Expression of a novel PSK-encoding gene from soybean improves seed growth and yield in transgenic plants

Small Peptides: Orchestrators of Plant Growth and Developmental Processes

Small peptides (SPs), ranging from 5 to 100 amino acids, play integral roles in plants due to their diverse functions. Despite their low abundance and small molecular weight, SPs intricately regulate critical aspects of plant life, including cell division, growth, differentiation, flowering, fruiting, maturation, and stress responses. As vital mediators of intercellular signaling, SPs have garnered significant attention in plant biology research. This comprehensive review delves into SPs' structure, classification, and identification, providing a detailed understanding of their significance. Additionally, we summarize recent findings on the biological functions and signaling pathways of prominent SPs that regulate plant growth and development. This review also offers a perspective on future research directions in peptide signaling pathways.

Sulfated peptides and their receptors: Key regulators of plant development and stress adaptation

Four distinct types of sulfated peptides have been identified in Arabidopsis thaliana. These peptides play crucial roles in regulating plant development and stress adaptation. Recent studies have revealed that Xanthomonas and Meloidogyne can secrete plant-like sulfated peptides, exploiting the plant sulfated peptide signaling pathway to suppress plant immunity. Over the past three decades, receptors for these four types of sulfated peptides have been identified, all of which belong to the leucine-rich repeat receptor-like protein kinase subfamily. A number of regulatory proteins have been demonstrated to play important roles in their corresponding signal transduction pathways. In this review, we comprehensively summarize the discoveries of sulfated peptides and their receptors, mainly in Arabidopsis thaliana. We also discuss their known biological functions in plant development and stress adaptation. Finally, we put forward a number of questions for reference in future studies.

A DNA demethylase reduces seed size by decreasing the DNA methylation of AT-rich transposable elements in soybean

Understanding how to increase soybean yield is crucial for global food security. The genetic and epigenetic factors influencing seed size, a major crop yield determinant, are not fully understood. We explore the role of DNA demethylase GmDMEa in soybean seed size. Our research indicates that GmDMEa negatively correlates with soybean seed size. Using CRISPR-Cas9, we edited GmDMEa in the Dongnong soybean cultivar, known for small seeds. Modified plants had larger seeds and greater yields without altering plant architecture or seed nutrition. GmDMEa preferentially demethylates AT-rich transposable elements, thus activating genes and transcription factors associated with the abscisic acid pathway, which typically decreases seed size. Chromosomal substitution lines confirm that these modifications are inheritable, suggesting a stable epigenetic method to boost seed size in future breeding. Our findings provide insights into epigenetic seed size control and suggest a strategy for improving crop yields through the epigenetic regulation of crucial genes. This work implies that targeted epigenetic modification has practical agricultural applications, potentially enhancing food production without compromising crop quality.

Phytosulfokine alpha enhances regeneration of transformed and untransformed protoplasts of Brassica oleracea

Phytosulfokine-α (PSK-α) is a disulfated pentapeptide (YIYTQ) acting as an intercellular signal peptide and growth factor. It was originally isolated from conditioned medium of asparagus mesophyll cell cultures in 1996 and later characterized as a hormone-like signal molecule with important roles in numerous processes of in vivo plant growth and development. It is currently becoming a valuable mitogenic factor in plant breeding and biotechnology due to its stimulatory effect on in vitro cell elongation, proliferation and differentiation. The focus of our work was to review current knowledge about the roles of PSK-α in plant biotechnology and to evaluate its influence on the regeneration of protoplasts of four Brassica oleracea cultivars (two cauliflower and two cabbage) cultured under two distinctive protocols and with different protoplast densities. Protoplast regeneration was studied due to its high value for plant genome editing, which is generally limited by the inefficient regeneration of treated protoplasts of numerous important plant genotypes. Our hypothesis was that the stress related to PEG-mediated protoplast transformation and the following decrease in viable protoplast density in culture could be alleviated by the addition of PSK-α to the culture medium. We therefore tested whether PSK-α could increase cell division at the early stages of culture (5 and 15 days after protoplast isolation) and stimulate the formation of microcallus colonies up to the 30st day of culture and to evaluate its influence on callus organogenesis leading to shoot regeneration. The PSK-α showed a strong stimulatory effect on untransformed protoplast regeneration already during the first days of culture, accelerating cell division up to 5.3-fold and the formation of multicellular microcallus colonies up to 37.0-fold. The beneficial influence was retained at later stages of regeneration, when PSK improved shoot organogenesis even if it was present only during the first 10 days of culture. The highest numbers of shoots, however, were regenerated when PSK was present during the first days of culture and later in solid shoot regeneration medium. Finally, the addition of PSK-α to PEG-transformed protoplasts significantly enhanced their division rate and the formation of microcallus colonies in selection media, up to 44.0-fold.

