 with CesA1.

Genome-wide characterization of the WAK gene family and expression analysis under plant hormone treatment in cotton

BACKGROUND

Wall-associated kinases (WAK), one of the receptor-like kinases (RLK), function directly in the connection and communication between the plant cell wall and the cytoplasm. WAK genes are highly conserved and have been identified in plants, such as rice, but there is little research on the WAK gene family in cotton.

RESULTS

In the present study, we identified 29 GhWAK genes in Gossypium hirsutum. Phylogenetic analysis showed that cotton WAK proteins can be divided into five clades. The results of synteny and Ka/Ks analysis showed that the GhWAK genes mainly originated from whole genome duplication (WGD) and were then mainly under purifying selection. Transcriptome data and real-time PCR showed that 97% of GhWAK genes highly expressed in cotton fibers and ovules. β-glucuronidase (GUS) staining assays showed that GhWAK5 and GhWAK16 expressed in Arabidopsis leaf trichomes. Fourteen GhWAK genes were found to possess putative gibberellin (GA) response elements in the promoter regions, 13 of which were significantly induced by GA treatment. Ten GhWAK genes contained auxin (IAA) response elements and the expression level of nine GhWAKs significantly increased under auxin treatment.

CONCLUSIONS

We provide a preliminary analysis of the WAK gene family in G. hirsutum, which sheds light on the potantial roles of GhWAK genes in cotton fiber cell development. Our data also provides a useful resource for future studies on the functional roles of GhWAK genes.

The β-ketoacyl-CoA synthase KCS13 regulates the cold response in cotton by modulating lipid and oxylipin biosynthesis

Cold stress is a key environmental factor that affects plant development and productivity. In this study, RNA-seq in cotton following cold-stress treatment resulted in the identification of 5239 differentially expressed genes (DEGs) between two cultivars with differing sensitivity to low temperatures, among which GhKCS13 was found to be involved in the response. Transgenic plants overexpressing GhKCS13 showed increased sensitivity to cold stress. KEGG analysis of 418 DEGs in both GhKCS13-overexpressing and RNAi lines after treatment at 4 °C indicated that lipid biosynthesis and linoleic acid metabolism were related to cold stress. ESI-MS/MS analysis showed that overexpression of GhKCS13 led to modifications in the composition of sphingolipids and glycerolipids in the leaves, which might alter the fluidity of the cell membrane under cold conditions. In particular, differences in levels of jasmonic acid (JA) in GhKCS13 transgenic lines suggested that, together with lysophospholipids, it might mediate the cold-stress response. Our results suggest that overexpression of GhKCS13 probably causes remodeling of lipids in the endoplasmic reticulum and biosynthesis of lipid-derived JA in chloroplasts, which might account for the increased sensitivity to cold stress in the transgenic plants. Complex interactions between lipid components, lipid signaling molecules, and JA appear to determine the response to cold stress in cotton.

Genome wide analysis and functional identification of MdKCS genes in apple

Apple fruit is covered by cuticle wax, which plays important roles protecting fruits from adverse environmental conditions. β-Ketoacyl-CoA synthase (KCS) is the key rate-limiting enzyme in plant wax synthesis. In this study, we identified 28 KCS gene family members from apple (Malus × domestica Borkh.) by homology analysis. Multi-sequence alignment and phylogenetic analyses revealed that the 28 MdKCS genes were divided into four subgroups, including KCS1-like, FAE1-like, FDH-like, and CER6. A chromosomal localization analysis revealed that 27 apple KCS genes were located on 11 chromosomes, while MdKCS28 was localized to the unassembled genomic scaffold. Most of the MdKCS proteins were hydrophilic proteins and they had similar secondary and tertiary structures. The prediction of cis-acting elements of the MdKCS gene promoters suggested that the MdKCS genes may be widely involved in hormone signaling and the stress response. Furthermore, the quantitative real-time polymerase chain reaction results showed that eight MdKCS genes were highly expressed in the apple pericarp, and were significantly induced by drought, abscisic acid (ABA), and NaCl treatments. We transformed the MdKCS21 gene into apple calli, and found the MdKCS21 overexpressing transgenic apple calli exhibited higher tolerance to ABA treatment. Finally, the MdKCS proteins were localized to the endoplasmic reticulum and vacuolar membrane by confocal laser microscopy. This study established a foundation to further analyze the function of KCS genes and provided candidate genes for molecular improvement of wax content in apple.

