The TOR-EIN2 axis mediates nuclear signalling to modulate plant growth.

The evolutionarily conserved target of rapamycin (TOR) kinase acts as a master regulator that coordinates cell proliferation and growth by integrating nutrient, energy, hormone and stress signals in all eukaryotes1,2. Research has focused mainly on TOR-regulated translation, but how TOR orchestrates the global transcriptional network remains unclear. Here we identify ethylene-insensitive protein 2 (EIN2), a central integrator3-5 that shuttles between the cytoplasm and the nucleus, as a direct substrate of TOR in Arabidopsis thaliana. Glucose-activated TOR kinase directly phosphorylates EIN2 to prevent its nuclear localization. Notably, the rapid global transcriptional reprogramming that is directed by glucose-TOR signalling is largely compromised in the ein2-5 mutant, and EIN2 negatively regulates the expression of a wide range of target genes of glucose-activated TOR that are involved in DNA replication, cell wall and lipid synthesis and various secondary metabolic pathways. Chemical, cellular and genetic analyses reveal that cell elongation and proliferation processes that are controlled by the glucose-TOR-EIN2 axis are decoupled from canonical ethylene-CTR1-EIN2 signalling, and mediated by different phosphorylation sites. Our findings reveal a molecular mechanism by which a central signalling hub is shared but differentially modulated by diverse signalling pathways using distinct phosphorylation codes that can be specified by upstream protein kinases.

High-density bin-based genetic map reveals a 530-kb chromosome segment derived from wild peanut contributing to late leaf spot resistance.

KEY MESSAGE: Twenty-eight QTLs for LLS disease resistance were identified using an amphidiploid constructed mapping population, a favorable 530-kb chromosome segment derived from wild species contributes to the LLS resistance. Late leaf spot (LLS) is one of the major foliar diseases of peanut, causing serious yield loss and affecting the quality of kernel and forage. Some wild Arachis species possess higher resistance to LLS as compared with cultivated peanut; however, ploidy level differences restrict utilization of wild species. In this study, a synthetic amphidiploid (Ipadur) of wild peanuts with high LLS resistance was used to cross with Tifrunner to construct TI population. In total, 200 recombinant inbred lines were collected for whole-genome resequencing. A high-density bin-based genetic linkage map was constructed, which includes 4,809 bin markers with an average inter-bin distance of 0.43 cM. The recombination across cultivated and wild species was unevenly distributed, providing a novel recombination landscape for cultivated-wild Arachis species. Using phenotyping data collected across three environments, 28 QTLs for LLS disease resistance were identified, explaining 4.35-20.42% of phenotypic variation. The major QTL located on chromosome 14, qLLS14.1, could be consistently detected in 2021 Jiyang and 2022 Henan with 20.42% and 12.12% PVE, respectively. A favorable 530-kb chromosome segment derived from Ipadur was identified in the region of qLLS14.1, in which 23 disease resistance proteins were located and six of them showed significant sequence variations between Tifrunner and Ipadur. Allelic variation analysis indicating the 530-kb segment of wild species might contribute to the disease resistance of LLS. These associate genomic regions and candidate resistance genes are of great significance for peanut breeding programs for bringing durable resistance through pyramiding such multiple LLS resistance loci into peanut cultivars.

Gene regulatory network controlling carpel number variation in cucumber.

The WUSCHEL-CLAVATA3 pathway genes play an essential role in shoot apical meristem maintenance and floral organ development, and under intense selection during crop domestication. The carpel number is an important fruit trait that affects fruit shape, size and internal quality in cucumber, but the molecular mechanism remains elusive. Here, we found that CsCLV3 expression was negatively correlated with carpel number in cucumber cultivars. CsCLV3-RNAi led to increased number of petals and carpels, whereas overexpression of CsWUS resulted in more sepals, petals and carpels, suggesting that CsCLV3 and CsWUS function as a negative and a positive regulator for carpel number variation, respectively. Biochemical analyses indicated that CsWUS directly bound to the promoter of CsCLV3 and activated its expression. Overexpression of CsFUL1A , a FRUITFULL-like MADS-box gene, resulted in more petals and carpels. CsFUL1A can directly bind to the CsWUS promoter to stimulate its expression. Furthermore, we found that auxin participated in carpel number variation in cucumber through interaction of CsARF14 with CsWUS. Therefore, we have identified a gene regulatory pathway involving CsCLV3, CsWUS, CsFUL1A and CsARF14 in determining carpel number variation in an important vegetable crop - cucumber.