Understanding the Molecular Regulatory Networks of Seed Size in Soybean

Soybean being a major cash crop provides half of the vegetable oil and a quarter of the plant proteins to the global population. Seed size traits are the most important agronomic traits determining the soybean yield. These are complex traits governed by polygenes with low heritability as well as are highly influenced by the environment as well as by genotype x environment interactions. Although, extensive efforts have been made to unravel the genetic basis and molecular mechanism of seed size in soybean. But most of these efforts were majorly limited to QTL identification, and only a few genes for seed size were isolated and their molecular mechanism was elucidated. Hence, elucidating the detailed molecular regulatory networks controlling seed size in soybeans has been an important area of research in soybeans from the past decades. This paper describes the current progress of genetic architecture, molecular mechanisms, and regulatory networks for seed sizes of soybeans. Additionally, the main problems and bottlenecks/challenges soybean researchers currently face in seed size research are also discussed. This review summarizes the comprehensive and systematic information to the soybean researchers regarding the molecular understanding of seed size in soybeans and will help future research work on seed size in soybeans.

Phytosulfokine peptides, their receptors, and functions

Phytosulfokines (PSKs) are a class of disulfated pentapeptides and are regarded as plant peptide hormones. PSK-α, -γ, -δ, and -ϵ are four bioactive PSKs that are reported to have roles in plant growth, development, and immunity. In this review, we summarize recent advances in PSK biosynthesis, signaling, and function. PSKs are encoded by precursor genes that are widespread in higher plants. PSKs maturation from these precursors requires a sulfation step, which is catalyzed by a tyrosylprotein sulfotransferase, as well as proteolytic cleavage by subtilisin serine proteases. PSK signaling is mediated by plasma membrane-localized receptors PSKRs that belong to the leucine-rich repeat receptor-like kinase family. Moreover, multiple biological functions can be attributed to PSKs, including promoting cell division and cell growth, regulating plant reproduction, inducing somatic embryogenesis, enhancing legume nodulation, and regulating plant resistance to biotic and abiotic stress. Finally, we propose several research directions in this field. This review provides important insights into PSKs that will facilitate biotechnological development and PSK application in agriculture.

Molecular, genetic, and genomic basis of seed size and yield characteristics in soybean

Soybean (Glycine max L. Merr.) is a crucial oilseed cash crop grown worldwide and consumed as oil, protein, and food by humans and feed by animals. Comparatively, soybean seed yield is lower than cereal crops, such as maize, rice, and wheat, and the demand for soybean production does not keep up with the increasing consumption level. Therefore, increasing soybean yield per unit area is the most crucial breeding objective and is challenging for the scientific community. Moreover, yield and associated traits are extensively researched in cereal crops, but little is known about soybeans' genetics, genomics, and molecular regulation of yield traits. Soybean seed yield is a complex quantitative trait governed by multiple genes. Understanding the genetic and molecular processes governing closely related attributes to seed yield is crucial to increasing soybean yield. Advances in sequencing technologies have made it possible to conduct functional genomic research to understand yield traits' genetic and molecular underpinnings. Here, we provide an overview of recent progress in the genetic regulation of seed size in soybean, molecular, genetics, and genomic bases of yield, and related key seed yield traits. In addition, phytohormones, such as auxin, gibberellins, cytokinins, and abscisic acid, regulate seed size and yield. Hence, we also highlight the implications of these factors, challenges in soybean yield, and seed trait improvement. The information reviewed in this study will help expand the knowledge base and may provide the way forward for developing high-yielding soybean cultivars for future food demands.

