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Epigenetic modification contributes to the regulation of gene expression and plant development under salinity stress. Here we describe the identification of 49 soybean transcription factors by microarray analysis as being inducible by salinity stress. A semi-quantitative RT-PCR-based expression assay confirmed the salinity stress inducibility of 45 of these 49 transcription factors, and showed that ten of them were up-regulated when seedlings were exposed to the demethylation agent 5-aza-2-deoxycytidine. Salinity stress was shown to affect the methylation status of four of these ten transcription factors (one MYB, one b-ZIP and two AP2/DREB family members) using a combination of bisulfite sequencing and DNA methylation-sensitive DNA gel blot analysis. ChIP analysis indicated that the activation of three of the four DNA methylated transcription factors was correlated with an increased level of histone H3K4 trimethylation and H3K9 acetylation, and/or a reduced level of H3K9 demethylation in various parts of the promoter or coding regions. Our results suggest a critical role for some transcription factors' activation/repression by DNA methylation and/or histone modifications in soybean tolerance to salinity stress.

Plant height is a key agronomic trait that affects yield and is controlled by both phytohormone gibberellin (GA) and ultraviolet-B (UV-B) irradiation. However, whether and how plant height is modulated by UV-B-mediated changes in GA metabolism are not well understood. It has not been reported that the E3 ubiquitin ligase Anaphase Promoting Complex/Cyclosome (APC/C) is involved in the regulation of plant growth in response to environmental factors. We perform a forward genetic screen in soybean and find that a mutation in Glycine max Increased Leaf Petiole Angle1 ( GmILPA1 ), encoding a subunit of the APC/C, lead to dwarfism under UV-B irradiation. UV-B promotes the accumulation of GmILPA1, which ubiquitinate the GA catabolic enzyme GA2 OXIDASE-like (GmGA2ox-like), resulting in its degradation in a UV-B-dependent manner. Another E3 ligase, GmUBL1, also ubiquitinate GmGA2ox-like and enhance the GmILPA1-mediated degradation of GmGA2ox-like, which suggest that GmILPA1-GmGA2ox-like module counteract the UV-B-mediated reduction of bioactive GAs. We also determine that GmILPA1 is a target of selection during soybean domestication and breeding. The deletion (Indel-665) in the promoter might facilitate the adaptation of soybean to high UV-B irradiation. This study indicates that an evolutionary GmILPA1 variant has the capability to develop ideal plant architecture with soybean cultivars. Gibberellins (GA) negatively regulate UVB-mediated suppression of plant height in plants. Here, the authors show that GmILPA1-mediated degradation of GmGA2ox-like protein counteract the UV-B-mediated reduction of bioactive GAs contributing to the linkage between the affection of UV-B and GA on plant height of soybean.

Plant adaptive responses to drought are coordinated by adjusting growth and developmental processes as well as molecular and cellular activities. The root system is the primary site that perceives drought stress signals, and its development is profoundly affected by soil water content. Various growth hormones, particularly abscisic acid (ABA) and auxin, play a critical role in root growth under drought through complex signaling networks. Here, we report that a R2R3-type MYB transcription factor, MYB96, regulates drought stress response by integrating ABA and auxin signals. The MYB96-mediated ABA signals are integrated into an auxin signaling pathway that involves a subset of GH3 genes encoding auxin-conjugating enzymes. A MYB96-overexpressing Arabidopsis (Arabidopsis thaliana) mutant exhibited enhanced drought resistance with reduced lateral roots. In the mutant, while lateral root primordia were normally developed, meristem activation and lateral root elongation were suppressed. In contrast, a T-DNA insertional knockout mutant was more susceptible to drought. Auxin also induces MYB96 primarily in the roots, which in turn induces the GH3 genes and modulates endogenous auxin levels during lateral root development. We propose that MYB96 is a molecular link that mediates ABA-auxin cross talk in drought stress response and lateral root growth, providing an adaptive strategy under drought stress conditions.

Class I KNOTTED-like homeobox ( KNOXI ) genes are parts of the regulatory network that control the evolutionary diversification of leaf morphology. Their specific spatiotemporal expression patterns in developing leaves correlate with the degrees of leaf complexity between simple-leafed and compound-leafed species. However, KNOXI genes are not involved in compound leaf formation in several legume species. Here, we identify a pathway for dual repression of MtKNOXI function in Medicago truncatula . PINNATE-LIKE PENTAFOLIATA1 ( PINNA1 ) represses the expression of MtKNOXI , while PINNA1 interacts with MtKNOXI and sequesters it to the cytoplasm. Further investigations reveal that UNUSUAL FLORAL ORGANS ( MtUFO ) is the direct target of MtKNOXI, and mediates the transition from trifoliate to pinnate-like pentafoliate leaves. These data suggest a new layer of regulation for morphological diversity in compound-leafed species, in which the conserved regulators of floral development, MtUFO , and leaf development, MtKNOXI , are involved in variation of pinnate-like compound leaves in M. truncatula . This study reveals a pathway in which the transformation of trifoliate leaves into pinnate-like pentafoliate leaves is regulated by the conserved regulators of floral development ( MtUFO ) and leaf development ( MtKNOXI ) in M. truncatula .