FATTY ACID DESATURASE5 Is Required to Induce Autoimmune Responses in Gigantic Chloroplast Mutants of Arabidopsis.

Chloroplasts mediate genetically controlled cell death via chloroplast-to-nucleus retrograde signaling. To decipher the mechanism, we examined chloroplast-linked lesion-mimic mutants of Arabidopsis (Arabidopsis thaliana) deficient in plastid division, thereby developing gigantic chloroplasts (GCs). These GC mutants, including crumpled leaf (crl), constitutively express immune-related genes and show light-dependent localized cell death (LCD), mirroring typical autoimmune responses. Our reverse genetic approach excludes any potential role of immune/stress hormones in triggering LCD. Instead, transcriptome and in silico analyses suggest that reactive electrophile species (RES) generated via oxidation of polyunsaturated fatty acids (PUFAs) or lipid peroxidation-driven signaling may induce LCD. Consistent with these results, the one of the suppressors of crl, dubbed spcrl4, contains a causative mutation in the nuclear gene encoding chloroplast-localized FATTY ACID DESATURASE5 (FAD5) that catalyzes the conversion of palmitic acid (16:0) to palmitoleic acid (16:1). The loss of FAD5 in the crl mutant might attenuate the levels of RES and/or lipid peroxidation due to the reduced levels of palmitic acid-driven PUFAs, which are prime targets of reactive oxygen species. The fact that fad5 also compromises the expression of immune-related genes and the development of LCD in other GC mutants substantiates the presence of an intrinsic retrograde signaling pathway, priming the autoimmune responses in a FAD5-dependent manner.

CsIVP functions in vasculature development and downy mildew resistance in cucumber.

Domesticated crops with high yield and quality are frequently susceptible to pathogen attack, whereas enhancement of disease resistance generally compromises crop yield. The underlying mechanisms of how plant development and disease resistance are coordinately programed remain elusive. Here, we showed that the basic Helix-Loop-Helix (bHLH) transcription factor Cucumis sativus Irregular Vasculature Patterning (CsIVP) was highly expressed in cucumber vascular tissues. Knockdown of CsIVP caused severe vasculature disorganization and abnormal organ morphogenesis. CsIVP directly binds to vascular-related regulators YABBY5 (CsYAB5), BREVIPEDICELLUS (CsBP), and AUXIN/INDOLEACETIC ACIDS4 (CsAUX4) and promotes their expression. Knockdown of CsYAB5 resulted in similar phenotypes as CsIVP-RNA interference (RNAi) plants, including disturbed vascular configuration and abnormal organ morphology. Meanwhile, CsIVP-RNAi plants were more resistant to downy mildew and accumulated more salicylic acid (SA). CsIVP physically interacts with NIM1-INTERACTING1 (CsNIMIN1), a negative regulator in the SA signaling pathway. Thus, CsIVP is a novel vasculature regulator functioning in CsYAB5-mediated organ morphogenesis and SA-mediated downy mildew resistance in cucumber.

AUXIN RESPONSE FACTOR3 Regulates Floral Meristem Determinacy by Repressing Cytokinin Biosynthesis and Signaling.

Successful floral meristem (FM) determinacy is critical for subsequent reproductive development and the plant life cycle. Although the phytohormones cytokinin and auxin interact to coregulate many aspects of plant development, whether and how cytokinin and auxin function in FM determinacy remain unclear. Here, we show that in Arabidopsis thaliana, cytokinin homeostasis is critical for FM determinacy. In this developmental context, auxin promotes the expression of AUXIN RESPONSE FACTOR3 (ARF3) to repress cytokinin activity. ARF3 directly represses the expression of ISOPENTENYLTRANSFERASE (IPT) family genes and indirectly represses LONELY GUY (LOG) family genes, both of which encode enzymes required for cytokinin biosynthesis. ARF3 also directly inhibits the expression of ARABIDOPSIS HISTIDINE KINASE4, a cytokinin receptor gene, resulting in reduced cytokinin activity. Consequently, ARF3 controls cell division by regulating cell cycle gene expression through cytokinin. In flowers, we show that AGAMOUS (AG) dynamically regulates the expression of ARF3 and IPTs, resulting in coordinated regulation of FM maintenance and termination through cell division. Moreover, genome-wide transcriptional profiling revealed both repressive and active roles for ARF3 in early flower development. Our findings establish a molecular link between AG and auxin/cytokinin and shed light on the mechanisms of stem cell maintenance and termination in the FM.