The Research Process of PSK Biosynthesis, Signaling Transduction, and Potential Applications in Brassica napus

Phytosulfokine (PSK) is a disulfated pentapeptide that acts as a growth regulator to control plant growth and development as well as adaptability to biotic and abiotic stress. In the last three decades, PSK has drawn increasing attention due to its various functions. Preproproteins that have been tyrosine sulfonylated and then cleaved by specific enzymes contribute to mature PSK. To transfer a signal from the apoplast to the inner cells, the PSK peptide must bind to the PSK receptors (PSKR1 and PSKR2) at the cell surface. The precise mechanism of PSK signal transduction is still unknown, given that PSKR combines receptor and kinase activity with a capacity to bind calmodulin (CaM). The binding of PSK and PSKR stimulates an abundance of cGMP downstream from PSKR, further activating a cation-translocating unit composed of cyclic nucleotide-gated channel 17 (CNGC17), H+-ATPases AHA1 and AHA2, and BRI-associated receptor kinase 1 (BAK1). Recently, it has been revealed that posttranslational ubiquitination is closely related to the control of PSK and PSKR binding. To date, the majority of studies related to PSK have used Arabidopsis. Given that rapeseed and Arabidopsis share a close genetic relationship, the relevant knowledge obtained from Arabidopsis can be further applied to rapeseed.

Rhizobium Soaking Promoted Maize Growth by Altering Rhizosphere Microbiomes and Associated Functional Genes

Rhizobium is a Gram-negative bacterium, which dissolves minerals, produces growth hormones, promotes root growth, and protects plants from different soil-borne pathogens. In the present study, roots, stalks, and fresh weight of maize (Zea mays L.) were significantly increased after soaking in Bradyrhizobium japonicum compared with the control. Subsequently, transcriptome sequencing results of the whole maize plant soaked in B. japonicum showed that multiple growth and development-related genes were up-regulated more than 100-fold compared to the control. Furthermore, the abundance of plant growth promoting bacteria, such as Acidobacteria Subgroup_6 and Chloroflexi KD4-96, were increased significantly. On the contrary, the abundance of multiple pathogens, such as Curvularia, Fusarium and Mycocentrospora, were significantly decreased. Moreover, inoculation with B. japonicum could inhibit the infection of the pathogen Fusarium graminearum in maize. These results suggest that soaking seeds in B. japonicum may affect the expression of maize growth and development-related genes as the bacteria changes the soil microorganism community structure. These findings may help to expand the application of B. japonicum in crop production and provide new opportunities for food security.

Major genetic locus with pleiotropism determined seed-related traits in cultivated and wild soybeans

KEY MESSAGE

Here, a novel pleiotropic QTL qSS14 simultaneously regulating four seed size traits and two consistently detected QTLs qSW17 and qSLW02 were identified across multiple years. Seed-related traits were the key agronomic traits that have been artificially selected during the domestication of wild soybean. Identifying the genetic loci and genes that regulate seed size could clarify the genetic variations in seed-related traits and provide novel insights into high-yield soybean breeding. In this study, we used a high-density genetic map constructed by F₁₀ RIL populations from a cross between Glycine max and Glycine soja to detect additive QTLs for seven seed-related traits over the last three years. As a result, we identified one novel pleiotropic QTL, qSS14, that simultaneously controlled four seed size traits (100-seed weight, seed length, seed width, and seed thickness) and two consistently detected QTLs, qSW17, and qSLW02, in multiple years of phenotypic data. Furthermore, we predicted two, two and three candidate genes within these three critical loci based on the parental resequencing data and gene function annotations. And the relative expression of four candidate genes GLYMA_14G155100, GLYMA_17G061000, GLYMA_02G273100, and GLYMA_02G273300 showed significant differences among parents and the extreme materials through qRT-PCR analysis. These findings could facilitate the determination of beneficial genes in wild soybean and contribute to our understanding of the soybean domestication process.

Novel Seed Size: A Novel Seed-Developing Gene in Glycine max

Soybean-seed development is controlled in multiple ways, as in many known regulating genes. Here, we identify a novel gene, Novel Seed Size (NSS), involved in seed development, by analyzing a T-DNA mutant (S006). The S006 mutant is a random mutant of the GmFTL4pro:GUS transgenic line, with phenotypes with small and brown seed coats. An analysis of the metabolomics and transcriptome combined with RT-qPCR in the S006 seeds revealed that the brown coat may result from the increased expression of chalcone synthase 7/8 genes, while the down-regulated expression of NSS leads to small seed size. The seed phenotypes and a microscopic observation of the seed-coat integument cells in a CRISPR/Cas9-edited mutant nss1 confirmed that the NSS gene conferred small phenotypes of the S006 seeds. As mentioned in an annotation on the Phytozome website, NSS encodes a potential DNA helicase RuvA subunit, and no such genes were previously reported to be involved in seed development. Therefore, we identify a novel gene in a new pathway controlling seed development in soybeans.

