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Structural variations (SVs) are critical factors affecting genome evolution and important traits. However, identification results and functional analyses of SVs in upland cotton are rare. Here, based on the genetic relationships, breeding history and cumulative planting area of upland cotton in China, nine predominant cultivars from the past 60 years (1950s-2010s) were selected for long read sequencing to uncover genic variations and breeding improvement targets for this crop. Based on the ZM24 reference genome, 0.88-1.47 × 10

Zanthoxylum armatum and Zanthoxylum bungeanum, known as 'Chinese pepper', are distinguished by their extraordinary complex genomes, phenotypic innovation of adaptive evolution and species-special metabolites. Here, we report reference-grade genomes of Z. armatum and Z. bungeanum. Using high coverage sequence data and comprehensive assembly strategies, we derived 66 pseudochromosomes comprising 33 homologous phased groups of two subgenomes, including autotetraploid Z. armatum. The genomic rearrangements and two whole-genome duplications created large (~4.5 Gb) complex genomes with a high ratio of repetitive sequences (82%) and high chromosome number (2n = 4x = 132). Further analysis of the high-quality genomes shed lights on the genomic basis of involutional reproduction, allomones biosynthesis and adaptive evolution in Chinese pepper, revealing a high consistent relationship between genomic evolution, environmental factors and phenotypic innovation. Our study provides genomic resources and new insights for investigating diversification and phenotypic innovation in Chinese pepper, with broader implications for the protection of plants under severe environmental changes.

Cotton fiber is a unicellular seed trichome, and lint fiber initials per seed as a factor determines fiber yield. However, the mechanisms controlling fiber initiation from ovule epidermis are not understood well enough. Here, with single-cell RNA sequencing (scRNA-seq), a total of 14,535 cells were identified from cotton ovule outer integument of Xu142_LF line at four developmental stages (1.5, 1, 0.5 days before anthesis and the day of anthesis). Three major cell types, fiber, non-fiber epidermis and outer pigment layer were identified and then verified by RNA in situ hybridization. A comparative analysis on scRNA-seq data between Xu142 and its fiberless mutant Xu142 fl further confirmed fiber cluster definition. The developmental trajectory of fiber cell was reconstructed, and fiber cell was identified differentiated at 1 day before anthesis. Gene regulatory networks at four stages revealed the spatiotemporal pattern of core transcription factors, and MYB25-like and HOX3 were demonstrated played key roles as commanders in fiber differentiation and tip-biased diffuse growth, respectively. A model for early development of a single fiber cell was proposed here, which sheds light on further deciphering mechanism of plant trichome and the improvement of cotton fiber yield.

N6-methyladenosine (m6A) is the most prevalent internal modification present in mRNAs, and is considered to participate in a range of developmental and biological processes. Drought response is highly regulated at the genomic, transcriptional and post-transcriptional levels. However, the biological function and regulatory mechanism of m6A modification in the drought stress response is still poorly understood. We generated a transcriptome-wide m6A map using drought-resistant and drought-sensitive varieties of cotton under different water deficient conditions to uncover patterns of m6A methylation in cotton response to drought stress. The results reveal that m6A represents a common modification and exhibit dramatic changes in distribution during drought stress. More 5'UTR m6A was deposited in the drought-resistant variety and was associated with a positive effect on drought resistance by regulating mRNA abundance. Interestingly, we observed that increased m6A abundance was associated with increased mRNA abundance under drought, contributing to drought resistance, and vice versa. The demethylase GhALKBH10B was found to decrease m6A levels, facilitating the mRNA decay of ABA signal-related genes (GhZEP, GhNCED4 and GhPP2CA) and Ca2+ signal-related genes (GhECA1, GhCNGC4, GhANN1 and GhCML13), and mutation of GhALKBH10B enhanced drought resistance at seedling stage in cotton. Virus-induced gene silencing (VIGS) of two Ca2+-related genes, GhECA1 and GhCNGC4, reduced drought resistance with the decreased m6A enrichment on silenced genes in cotton. Collectively, we reveal a novel mechanism of post-transcriptional modification involved in affecting drought response in cotton, by mediating m6A methylation on targeted transcripts in the ABA and Ca2+ signalling transduction pathways.