The production of phytochelatins (PCs) provides an important means for plants to achieve tolerance to cadmium (Cd) toxicity. A reed gene encoding PC synthase (PaPCS) was isolated and its function tested through its heterologous expression in a strain of yeast sensitive to Cd. Subsequently, the Cd sensitive and high biomass accumulating species tall fescue was transformed either with PaPCS or PaGCS (a glutamyl cysteine synthetase gene of reed) on their own (single transformants), or with both genes together in the same transgene cassette (double transformant). The single and double transformants showed greater Cd tolerance and accumulated more Cd and PC than wild type plants, and their Cd leaf/root ratio content was higher. The ranking in terms of Cd and PC content for the various transgenic lines was double transformants>PaGCS single transformants>PaPCS single transformants>wild type. Thus PaGCS appears to exert a greater influence than PaPCS over PC synthesis and Cd tolerance/accumulation. The double transformant has interesting potential for phytoremediation.

Soybean (Glycine max) is a major source of dietary protein and vegetable oil, but its production is severely reduced by salt stress. The regulatory mechanisms and utilization of salt‐tolerant genes have not been deeply studied. Salt‐Induced NAC 1 (GmSIN1) positively regulates salt tolerance in soybean, enhancing growth and yield in saline soil. Here, we found that GmSIN1 is degraded via the 26S proteasome pathway, and this process is suppressed by salt. GmRNF1a mediates the ubiquitination‐dependent degradation of GmSIN1 as an E3 ubiquitin ligase, whereas GmCSN5a (a homolog of COP9 signalosome subunit) directly inhibits its E3 ligase activity. GmRNF1a negatively regulates salt tolerance while GmCSN5a functions as a positive regulator. We further identified elite haplotypes of GmSIN1, GmRNF1a, and GmCSN5a that associate with grain weight per plant under both normal and saline conditions. Gene‐pyramided lines carrying elite alleles (GmSIN1Hap1‐GmRNF1aHap2‐GmCSN5aHap1) exhibit boosted grain yield under both conditions. In conclusion, our study reveals that the GmSIN1‐GmRNF1a‐GmCSN5a module enhances soybean salt tolerance by maintaining GmSIN1 orthostasis. Pyramiding elite haplotypes establishes an innovative haplotype‐based breeding strategy for developing salt‐tolerant and high‐yielding soybean cultivars by harnessing natural variation. Soybean production is severely threatened by salt stress. This study reveals that the GmSIN1‐GmRNF1a‐GmCSN5a module enhances salt tolerance by stabilizing the GmSIN1 protein. GmRNF1a acts as an E3 ligase to ubiquitinate GmSIN1 for degradation, a process inhibited by GmCSN5a. Pyramiding elite haplotypes of these genes significantly boosts yield under both normal and saline conditions, offering a novel haplotype‐based breeding strategy for salt‐tolerant, high‐yielding soybeans.

Salt stress limits soybean quality and yield. Despite the genetic validation of many salinity tolerance genes, the roles and regulatory mechanisms of their natural variations in population‐level salt tolerance remain unclear. This study identifies seed maturation protein PM30 (GmPM30), a late embryogenesis abundant (LEA) gene, as enhancing soybean salt tolerance. A significant T/C nonsynonymous polymorphism in the coding region of GmPM30 confers haplotype HapT with greater salt tolerance than HapC via stronger GmLEA1‐GmPM30‐GmLEC1 (Lectin) interactions, reducing ion leakage, malondialdehyde (MDA) content, and hydrogen peroxide (H2O2) accumulation under salt stress. RNA‐seq demonstrates that GmPM30‐HapT activates more extensive and robust stress response pathways than HapC. Evolutionary analyses reveal artificial selection of the GmLEA1‐GmPM30‐GmLEC1 module during soybean domestication and breeding, with GmPM30 being geographically adapted to high‐latitude regions with greater saline‐alkaline stress. Pyramiding lines with elite alleles (GmLEA1‐Hap3‐GmPM30‐HapT‐GmLEC1‐Hap3) boosts grain yield on saline soil. An efficient marker developed for GmPM30‐HapT enables marker‐assisted selection (MAS) breeding, and haplotype hybrids with successful GmPM30‐HapT integration exhibit improved yield‐related traits in saline farmlands. This study establishes a novel workflow linking evolutionary genomics, molecular mechanisms, and breeding applications through the GmLEA1‐GmPM30‐GmLEC1 module, providing a replicable blueprint for rapid crop improvement by using natural selection strategies. A natural variation in soybean PM30, GmPM30‐HapT, confers greater salt tolerance than GmPM30‐HapC via stronger GmLEA1‐GmPM30‐GmLEC1 interactions. Pyramiding their elite haplotypes yields additive gains in salt tolerance and yield, establishing a novel workflow linking evolutionary genomics, molecular mechanisms, and breeding applications via the module to guide soybean salt tolerance research using natural selection.