Genome sequence of Gossypium herbaceum and genome updates of Gossypium arboreum and Gossypium hirsutum provide insights into cotton A-genome evolution

Upon assembling the first Gossypium herbaceum (A1) genome and substantially improving the existing Gossypium arboreum (A2) and Gossypium hirsutum ((AD)1) genomes, we showed that all existing A-genomes may have originated from a common ancestor, referred to here as A0, which was more phylogenetically related to A1 than A2. Further, allotetraploid formation was shown to have preceded the speciation of A1 and A2. Both A-genomes evolved independently, with no ancestor-progeny relationship. Gaussian probability density function analysis indicates that several long-terminal-repeat bursts that occurred from 5.7 million years ago to less than 0.61 million years ago contributed compellingly to A-genome size expansion, speciation and evolution. Abundant species-specific structural variations in genic regions changed the expression of many important genes, which may have led to fiber cell improvement in (AD)1. Our findings resolve existing controversial concepts surrounding A-genome origins and provide valuable genomic resources for cotton genetic improvement.

Genome-wide mining and comparative analysis of fatty acid elongase gene family in Brassica napus and its progenitors

Very long chain fatty acids (VLCFAs) that are structural components of cell membrane lipid, cuticular waxes and seed oil, play crucial roles in plant growth, development and stress response. Fatty acid elongases (FAEs) comprising KCS and ELO, are key enzymes for VLCFA biosynthesis in plants. Although reference genomes of Brassica napus and its parental speices both have been sequenced, whole-genome analysis of FAE gene family in these Brassica speices is not reported. Here, 58, 33 and 30 KCS genes were identified in B. napus, B. rapa and B. oleracea genomes, respectively, whereas 14, 6 and 8 members were obtained for ELO genes. These KCS genes were unevenly located in 37 chromosomes and 3 scaffolds of 3 Brassica species, while these ELO genes were mapped to 19 chromosomes. The KCS and ELO proteins were divided into 8 and 4 subclasses, respectively. Gene structure and protein motifs remained highly conserved in each KCS or ELO subclass. Most promoters of KCS and ELO genes harbored various plant growth-, phytohormone-, and stress response-related cis-acting elements. 20 SSR loci existed in the KCS and ELO genes/promoters. The whole-genome duplication and segmental duplication mainly contributed to expansion of KCS and ELO genes in these genomes. Transcriptome analysis showed that KCS and ELO genes in 3 Brassica species were expressed in various tissues/organs with different levels, whereas 1 BnELO gene and 6 BnKCS genes might be pathogen-responsive genes. The qRT-PCR assay showed that BnKCS22 and BnELO04 responded to various phytohormone treatments and abiotic stresses. This work lays the foundation for further function identification of KCS and ELO genes in B. napus and its progenitors.

Long-Chain acyl-CoA Synthetase LACS2 Contributes to Submergence Tolerance by Modulating Cuticle Permeability in Arabidopsis

In Arabidopsis thaliana, LONG-CHAIN ACYL-COA SYNTHETASEs (LACSs) catalyze the synthesis of long-chain acyl-CoAs and function in diverse biological processes. We have recently revealed that LACS2 is primarily involved in the production of polyunsaturated linolenoyl-CoA, essential for the activation of ethylene response transcription factors-mediated hypoxia signaling. Here, we further reported the dual role of LACS2 in the regulation of submergence tolerance by modulating cuticle permeability in Arabidopsis cells. LACS2-overexpressors (LACS2-OEs) showed improved tolerance to submergence, with higher accumulation of cuticular wax and cutin in their rosettes. In contrast, knockout of LACS2 in the lacs2-3 mutant resulted in hypersensitivity to submergence with reduced wax crystals and thinner cutin layer. By analyses of plant surface permeability, we observed that the hypoxic sensitivities in the LACS2-OEs and lacs2-3 mutant were physiologically correlated with chlorophyll leaching, water loss rates, ionic leakage, and gas exchange. Thus, our findings suggest the role of LACS2 in plant response to submergence by modulating cuticle permeability in plant cells.

Comprehensive analysis of the Gossypium hirsutum L. respiratory burst oxidase homolog (Ghrboh) gene family

BACKGROUND

Plant NADPH oxidase (NOX), also known as respiratory burst oxidase homolog (rboh), encoded by the rboh gene, is a key enzyme in the reactive oxygen species (ROS) metabolic network. It catalyzes the formation of the superoxide anion (O2•-), a type of ROS. In recent years, various studies had shown that members of the plant rboh gene family were involved in plant growth and developmental processes as well as in biotic and abiotic stress responses, but little is known about its functional role in upland cotton.

RESULTS

In the present study, 26 putative Ghrboh genes were identified and characterized. They were phylogenetically classified into six subfamilies and distributed at different densities across 18 of the 26 chromosomes or scaffolds. Their exon-intron structures, conserved domains, synteny and collinearity, gene family evolution, regulation mediated by cis-acting elements and microRNAs (miRNAs) were predicted and analyzed. Additionally, expression profiles of Ghrboh gene family were analyzed in different tissues/organs and at different developmental stages and under different abiotic stresses, using RNA-Seq data and real-time PCR. These profiling studies indicated that the Ghrboh genes exhibited temporal and spatial specificity with respect to expression, and might play important roles in cotton development and in stress tolerance through modulating NOX-dependent ROS induction and other signaling pathways.