Interlinked regulatory loops of ABA catabolism and biosynthesis coordinate fruit growth and ripening in woodland strawberry.

Fruit growth and ripening are controlled by multiple phytohormones. How these hormones coordinate and interact with each other to control these processes at the molecular level is unclear. We found in the early stages of Fragaria vesca (woodland strawberry) fruit development, auxin increases both widths and lengths of fruits, while gibberellin [gibberellic acid (GA)] mainly promotes their longitudinal elongation. Auxin promoted GA biosynthesis and signaling by activating GA biosynthetic and signaling genes, suggesting auxin function is partially dependent on GA function. To prevent the repressive effect of abscisic acid (ABA) on fruit growth, auxin and GA suppressed ABA accumulation during early fruit development by activating the expression of FveCYP707A4a encoding cytochrome P450 monooxygenase that catalyzes ABA catabolism. At the onset of fruit ripening, both auxin and GA levels decreased, leading to a steep increase in the endogenous level of ABA that drives fruit ripening. ABA repressed the expression of FveCYP707A4a but promoted that of FveNCED, a rate-limiting step in ABA biosynthesis. Accordingly, altering FveCYP707A4a expression changed the endogenous ABA levels and affected FveNCED expression. Hence, ABA catabolism and biosynthesis are tightly linked by feedback and feedforward loops to limit ABA contents for fruit growth and to quickly increase ABA contents for the onset of fruit ripening. These results indicate that FveCYP707A4a not only regulates ABA accumulation but also provides a hub to coordinate fruit size and ripening times by relaying auxin, GA, and ABA signals.

Populus cathayana genome and population resequencing provide insights into its evolution and adaptation.

Populus cathayana Rehder, an indigenous poplar species of ecological and economic importance, is widely distributed in a high-elevation range from southwest to northeast China. Further development of this species as a sustainable poplar resource has been hindered by a lack of genome information the at the population level. Here, we produced a chromosome-level genome assembly of P. cathayana, covering 406.55 Mb (scaffold N50 = 20.86 Mb) and consisting of 19 chromosomes, with 35 977 protein-coding genes. Subsequently, we made a genomic variation atlas of 438 wild individuals covering 36 representative geographic areas of P. cathayana, which were divided into four geographic groups. It was inferred that the Northwest China regions served as the genetic diversity centers and a population bottleneck happened during the history of P. cathayana. By genotype-environment association analysis, 947 environment-association loci were significantly associated with temperature, solar radiation, precipitation, and altitude variables. We identified local adaptation genes involved in DNA repair and UV radiation response, among which UVR8, HY5, and CUL4 had key roles in high-altitude adaptation of P. cathayana. Predictions of adaptive potential under future climate conditions showed that P. cathayana populations in areas with drastic climate change were anticipated to have greater maladaptation risk. These results provide comprehensive insights for understanding wild poplar evolution and optimizing adaptive potential in molecular breeding.

The Torreya grandis genome illuminates the origin and evolution of gymnosperm-specific sciadonic acid biosynthesis.

Torreya plants produce dry fruits with assorted functions. Here, we report the 19-Gb chromosome-level genome assembly of T. grandis. The genome is shaped by ancient whole-genome duplications and recurrent LTR retrotransposon bursts. Comparative genomic analyses reveal key genes involved in reproductive organ development, cell wall biosynthesis and seed storage. Two genes encoding a C18 Δ9-elongase and a C20 Δ5-desaturase are identified to be responsible for sciadonic acid biosynthesis and both are present in diverse plant lineages except angiosperms. We demonstrate that the histidine-rich boxes of the Δ5-desaturase are crucial for its catalytic activity. Methylome analysis reveals that methylation valleys of the T. grandis seed genome harbor genes associated with important seed activities, including cell wall and lipid biosynthesis. Moreover, seed development is accompanied by DNA methylation changes that possibly fuel energy production. This study provides important genomic resources and elucidates the evolutionary mechanism of sciadonic acid biosynthesis in land plants.

Draft genomes assembly and annotation of Carex parvula and Carex kokanica reveals stress-specific genes.