Despite the established significance of WRKY proteins and phenylpropanoid metabolism in plant immunity, how WRKY proteins modulate aspects of the phenylpropanoid pathway remains undetermined. To understand better the role of WRKY proteins in plant defence, we identified a cotton (Gossypium hirsutum) protein, GhWRKY41, that is, universally and rapidly induced in three disease-resistant cotton cultivars following inoculation with the plant pathogenic fungus, Verticillium dahliae. We show that overexpression of GhWRKY41 in transgenic cotton and Arabidopsis enhances resistance to V. dahliae, while knock-down increases cotton more susceptibility to the fungus. GhWRKY41 physically interacts with itself and directly activates its own transcription. A genome-wide chromatin immunoprecipitation and high-throughput sequencing (ChIP-seq), in combination with RNA sequencing (RNA-seq) analyses, revealed that 43.1% of GhWRKY41-binding genes were up-regulated in cotton upon inoculation with V. dahliae, including several phenylpropanoid metabolism master switches, receptor kinases, and disease resistance-related proteins. We also show that GhWRKY41 homodimer directly activates the expression of GhC4H and Gh4CL, thereby modulating the accumulation of lignin and flavonoids. This finding expands our understanding of WRKY-WRKY protein interactions and provides important insights into the regulation of the phenylpropanoid pathway in plant immune responses by a WRKY protein.

The pollen wall exine provides a protective layer for the male gametophyte and is largely composed of sporopollenin, which comprises fatty acid derivatives and phenolics. However, the biochemical nature of the external exine is poorly understood. Here, we show that the male sterile line 1355A of cotton mutated in NO SPINE POLLEN (GhNSP) leads to defective exine formation. The GhNSP locus was identified through map-based cloning and confirmed by genetic analysis (co-segregation test and allele prediction using the CRISPR/Cas9 system). In situ hybridization showed that GhNSP is highly expressed in tapetum. GhNSP encodes a polygalacturonase protein homologous to AtQRT3, which suggests a function for polygalacturonase in pollen exine formation. These results indicate that GhNSP is functionally different from AtQRT3, the latter has the function of microspore separation. Biochemical analysis showed that the percentage of de-esterified pectin was significantly increased in the 1355A anthers at developmental stage 8. Furthermore, immunofluorescence studies using antibodies to the de-esterified and esterified homogalacturonan (JIM5 and JIM7) showed that the Ghnsp mutant exhibits abundant of de-esterified homogalacturonan in the tapetum and exine, coupled with defective exine formation. The characterization of GhNSP provides new understanding of the role of polygalacturonase and de-esterified homogalacturonan in pollen exine formation.

Plants respond to environmental stresses through controlled stem cell maintenance and meristem activity. One level of gene regulation is RNA alternative splicing. However, the mechanistic link between stress, meristem function and RNA splicing is poorly understood. The MERISTEM-DEFECTIVE (MDF) Arabidopsis gene encodes an SR-related family protein, required for meristem function and leaf vascularization, and is the likely orthologue of the human SART1 and yeast Snu66 splicing factors. MDF is required for the correct splicing and expression of key transcripts associated with root meristem function. We identified RSZ33 and ACC1, both known to regulate cell patterning, as splicing targets required for MDF function in the meristem. MDF expression is modulated by osmotic and cold stress, associated with differential splicing and specific isoform accumulation and shuttling between nucleus and cytosol, and acts in part via a splicing target SR34. We propose a model in which MDF controls splicing in the root meristem to promote stemness and to repress stress response, cell differentiation and cell death pathways.