Phytosulfokine-δ: A Small Peptide, but a Big Player in Symbiosis Gene Regulation

Nitrogen availability is one of the critical determinants of agricultural yield. Biological nitrogen fixation, such as legume–rhizobia symbiotic association, might function as a solution to fix nitrogen. Using phytosulfokine (PSK)-α sequences as a query, Yu et al., 2022 performed a comprehensive genome-wide search of legume species to identify PSK-δ, a divergent pentapeptide differing in single amino acid. Furthermore, PSK-δ exhibited nodule-specific expression with lower expression in the root, substantiating the nodule-specific temporal expression and suggesting its role in nodule development and nitrogen fixation. Additionally, in planta functional characterization in Medicago truncatula using overexpression and Tnt1-insertion mutant analysis indicated the role of PSK-δ in symbiotic nodulation. Interestingly, a similar phenotype of MtPSKδ mutant (mtpskδ) with that of wild-type control led to the hypothesis of its functional redundancy with PSK-α in nodule organogenesis. Further investigation regarding its position in the Nod-factor signaling pathway revealed the downstream function of PSK-δ in association with MtENOD11 in regulating nodule formation.

A novel type of phytosulfokine, PSK-ε, positively regulates root elongation and formation of lateral roots and root nodules in Medicago truncatula

Phytosulfokines (PSKs) are a class of tyrosine-sulfated pentapeptides. PSK-α, PSK-γ, and PSK-δ are three reported PSK members involved in regulating plant growth, development, and resistance to biotic and abiotic stresses. Here, we reported a novel type of PSK, PSK-ε with the sequence Y_SO3VY_SO3TN, and its precursor proteins (MtPSKε, LjPSKε, and GmPSKε), specifically from legume species. PSK-ε peptide differs from PSK-δ by one amino acid and is close to PSK-δ in the phylogenetic relationship. Expression profile analysis showed that MtPSKε was highly expressed in Medicago truncatula roots, especially in root tips and emerged lateral roots. Application of the synthetic sulfated PSK-ε peptide and overexpression of MtPSKε significantly promoted M. truncatula root elongation and increased lateral root number, probably by inducing cell division and expansion in roots. Furthermore, MtPSKε expression was induced by rhizobia infection and was detected in root nodules including nodule primordia. Both PSK-ε peptide treatment and MtPSKε overexpression significantly increased nodule number in M. truncatula. Taken together, these results demonstrate that PSK-ε, a novel type of phytosulfokine, positively regulates root elongation and formation of lateral root and root nodule in M. truncatula.

An enhancing effect attributed to a nonsynonymous mutation in SOYBEAN SEED SIZE 1, a SPINDLY-like gene, is exploited in soybean domestication and improvement

Soybean (Glycine max) was domesticated from its wild relative Glycine soja. One-hundred-seed weight is one of the most important domesticated traits determining soybean yield; however, its underlying genetic basis remains elusive. We characterized a soybean seed size 1 (sss1) mutant featuring large seeds compared to its wild-type background. Positional cloning revealed that the candidate gene GmSSS1 encoded a SPINDLY homolog and was co-located in a well-identified quantitative trait locus (QTL)-rich region on chromosome 19. Knocking out GmSSS1 resulted in small seeds, while overexpressing GmSSS1/Gmsss1 induced large seeds. Modulating GmSSS1/Gmsss1 in transgenic plants can positively influence cell expansion and cell division. Relative to GmSSS1, one mutation leading to an E to Q substitution at the 182^nd residue in Gmsss1 conferred an enhancing effect on seed weight. GmSSS1 underwent diversification in wild-type and cultivated soybean, and the alleles encoding the Gmsss1-type substitution of 182^nd -Q, which originated along the central and downstream parts of the Yellow River, were selected and expanded during soybean domestication and improvement. We cloned the causative gene for the sss1 mutant, which is linked with a seed weight QTL, identified an elite allele of this gene for increasing seed weight, and provided new insights into soybean domestication and breeding.