CONCLUSIONS

This comprehensive analysis of the characteristics of the Ghrboh gene family determined features such as sequence, synteny and collinearity, phylogenetic and evolutionary relationship, expression patterns, and cis-element- and miRNA-mediated regulation of gene expression. Our results will provide valuable information to help with further gene cloning, evolutionary analysis, and biological function analysis of cotton rbohs.

Genome-Wide Identification of Peanut KCS Genes Reveals That AhKCS1 and AhKCS28 Are Involved in Regulating VLCFA Contents in Seeds

The peanut (Arachis hypogaea L.) is an important oilseed crop worldwide. Compared to other common edible vegetable oils, peanut oil contains a higher content of saturated fatty acids (SFAs), approximately 20-40% of which are very long chain fatty acids (VLCFAs). To understand the basis for this oil profile, we interrogated genes for peanut β-ketoacyl-CoA synthase (KCS), which is known to be a key enzyme in VLCFA biosynthesis. A total of 30 AhKCS genes were identified in the assembled genome of the peanut. Based on transcriptome data, nine AhKCS genes with high expression levels in developing seeds were cloned and expressed in yeast. All these AhKCSs could produce VLCFAs but result in different profiles, indicating that the AhKCSs catalyzed fatty acid elongation with different substrate specificities. Expression level analysis of these nine AhKCS genes was performed in developing seeds from six peanut germplasm lines with different VLCFA contents. Among these genes, the expression levels of AhKCS1 or AhKCS28 were, 4-10-fold higher than that of any other AhKCS. However, only the expression levels of AhKCS1 and AhKCS28 were significantly and positively correlated with the VLCFA content, suggesting that AhKCS1 and AhKCS28 were involved in the regulation of VLCFA content in the peanut seed. Further subcellular localization analysis indicated that AhKCS1 and AhKCS28 were located at the endoplasmic reticulum (ER). Overexpression of AhKCS1 or AhKCS28 in Arabidopsis increased the contents of VLCFAs in the seed, especially for very long chain saturated fatty acids (VLCSFAs). Taken together, this study suggests that AhKCS1 and AhKCS28 could be key genes in regulating VLCFA biosynthesis in the seed, which could be applied to improve the health-promoting and nutritional qualities of the peanut.

Comprehensive analyses of ZFP gene family and characterization of expression profiles during plant hormone response in cotton

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.

Genome-Wide Association Study Identifies Candidate Genes Related to Seed Oil Composition and Protein Content in Gossypium hirsutum L

Cotton (Gossypium spp.) is a leading natural fiber crop and an important source of vegetable protein and oil for humans and livestock. To investigate the genetic architecture of seed nutrients in upland cotton, a genome-wide association study (GWAS) was conducted in a panel of 196 germplasm resources under three environments using a CottonSNP80K chip of 77,774 loci. Relatively high genetic diversity (average gene diversity being 0.331) and phenotypic variation (coefficient of variation, CV, exceeding 3.9%) were detected in this panel. Correlation analysis revealed that the well-documented negative association between seed protein (PR) and oil may be to some extent attributable to the negative correlation between oleic acid (OA) and PR. Linkage disequilibrium (LD) was unevenly distributed among chromosomes and subgenomes. It ranged from 0.10-0.20 Mb (Chr19) to 5.65-5.75 Mb (Chr25) among the chromosomes and the range of Dt-subgenomes LD decay distances was smaller than At-subgenomes. This panel was divided into two subpopulations based on the information of 41,815 polymorphic single-nucleotide polymorphism (SNP) markers. The mixed linear model considering both Q-matrix and K-matrix [MLM(Q+K)] was employed to estimate the association between the SNP markers and the seed nutrients, considering the false positives caused by population structure and the kinship. A total of 47 SNP markers and 28 candidate quantitative trait loci (QTLs) regions were found to be significantly associated with seven cottonseed nutrients, including protein, total fatty acid, and five main fatty acid compositions. In addition, the candidate genes in these regions were analyzed, which included three genes, Gh_D12G1161, Gh_D12G1162, and Gh_D12G1165 that were most likely involved in the control of cottonseed protein concentration. These results improved our understanding of the genetic control of cottonseed nutrients and provided potential molecular tools to develop cultivars with high protein and improved fatty acid compositions in cotton breeding programs through marker-assisted selection.