Plants respond to environmental stresses through controlled stem cell maintenance and meristem activity. One level of transcriptional control is RNA alternative splicing. However the mechanistic link between stress, meristem function and RNA splicing is poorly understood. TheMERISTEM-DEFECTIVE(MDF)/DEFECTIVELY ORGANIZED TRIBUTARIES(DOT2) gene of Arabidopsis encodes a SR-related family protein, required for meristem function and leaf vascularization, and is the likely orthologue of the human SART1 and yeast snu66 splicing factors. MDF is required for the correct splicing and expression of key transcripts associated with root meristem function. We identifiedRSZ33andACC1, both known to regulate cell patterning, as splicing targets required for MDF function in the meristem.MDFexpression is modulated by osmotic and cold stress, associated with differential splicing and specific isoform accumulation and shuttling between nucleus and cytosol, and acts in part via a splicing targetSR34. We propose a model in which MDF controls splicing in the root meristem to promote stemness and repress stress response and cell differentiation pathways.Summary statementThe protein MERISTEM-DEFECTIVE regulates Arabidopsis meristem function through its role as a splicing factor, mediated through splicing targets RSZ33, ACC1 and SR34.

Wounded plant cells can form callus to seal the wound site. Alternatively, wounding can cause adventitious organogenesis or somatic embryogenesis. These distinct developmental pathways require specific cell fate decisions. Here, we identify GhTCE1, a basic helix–loop–helix family transcription factor, and its interacting partners as a central regulatory module of early cell fate transition during in vitro dedifferentiation of cotton (Gossypium hirsutum). RNAi- or CRISPR/Cas9-mediated loss of GhTCE1 function resulted in excessive accumulation of reactive oxygen species (ROS), arrested callus cell elongation, and increased adventitious organogenesis. In contrast, GhTCE1-overexpressing tissues underwent callus cell growth, but organogenesis was repressed. Transcriptome analysis revealed that several pathways depend on proper regulation of GhTCE1 expression, including lipid transfer pathway components, ROS homeostasis, and cell expansion. GhTCE1 bound to the promoters of the target genes GhLTP2 and GhLTP3, activating their expression synergistically, and the heterodimer TCE1-TCEE1 enhances this activity. GhLTP2- and GhLTP3-deficient tissues accumulated ROS and had arrested callus cell elongation, which was restored by ROS scavengers. These results reveal a unique regulatory network involving ROS and lipid transfer proteins, which act as potential ROS scavengers. This network acts as a switch between unorganized callus growth and organized development during in vitro dedifferentiation of cotton cells.

Verticillium dahliae is a soil-borne hemi-biotrophic fungal pathogen and inflicts major losses in agricultural production worldwide. Although the pathogenicity of the fungus and plant immunity have been extensively studied, how cotton leaf necrosis is induced by defoliating strains of V. dahliae is poorly understood. In this study, reference-grade genomes were determined for two representative V. dahliae isolates: V991, which is defoliating and aggressive, and 1cd3-2, which is non-defoliating and has weak pathogenicity. Transcriptome analysis showed that cotton resistance to V. dahliae mainly depends on cell wall structure or physical barrier generation in the early stage of infection (3-9 days post inoculation, dpi). However, a large number of pathogenic factors could be detected from 12 dpi and accumulated quickly in cotton stems, accompanied by the burst of reactive oxygen species (ROS), leaf necrosis and defoliation. A V991 specific virulence gene SP3 was identified through comparative genome analysis and found to be highly expressed after colonization. Knock-out of SP3 clearly attenuated pathogenicity, with less ROS produced. These results indicate that disease symptoms in cotton may be due to abnormal immune activation and excessive ROS induced by the pathogen. To further investigate this, Polyethyleneimine coated MXene quantum dots (PEI-MQDs), a type of nano material that possesses the ability to remove ROS in vitro, were used. Cotton seedlings maintain ROS homeostasis with enhanced peroxidase (POD), catalase (CAT) and glutathione peroxidase (GSH-Px) activities after exogenous treatment with PEI-MQDs and show significant tolerance to V. dahliae isolate V991. Our results suggest that excessive ROS and constitutive immune activation in cotton induced by the defoliating strain of V. dahliae is responsible for disease symptoms such as leaf necrosis, and PEI-MQDs application improve cotton tolerance to V. dahliae by maintaining ROS homeostasis.