Kobresia plants are important forage resources on the Qinghai-Tibet Plateau and are essential in maintaining the ecological balance of grasslands. Therefore, it is beneficial to obtain Kobresia genome resources and study the adaptive characteristics of Kobresia plants on the Qinghai-Tibetan Plateau. Previously, we have assembled the genome of Carex littledalei (Kobresia littledalei), which is a diploid with 29 chromosomes. In this study, we assembled genomes of Carex parvula (Kobresia pygmaea) and Carex kokanica (Kobresia royleana) via using Illumina and PacBio sequencing data, which were about 783.49 Mb and 673.40 Mb in size, respectively. And 45,002 or 36,709 protein-coding genes were further annotated in the genome of C. parvula or C. kokanica. Phylogenetic analysis indicated that Kobresia in Cyperaceae separated from Poaceae about 101.5 million years ago after separated from Ananas comosus in Bromeliaceae about 117.2 million years ago. C. littledalei and C. parvula separated about 5.0 million years ago, after separated from C. kokanica about 6.2 million years ago. In this study, transcriptome data of C. parvula at three different altitudes were also measured and analyzed. Kobresia plants genomes assembly and transcriptome analysis will assist research into mechanisms of plant adaptation to environments with high altitude and cold weather.

Dysfunction of histone demethylase IBM1 in Arabidopsis causes autoimmunity and reshapes the root microbiome.

Root microbiota is important for plant growth and fitness. Little is known about whether and how the assembly of root microbiota may be controlled by epigenetic regulation, which is crucial for gene transcription and genome stability. Here we show that dysfunction of the histone demethylase IBM1 (INCREASE IN BONSAI METHYLATION 1) in Arabidopsis thaliana substantially reshaped the root microbiota, with the majority of the significant amplicon sequence variants (ASVs) being decreased. Transcriptome analyses of plants grown in soil and in sterile growth medium jointly disclosed salicylic acid (SA)-mediated autoimmunity and production of the defense metabolite camalexin in the ibm1 mutants. Analyses of genome-wide histone modifications and DNA methylation highlighted epigenetic modifications permissive for transcription at several important defense regulators. Consistently, ibm1 mutants showed increased resistance to the pathogen Pseudomonas syringae DC3000 with stronger immune responses. In addition, ibm1 showed substantially impaired plant growth promotion in response to beneficial bacteria; the impairment was partially mimicked by exogenous application of SA to wild-type plants, and by a null mutation of AGP19 that is important for cell expansion and that is repressed with DNA hypermethylation in ibm1. IBM1-dependent epigenetic regulation imposes strong and broad impacts on plant-microbe interactions and thereby shapes the assembly of root microbiota.

A high-quality chromosome-scale assembly of the centipedegrass [Eremochloa ophiuroides (Munro) Hack.] genome provides insights into chromosomal structural evolution and prostrate growth habit.

Centipedegrass [Eremochloa ophiuroides (Munro) Hack.], a member of the Panicoideae subfamily, is one of the most important warm-season turfgrasses originating from China. This grass has an extremely developed prostrate growth habit and has been widely used in transitional and warm climatic regions. To better understand the genetic basis of important biological characteristics, such as prostrate growth and seed yield, in warm-season turfgrasses, we present a high-quality reference genome for centipedegrass and use PacBio, BioNano, and Hi-C technologies to anchor the 867.43 Mb genome assembly into nine pseudochromosomes, with a scaffold N50 of 86.05 Mb and 36,572 annotated genes. Centipedegrass was most closely related to sorghum and diverged from their common ancestor ~16.8 Mya. We detected a novel chromosome reshuffling event in centipedegrass, namely, the nest chromosome fusion event in which fusion of chromosomes 8 and 10 of sorghum into chromosome 3 of centipedegrass likely occurred after the divergence of centipedegrass from sorghum. The typical prostrate growth trait in centipedegrass may be linked to the expansion of candidate PROSTRATE GROWTH 1 (PROG1) genes on chromosome 2. Two orthologous genes of OsPROG1, EoPROG1, and EoPROG2, were confirmed to increase the stem number and decrease the stem angle in Arabidopsis. Collectively, our assembled reference genome of centipedegrass offers new knowledge and resources to dissect the genome evolution of Panicoideae and accelerate genome-assisted breeding and improvement of plant architecture in turf plants.

Plant Transcriptome Reprograming and Bacterial Extracellular Metabolites Underlying Tomato Drought Resistance Triggered by a Beneficial Soil Bacteria.