Downregulation of a gibberellin 3β-hydroxylase enhances photosynthesis and increases seed yield in soybean

Seed yield, determined mainly by seed numbers and seed weight, is the primary target of soybean breeding. Identifying the genes underlying yield-related traits is of great significance. Through joint linkage mapping and a genome-wide association study for 100-seed weight, we cloned GmGA3ox1, a gene encoding gibberellin 3β-hydroxylase, which is the key enzyme in the gibberellin synthesis pathway. Genome resequencing identified a beneficial GmGA3ox1 haplotype contributing to high seed weight, which was further confirmed by soybean transformants. CRISPR/Cas9-generated gmga3ox1 mutants showed lower seed weight, but promoted seed yield by increasing seed numbers. The gmga3ox1 mutants reduced gibberellin biosynthesis while enhancing photosynthesis. Knockout of GmGA3ox1 resulted in the upregulation of numerous photosynthesis-related genes, particularly the GmRCA family encoding ribulose-1,5-bispho-sphate carboxylase-oxygenase (Rubisco) activases. The basic leucine zipper transcription factors GmbZIP97 and GmbZIP159, which were both upregulated in the gmga3ox1 mutants and induced by the gibberellin synthesis inhibitor uniconazole, could bind to the promoter of GmRCAβ and activate its expression. Analysis of genomic sequences with over 2700 soybean accessions suggested that GmGA3ox1 is being gradually utilized in modern breeding. Our results elucidated the important role of GmGA3ox1 in soybean yield. These findings reveal important clues for future high-yield breeding in soybean and other crops.

A legume-specific novel type of phytosulfokine, PSK-δ, promotes nodulation by enhancing nodule organogenesis

Phytosulfokine-α (PSK-α), a tyrosine-sulfated pentapeptide with the sequence YSO3IYSO3TQ, is widely distributed across the plant kingdom and plays multiple roles in plant growth, development, and immune response. Here, we report a novel type of phytosulfokine, PSK-δ, and its precursor proteins (MtPSKδ, LjPSKδ, and GmPSKδ1), specifically from legume species. The sequence YSO3IYSO3TN of sulfated PSK-δ peptide is different from PSK-α at the last amino acid. Expression pattern analysis revealed PSK-δ-encoding precursor genes to be expressed primarily in legume root nodules. Specifically, in Medicago truncatula, MtPSKδ expression was detected in root cortical cells undergoing nodule organogenesis, in nodule primordia and young nodules, and in the apical region of mature nodules. Accumulation of sulfated PSK-δ peptide in M. truncatula nodules was detected by LC/MS. Application of synthetic PSK-δ peptide significantly increased nodule number in legumes. Similarly, overexpression of MtPSKδ in transgenic M. truncatula markedly promoted symbiotic nodulation. This increase in nodule number was attributed to enhanced nodule organogenesis induced by PSK-δ. Additional genetic evidence from the MtPSKδ mutant and RNA interference assays suggested that the PSK-δ and PSK-α peptides function redundantly in regulating nodule organogenesis. These results suggest that PSK-δ, a legume-specific novel type of phytosulfokine, promotes symbiotic nodulation by enhancing nodule organogenesis.

Progress in soybean functional genomics over the past decade

Soybean is one of the most important oilseed and fodder crops. Benefiting from the efforts of soybean breeders and the development of breeding technology, large number of germplasm has been generated over the last 100 years. Nevertheless, soybean breeding needs to be accelerated to meet the needs of a growing world population, to promote sustainable agriculture and to address future environmental changes. The acceleration is highly reliant on the discoveries in gene functional studies. The release of the reference soybean genome in 2010 has significantly facilitated the advance in soybean functional genomics. Here, we review the research progress in soybean omics (genomics, transcriptomics, epigenomics and proteomics), germplasm development (germplasm resources and databases), gene discovery (genes that are responsible for important soybean traits including yield, flowering and maturity, seed quality, stress resistance, nodulation and domestication) and transformation technology during the past decade. At the end, we also briefly discuss current challenges and future directions.

Overexpression of PSK-γ in Arabidopsis promotes growth without influencing pattern-triggered immunity

Phytosulfokine-α (PSK-α) is a disulfated pentapeptide with the sequence YIYTQ. As a new peptide hormone, PSK-α promotes plant growth and development but represses pattern-triggered immunity (PTI) against bacterial pathogens. Our recent study identified a novel phytosulfokine, PSK-γ, from soybean. The sequence of PSK-γ is YVYTQ in which the tyrosines are sulfated. Expression of PSK-γ significantly increased seed size and weight in transgenic plants by inducing embryo cell expansion. In this study, we further found that the constitutive expression of PSK-γ in Arabidopsis promotes the growth of vegetative organs as well as seeds. Moreover, overexpressed PSK-γ does not influence plant PTI against bacterial pathogens. These findings demonstrate a potential use of PSK-γ in genetic improvement of crop growth and yield by molecular breeding.