Summary Eukaryotic genomes are highly folded for packing into higher‐order chromatin structures in the nucleus. With the emergence of state‐of‐the‐art chromosome conformation capture methods and microscopic imaging techniques, the spatial organization of chromatin and its functional implications have been interrogated. Our knowledge of 3D chromatin organization in plants has improved dramatically in the past few years, building on the early advances in animal systems. Here, we review recent advances in 3D genome mapping approaches, our understanding of the sophisticated organization of spatial structures, and the application of 3D genomic principles in plants. We also discuss directions for future developments in 3D genomics in plants.

Summary The growth and development of root systems is influenced by mechanical properties of the substrate in which the plants grow. Mechanical impedance, such as by compacted soil, can reduce root elongation and limit crop productivity.To understand better the mechanisms involved in plant root responses to mechanical impedance stress, we investigated changes in the root transcriptome and hormone signalling responses of Arabidopsis to artificial root barrier systems in vitro.We demonstrate that upon encountering a barrier, reduced Arabidopsis root growth and a characteristic ‘step‐like’ growth pattern is due to a reduction in cell elongation associated with changes in signalling gene expression. Data from RNA‐sequencing combined with reporter line and mutant studies identified essential roles for reactive oxygen species, ethylene and auxin signalling during the barrier response.We propose a model in which early responses to mechanical impedance include reactive oxygen signalling integrated with ethylene and auxin responses to mediate root growth changes. Inhibition of ethylene responses allows improved growth in response to root impedance, an observation that may inform future crop breeding programmes., See also the Commentary on this article by Del Bianco & Kepinski 231: 8–10.

Urban agriculture plays a vital role in ensuring the self-sufficiency of a great variety of fresh vegetables and nutrients. It promotes a sustainable food system as well as reducing the dependency on imports for the growing population. Urban farming has made it possible for agriculture practices to be implemented anywhere at any time in a sophisticated way. Hydrogel has been introduced in urban agriculture in the past few decades. However, the application of hydrogel in urban agriculture is still being explored in terms of hydrogel types, structure, physical and chemical properties, change due to external factors, and its suitability for different plant species. This review discusses the potentials and limitations of hydrogel in different application conditions. We present the state of knowledge on hydrogel production and crosslinking methods, hydrogel characteristics, water absorption and release mechanisms of hydrogel, hydrogel advantages and limitations, and current and future applications in urban farming.

The potassium ion (K+) is vital for plant growth and development, and K+-deprivation leads to reduced crop yields. Here we describe phenotypic, transcriptomic, and mutant analyses to investigate the signaling mechanisms mediating root architectural changes in Arabidopsis (Arabidopsis thaliana) Columbia. We showed effects on root architecture are mediated through a reduction in cell division in the lateral root (LR) meristems, the rate of LR initiation is reduced but LR density is unaffected, and primary root growth is reduced only slightly. This was primarily regulated through gibberellic acid (GA) signaling, which leads to the accumulation of growth-inhibitory DELLA proteins. The short LR phenotype was rescued by exogenous application of GA but not of auxin or by the inhibition of ethylene signaling. RNA-seq analysis showed upregulation by K+-deprivation of the transcription factors JUNGBRUNNEN1 (JUB1) and the C-repeat-binding factor (CBF)/dehydration-responsive element-binding factor 1 regulon, which are known to regulate GA signaling and levels that regulate DELLAs. Transgenic overexpression of JUB1 and CBF1 enhanced responses to K+ stress. Attenuation of the reduced LR growth response occurred in mutants of the CBF1 target gene SFR6, implicating a role for JUB1, CBF1, and SFR6 in the regulation of LR growth in response to K+-deprivation via DELLAs. We propose this represents a mechanism to limit horizontal root growth in conditions where K+ is available deeper in the soil.