Water deficit is one of the major constraints to crop production and food security worldwide. Some plant growth-promoting rhizobacteria (PGPR) strains are capable of increasing plant drought resistance. Knowledge about the mechanisms underlying bacteria-induced plant drought resistance is important for PGPR applications in agriculture. In this study, we show the drought stress-mitigating effects on tomato plants by the Bacillus megaterium strain TG1-E1, followed by the profiling of plant transcriptomic responses to TG1-E1 and the profiling of bacterial extracellular metabolites. Comparison between the transcriptomes of drought-stressed plants with and without TG1-E1 inoculation revealed bacteria-induced transcriptome reprograming, with highlights on differentially expressed genes belonging to the functional categories including transcription factors, signal transduction, and cell wall biogenesis and organization. Mass spectrometry-based analysis identified over 40 bacterial extracellular metabolites, including several important regulators or osmoprotectant precursors for increasing plant drought resistance. These results demonstrate the importance of plant transcriptional regulation and bacterial metabolites in PGPR-induced plant drought resistance.

Genome sequence of Kobresia littledalei, the first chromosome-level genome in the family Cyperaceae.

Kobresia plants are important forage resources in the Qinghai-Tibet Plateau and are essential in maintaining the ecological balance of grasslands. Therefore, it is beneficial to obtain Kobresia genome resources and study the adaptive characteristics of Kobresia plants in the Qinghai-Tibetan Plateau. We assembled the genome of Kobresia littledalei C. B. Clarke, which was about 373.85 Mb in size. 96.82% of the bases were attached to 29 pseudo-chromosomes, combining PacBio, Illumina and Hi-C sequencing data. Additional investigation of the annotation identified 23,136 protein-coding genes. 98.95% of these were functionally annotated. According to phylogenetic analysis, K. littledalei in Cyperaceae separated from Poaceae about 97.6 million years ago after separating from Ananas comosus in Bromeliaceae about 114.3mya. For K. littledalei, we identified a high-quality genome at the chromosome level. This is the first time a reference genome has been established for a species of Cyperaceae. This genome will help additional studies focusing on the processes of plant adaptation to environments with high altitude and cold weather.

DNA demethylases are required for myo-inositol-mediated mutualism between plants and beneficial rhizobacteria.

Root-associated soil bacteria can strongly influence plant fitness. DNA methylation is an epigenetic mark important to many fundamental biological processes; however, its roles in plant interactions with beneficial microbes remain elusive. Here, we report that active DNA demethylation in Arabidopsis controls root secretion of myo-inositol and consequently plant growth promotion triggered by Bacillus megaterium strain YC4. Root-secreted myo-inositol is critical for YC4 colonization and preferentially attracts B. megaterium among the examined bacteria species. Active DNA demethylation antagonizes RNA-directed DNA methylation in controlling myo-inositol homeostasis. Importantly, we demonstrate that active DNA demethylation controls myo-inositol-mediated mutualism between YC4 and Solanum lycopersicum, thus suggesting a conserved nature of this epigenetic regulatory mechanism.

Partial defoliation of Brachypodium distachyon plants grown in petri dishes under low light increases P and other nutrient levels concomitantly with transcriptional changes in the roots.

BACKGROUND: There have been few studies on the partial defoliation response of grass. It has been unclear how partial defoliation may affect roots at the levels of nutrient accumulation and transcriptional regulation. Hereby we report a comprehensive investigation on molecular impacts of partial defoliation by using a model grass species, Brachypodium distachyon. RESULTS: Our Inductively Coupled Plasma Mass Spectrometry analyses of B. distachyon revealed shoot- and root-specific accumulation patterns of a group of macronutrients including potassium (K), Phosphorus (P), Calcium (Ca), Magnesium (Mg), and micronutrients including Sodium (Na), iron (Fe), and Manganese (Mn). Meanwhile, our genome-wide profiling of gene expression patterns depicts transcriptional impacts on B. distachyon roots by cutting the aerial portion. The RNAseq analyses identified a total of 1,268 differentially expressed genes in B. distachyon with partial defoliation treatment. Our comprehensive analyses by means of multiple approaches, including Gene Ontology, InterPro and Pfam protein classification, KEGG pathways, and Plant TFDB, jointly highlight the involvement of hormone-mediated wounding response, primary and secondary metabolites, and ion homeostasis, in B. distachyon after the partial defoliation treatment. In addition, evidence is provided that roots respond to partial defoliation by modifying nutrient uptake and rhizosphere acidification rate, indicating that an alteration of the root/soil interaction occurs in response to this practice. CONCLUSIONS: This study reveals how partial defoliation alters ion accumulation levels in shoots and roots, as well as partial defoliation-induced transcriptional reprogramming on a whole-genome scale, thereby providing insight into the molecular mechanisms underlying the recovery process of grass after partial defoliation.