Soil stress, such as salinity, is a primary cause of global crop yield reduction. Existing crop phenotyping platforms cannot fully meet the specific needs of phenomics studies of plant response to soil stress in terms of throughput, environmental controllability, or root phenotypic acquisition. Here, we report the WinRoots, a low-cost and high-throughput plant soil cultivation and phenotyping system that can provide uniform, controlled soil stress conditions and accurately quantify the whole-plant phenome, including roots. Using soybean seedlings exposed to salt stress as an example, we demonstrate the uniformity and controllability of the soil environment in this system. A high-throughput multiple-phenotypic assay among 178 soybean cultivars reveals that the cotyledon character can serve as a non-destructive indicator of the whole-seedling salt tolerance. Our results demonstrate that WinRoots is an effective tool for high-throughput plant cultivation and soil stress phenomics studies.

The flower buds of Lonicera japonica are a rich source of antioxidants, comprising mostly flavonoids and phenolic acids, and in particular chlorogenic acid (5-caffeoylquinic acid, CGA), dicaffeoylquinic acid and caffeic acid. Hydroxycinnamoyl-CoA transferases are important for the synthesis of CGA. Here, the isolation and characterization of a Lonicera japonica gene encoding a hydroxycinnamoyl-CoA quinate transferase (HQT) is described. The recombinant LjHQT, produced by heterologously expressing the gene in Escherichia coli , favored p -coumaroyl-CoA over caffeoyl-CoA as its acyl donor, and expressed a higher affinity for quinate over shikimate as its its acyl acceptor. Southern blot analysis showed that the L. japonica genome harbors at least two copies of LjHQT. LjHQT transcript abundance was promoted both by spraying the leaves with salicylic acid or abscisic acid, and exposing them to a period of low temperature. The constitutive expression of LjHQT in Arabidopsis thaliana resulted in the production of CGA in the leaf and an higher level of resistance to the bacterial pathogen Pseudomonas syringae . CGA synthesis was positively correlated with LjHQT transcript abundance. When a fusion between the LjHQT promoter and GUS was expressed in A. thaliana , GUS expression was observed mainly in the sepal, vascular bundle, stigma and axillary bud.

Background The wild herb Swertia mussotii is a source of the anti-hepatitis compounds swertiamarin, mangiferin and gentiopicroside. Its over-exploitation has raised the priority of producing these compounds heterologously. Somatic hybridization represents a novel approach for introgressing Swertia mussotii genes into a less endangered species. Results Protoplasts derived from calli of Bupleurum scorzonerifolium and S. mussotii were fused to produce 194 putative hybrid cell lines, of which three (all derived from fusions where the S. mussotii protoplasts were pre-treated for 30 s with UV light) later differentiated into green plants. The hybridity of the calli was confirmed by a combination of isozyme, RAPD and chromosomal analysis. The hybrid calli genomes were predominantly B. scorzonerifolium. GISH analysis of mitotic chromosomes confirmed that the irradiation of donor protoplasts increased the frequency of chromosome elimination and fragmentation. RFLP analysis of organellar DNA revealed that mitochondrial and chloroplast DNA of both parents coexisted and recombined in some hybrid cell lines. Some of the hybrid calli contained SmG10H from donor, and produced swertiamarin, mangiferin and certain volatile compounds characteristic of S. mussotii. The expression of SmG10H (geraniol 10-hydroxylase) was associated with the heterologous accumulation of swertiamarin. Conclusions Somatic hybrids between B. scorzonerifolium and S. mussotii were obtained, hybrids selected all contained introgressed nuclear and cytoplasmic DNA from S. mussotii; and some produced more mangiferin than the donor itself. The introgression of SmG10H was necessary for the accumulation of swertiamarin.