Bloom et al. (2019) proposed that rising atmospheric CO2 concentrations “inhibit malate production in chloroplasts and thus impede assimilation of nitrate into protein of C3 plants, a phenomenon that will strongly influence primary productivity and food security under the environmental conditions anticipated during the next few decades”. Previously we argued that the weight of evidence in the literature indicated that elevated atmospheric [CO2] does not inhibit NO3‐ assimilation in C3 plants (Andrews et al. 2019). New data for common bean (Phaseolus vulgaris) and wheat (Triticum aestivum) were presented that supported this view and indicated that the effects of elevated atmospheric [CO2] on nitrogen (N) assimilation and growth of C3 vascular plants were similar regardless of the form of N assimilated. Bloom et al. (2019) strongly criticised the arguments presented in Andrews et al. (2019). Here we respond to these criticisms and again conclude that the available data indicate that elevated atmospheric [CO2] does not inhibit NO3‐ assimilation of C3 plants. Measurement of the partitioning of NO3‐ assimilation between root and shoot of C3 species under different NO3‐ supply, at ambient and elevated CO2 would determine if their NO3‐ assimilation is inhibited in shoots but enhanced in roots at elevated atmospheric CO2.

Cotton (Gossypium hirsutum) is an allotetraploid species and a typical thermophilic crop that can survive and grow well under temperatures up to 45°C. CRISPR/LbCpf1 (LbCas12a) is a temperature‐sensitive system for plant genome editing (Malzahn et al., 2019) and has been successfully applied in species such as rice, soybean, tobacco, maize and cotton (Lee et al., 2019; Li et al., 2018; Tang et al., 2017; Xu et al., 2019). However, the temperature sensitivity of LbCpf1 has not been tested in cotton yet, a high temperature‐resistant crop. In order to improve LbCpf1 efficiency and determine the optimum temperature for cotton genome editing, we investigated the effects of different temperatures on LbCpf1 activity and genome editing efficiency. Moreover, we created nontransgenic and glandless cotton plants with seeds free of gossypol, representing a valuable germplasm resource for cotton breeding.

Summary The base‐editing technique using CRISPR/nCas9 (Cas9 nickase) or dCas9 (deactivated Cas9) fused with cytidine deaminase is a powerful tool to create point mutations. In this study, a novel G. hirsutum‐Base Editor 3 (GhBE3) base‐editing system has been developed to create single‐base mutations in the allotetraploid genome of cotton (Gossypium hirsutum). A cytidine deaminase sequence (APOBEC) fused with nCas9 and uracil glycosylase inhibitor (UGI) was inserted into our CRISPR/Cas9 plasmid (pRGEB32‐GhU6.7). Three target sites were chosen for two target genes, GhCLA and GhPEBP, to test the efficiency and accuracy of GhBE3. The editing efficiency ranged from 26.67 to 57.78% at the three target sites. Targeted deep sequencing revealed that the C→T substitution efficiency within an ‘editing window’, approximately six‐nucleotide windows of −17 to −12 bp from the PAM sequence, was up to 18.63% of the total sequences. The 27 most likely off‐target sites predicted by CRISPR‐P and Cas‐OFFinder tools were analysed by targeted deep sequencing, and it was found that rare C→T substitutions (average

Fusarium wilt (FW) disease of cotton, caused by the fungus Fusarium oxysporum f. sp. vasinfectum (Fov), causes severe losses in cotton production worldwide. Though significant advancements have been made in development of FW‐resistant Upland cotton (Gossypium hirsutum) in resistance screening programs, the precise resistance genes and the corresponding molecular mechanisms for resistance to Fov remain unclear. Herein it is reported that Fov7, a gene unlike canonical plant disease‐resistance (R) genes, putatively encoding a GLUTAMATE RECEPTOR‐LIKE (GLR) protein, confers resistance to Fov race 7 in Upland cotton. A single nucleotide polymorphism (SNP) (C/A) in GhGLR4.8, resulting in an amino acid change (L/I), is associated with Fov resistance. A PCR‐based DNA marker (GhGLR4.8SNP(A/C)) is developed and shown to cosegregate with the Fov resistance. CRISPR/Cas9‐mediated knockout of Fov7 results in cotton lines extremely susceptible to Fov race 7 with a loss of the ability to induce calcium influx in response to total secreted proteins (SEPs) of Fov. Furthermore, coinfiltration of SEPs with GhGLR4.8A results in a hypersensitive response. This first report of a GLR‐encoding gene that functions as an R gene provides a new insight into plant–pathogen interactions and a new handle to develop cotton cultivars with resistance to Fov race 7., Fusarium oxysporum f. sp. vasinfectum (Fov) is a widely distributed fungal pathogen seriously threatening cotton production. Herein, a GLUTAMATE RECEPTOR‐LIKE gene (GhGLR4.8) is identified as an atypical disease‐resistance gene specifying resistance to Fov race 7 through a genome‐wide association study in upland cotton, which provides a new insight into plant–pathogen interactions and facilitates the development of elite Fov‐resistant cultivars.