Genome-wide identification of the GhARF gene family reveals that GhARF2 and GhARF18 are involved in cotton fibre cell initiation

Auxin signalling plays an essential role in regulating plant development. Auxin response factors (ARFs), which are critical components of auxin signalling, modulate the expression of early auxin-responsive genes by binding to auxin response factor elements (AuxREs). However, there has been no comprehensive characterization of this gene family in cotton. Here, we identified 56 GhARF genes in the assembled Gossypium hirsutum genome. This gene family was divided into 17 subfamilies, and 44 members of them were distributed across 21 chromosomes. GhARF6 and GhARF11 subfamily genes were predominantly expressed in vegetative tissues, whereas GhARF2 and GhARF18 subfamily genes were highly expressed during seed fibre cell initiation. GhARF2-1 and GhARF18-1 were exclusively expressed in trichomes, organs similar to cotton seed fibre cells, and overexpression of these genes in Arabidopsis enhances trichome initiation. Comparative transcriptome analysis combined with AuxRE prediction revealed 11 transcription factors as potential target genes of GhARF2 and GhARF18. Six of these genes were significantly expressed during seed fibre cell initiation and were bound by GhARF2-1 and GhARF18-1 in yeast one-hybrid assays. Our results suggest that GhARF2 and GhARF18 genes may be key regulators of cotton seed fibre initiation by regulating the expression of several transcription factor genes. This study deepens our understanding of auxin-mediated initiation of cotton seed fibre cells and helps us in breeding better cotton varieties in the future.

Effect of ancymidol on cell wall metabolism in growing maize cells

Ancymidol inhibits the incorporation of cellulose into cell walls of maize cell cultures in a gibberellin-independent manner, impairing cell growth; the reduction in the cellulose content is compensated with xylans. Ancymidol is a plant growth retardant which impairs gibberellin biosynthesis. It has been reported to inhibit cellulose synthesis by tobacco cells, based on its cell-malforming effects. To ascertain the putative role of ancymidol as a cellulose biosynthesis inhibitor, we conducted a biochemical study of its effect on cell growth and cell wall metabolism in maize cultured cells. Ancymidol concentrations ≤ 500 µM progressively reduced cell growth and induced globular cell shape without affecting cell viability. However, cell growth and viability were strongly reduced by ancymidol concentrations ≥ 1.5 mM. The I₅₀ value for the effect of ancymidol on FW gain was 658 µM. A reversal of the inhibitory effects on cell growth was observed when 500 µM ancymidol-treated cultures were supplemented with 100 µM GA₃. Ancymidol impaired the accumulation of cellulose in cell walls, as monitored by FTIR spectroscopy. Cells treated with 500 µM ancymidol showed a ~ 60% reduction in cellulose content, with no further change as the ancymidol concentration increased. Cellulose content was partially restored by 100 µM GA₃. Radiolabeling experiments confirmed that ancymidol reduced the incorporation of [¹⁴C]glucose into α-cellulose and this reduction was not reverted by the simultaneous application of GA₃. RT-PCR analysis indicated that the cellulose biosynthesis inhibition caused by ancymidol is not related to a downregulation of ZmCesA gene expression. Additionally, ancymidol treatment increased the incorporation of [³H]arabinose into a hemicellulose-enriched fraction, and up-regulated ZmIRX9 and ZmIRX10L gene expression, indicating an enhancement in the biosynthesis of arabinoxylans as a compensatory response to cellulose reduction.

Genome-wide investigation and expression profiling of APX gene family in Gossypium hirsutum provide new insights in redox homeostasis maintenance during different fiber development stages

Ascorbate peroxidase (APX) is a member of heme-containing peroxidases which catalyze the H₂O₂-dependent oxidation of a wide range of substrates in plants and animals. As is known, H₂O₂ acts as a signaling molecule in the regulation of fiber development. Our previous work reported that ascorbate peroxidase 1 (GhAPX1) was important for cotton fiber elongation. However, knowledge about APX gene family members and their evolutionary and functional characteristics in cotton is limited. Here, we report 26 GhAPX genes by genome-wide investigation of tetraploid cotton Gossypium hirsutum. Phylogenetic and gene structure analyses classified these APX members into five clades and syntenic analysis suggested two duplication events. Expression profiling of the 26 APXs revealed that ten members are expressed in cotton fibers. Notably, GhAPX10A, GhAPX10D, GhAPX12A, and GhAPX12D showed high expression levels in 30-day fiber, while GhAPX1A/D, GhAPX3A/D, and GhAPX6A/D showed very low expression levels. The enzyme activity and H₂O₂ content assays revealed that cotton fiber kept high enzyme activity and the lowest H₂O₂ level in 30-day fibers, indicating that other than GhAPX1, the newly reported APX members are responsible for the reactive oxygen species homeostasis in the cotton fiber maturation stages. Expression profiling of ten fiber-expressed APXs after phytohormone treatments revealed their regulation patterns by different stimuli, suggesting that GhAPX1, GhAPX12A, and GhAPX12D are responsible to most phytohormone treatments. Our data provided evolutionary and functional information of GhAPX gene family members and revealed that different members are responsible to redox homeostasis during different cotton fiber development stages.