Polyamines (PAs) dramatically affect root architecture and development, mainly by unknown mechanisms, however, accumulating evidence points to hormone signaling and reactive oxygen species (ROS) as candidate mechanisms. To test this hypothesis, PA levels were modified by progressively reducing ADC1/2 activity and Put levels, and then changes in root meristematic zone (MZ) size, ROS, and auxin and cytokinin (CK) signaling were investigated. Decreasing putrescine resulted in an interesting inverted-U-trend in primary root growth and a similar trend in MZ size, and differential changes in putrescine (Put), spermidine (Spd), and combined spermine (Spm) plus thermospermine (Tspm) levels. At low Put concentrations, ROS accumulation increased coincidently with decreasing MZ size, and treatment with ROS scavenger KI partially rescued this phenotype. Analysis of double AtrbohD/F loss-of-function mutants indicated that NADPH oxidases were not involved in H2O2 accumulation and that elevated ROS levels were due to changes in PA back-conversion, terminal catabolism, PA ROS scavenging, or another pathway. Decreasing Put resulted in a non-linear trend in auxin signaling, whereas CK signaling decreased, re-balancing auxin and CK signaling. Different levels of Put modulated the expression of PIN1 and PIN2 auxin transporters, indicating changes to auxin distribution. These data strongly suggest that PAs modulate MZ size through both hormone signaling and ROS accumulation in Arabidopsis.

Salicylic acid (SA) and brassinosteroids (BRs) are well known to regulate diverse processes of plant development and stress responses, but the mechanisms by which these phytohormones mediate the growth and defense trade-off are largely unclear. In addition, little is known about the roles of DEHYDRATION RESPONSIVE ELEMENT BINDING transcription factors, especially in biotic stress and plant growth. Here, we identified a cotton (Gossypium hirsutum) APETALA2/ETHYLENE RESPONSIVE FACTOR gene GhTINY2 that is strongly induced by Verticillium dahliae. Overexpression of GhTINY2 in cotton and Arabidopsis enhanced tolerance to V. dahliae, while knockdown of expression increased the susceptibility of cotton to the pathogen. GhTINY2 was found to promote SA accumulation and SA signaling transduction by directly activating expression of WRKY51. Moreover, GhTINY2-overexpressing cotton and Arabidopsis showed retardation of growth, increased sensitivity to inhibitors of BR biosynthesis, down-regulation of several BR-induced genes, and up-regulation of BR-repressed genes, while GhTINY2-RNAi cotton showed the opposite effects. We further determined that GhTINY2 negatively regulates BR signaling by interacting with BRASSINAZOLE-RESISTANT 1 (BZR1) and restraining its transcriptional activation of the expression of INDOLE-3-ACETIC ACID INDUCIBLE 19 (IAA19). These findings indicate that GhTINY2 fine-tunes the trade-off between immunity and growth via indirect crosstalk between WRKY51-mediated SA biosynthesis and BZR1-IAA19-regulated BR signaling.

Plant bugs (Miridae species) have become major agricultural pests that cause increasing and severe economic damage. Plant-mediated RNA interference (RNAi) is emerging as an eco-friendly, efficient, and reliable strategy for pest management. In this study, we isolated and characterized a lethal gene of Apolygus lucorum and named it Apolygus lucorum LIM (AlLIM), which produced A. lucorum mortality rates ranging from 38% to 81%. Downregulation of the AlLIM gene expression in A. lucorum by injection of a double-stranded RNA (dsRNA) led to muscle structural disorganization that resulted in metamorphosis deficiency and increased mortality. Then we constructed a plant expression vector that enabled transgenic cotton to highly and stably express dsRNA of AlLIM (dsAlLIM) by Agrobacterium-mediated genetic transformation. In the field bioassay, dsAlLIM transgenic cotton was protected from A. lucorum damage with high efficiency, with almost no detectable yield loss. Therefore, our study successfully provides a promising genetically modified strategy to overpower A. lucorum attack.

Summary The plant hormone auxin and its directional intercellular transport play a major role in diverse aspects of plant growth and development. The establishment of auxin gradients requires the asymmetric distribution of members of the auxin efflux carrier PIN‐FORMED (PIN) protein family to the plasma membrane. An endocytic pathway regulates the recycling of PIN proteins between the plasma membrane and endosomes, providing a mechanism for dynamic localisation. N‐Ethylmaleimide‐sensitive factor adaptor protein receptors (SNAP receptors, SNAREs) mediate fusion between vesicles and target membranes and are classed as Q‐ or R‐SNAREs based on their sequence. We analysed gain‐ and loss‐of‐function mutants, dominant‐negative transgenics and localisation of the Arabidopsis R‐SNARE VAMP714 protein to understand its function.We demonstrate that VAMP714 is essential for the insertion of PINs into the plasma membrane, for polar auxin transport, root gravitropism and morphogenesis. VAMP714 gene expression is upregulated by auxin, and the VAMP714 protein co‐localises with endoplasmic reticulum and Golgi vesicles and with PIN proteins at the plasma membrane.It is proposed that VAMP714 mediates the delivery of PIN‐carrying vesicles to the plasma membrane, and that this forms part of a positive regulatory loop in which auxin activates a VAMP714‐dependent PIN/auxin transport system to control development.

The cotton fiber serves as a valuable experimental system to study cell wall synthesis in plants, but our understanding of the genetic regulation of this process during fiber development remains limited. We performed a genome‐wide association study (GWAS) and identified 28 genetic loci associated with fiber quality in allotetraploid cotton. To investigate the regulatory roles of these loci, we sequenced fiber transcriptomes of 251 cotton accessions and identified 15,330 expression quantitative trait loci (eQTL). Analysis of local eQTL and GWAS data prioritized 13 likely causal genes for differential fiber quality in a transcriptome‐wide association study (TWAS). Characterization of distal eQTL revealed unequal genetic regulation patterns between two subgenomes, highlighted by an eQTL hotspot (Hot216) that establishes a genome‐wide genetic network regulating the expression of 962 genes. The primary regulatory role of Hot216, and specifically the gene encoding a KIP‐related protein, was found to be the transcriptional regulation of genes responsible for cell wall synthesis, which contributes to fiber length by modulating the developmental transition from rapid cell elongation to secondary cell wall synthesis. This study uncovers the genetic regulation of fiber‐cell development and reveals the molecular basis of the temporal modulation of secondary cell wall synthesis during plant cell elongation.

Summary Global warming has reduced the productivity of many field‐grown crops, as the effects of high temperatures can lead to male sterility in such plants. Genetic regulation of the high temperature (HT) response in the major crop cotton is poorly understood.We determined the functionality and transcriptomes of the anthers of 218 cotton accessions grown under HT stress. By analyzing transcriptome divergence and implementing a genome‐wide association study (GWAS), we identified three thermal tolerance associated loci which contained 75 protein coding genes and 27 long noncoding RNAs, and provided expression quantitative trait loci (eQTLs) for 13 132 transcripts.A transcriptome‐wide association study (TWAS) confirmed six causal elements for the HT response (three genes overlapped with the GWAS results) which are involved in protein kinase activity. The most susceptible gene, GhHRK1, was confirmed to be a previously uncharacterized negative regulator of the HT response in both cotton and Arabidopsis.These functional variants provide a new understanding of the genetic basis for HT tolerance in male reproductive organs.