GmJAZ3 interacts with GmRR18a and GmMYC2a to regulate seed traits in soybean

Genome-wide survey and expression analysis of JAZ genes in watermelon (Citrullus lanatus)

BACKGROUND JAZ: (Jasmonate ZIM-domain) genes play important roles in plant growth and JA signaling pathway which is correlated with fruit ripening process. However, there have been few reports on the genome-wide identification of JAZ genes in watermelon and its relationship with fruit ripening. METHODS AND RESULTS: In this study, bioinformatics approaches were employed to identify ClaJAZ genes of watermelon at the genome-wide levels. Further exploration delved into the phylogenetic relationships, chromosomal mappings, promoter dynamics, expression, and architectural features of the JAZ genes. The results showed that a total of 9 ClaJAZ genes unevenly distributed across six chromosomes were identified in the watermelon genome, and they all have conserved Jas and TIFY domains. These JAZ genes were divided into four distinct groups with five genes involved in inter-chromosomal tandem duplication events, and members of the same subgroup exhibited a high degree of similarity in their gene structure and protein motif patterns. Analysis of the promoter regions of the ClaJAZ genes indicated the presence of cis-acting elements associated with hormonal responses, stress, and developmental processes. Gene expression analysis through real-time quantitative PCR (qRT-PCR) showed that there were spatiotemporal differences in the expression of ClaJAZ genes at various stages of fruit development. Among them, ClaJAZ7 has the highest level of transcriptional expression and showed strong promoter activity. CONCLUSIONS: This study conducted a comprehensive analysis of the ClaJAZ genes and provided insights into the role of ClaJAZ in the development and ripening of watermelon fruit.

Fruit traits of different variants of Zanthoxylum planispinum var. dingtanensis in the karst plateau valley area of Guizhou Province, Southwest China

BACKGROUND

Many studies have shown that seed traits, which are among the most important plant traits, can be inherited stably, a finding which is of great value for the improvement of seed germination, seed propagation, seedling establishment, plant breeding, and ecological restoration. The differences in phenotype and nutritional traits and their interactions in Zanthoxylum planispinum var. dingtanensis were ascertained, and the nutrient input rule and the strategy of resource balancing were analyzed in order to provide a scientific basis for the screening of improved variants of the test plant.

RESULTS

The nutrient distribution with in the tissues of Z. planispinum var. dingtanensis fruit was that the pericarp had adequate concentrations of N and P concentrations and the seed was also sufficient in P, but low in N concentration. Inorganic nutrients were particularly invested in the pericarp, while organic nutrients are more likely to be stored in the seed. In the economic spectrum of seed traits, the large leaf Zanthoxylum variant represented the low-investment economic type, the tufted leaf Zanthoxylum variant represented the high-investment luxury type, and the safflower Zanthoxylum and acutifoliate leaf Zanthoxylum variants represented transitional types.

CONCLUSIONS

Inorganic nutrients were more invested in the pericarp to produce secondary metabolites, while organic nutrients are more likely to be stored in the seed to ensure seed germination and seedling establishment in order to achieve inheritance. The variants of Z. planispinum var. dingtanensis differ in terms of resource allocation and balance, which could be further exploited through combining characters in breeding programs.

Transcriptional and Metabolomic Analyses Reveal That GmESR1 Increases Soybean Seed Protein Content Through the Phenylpropanoid Biosynthesis Pathway

Soybeans are an economically vital food crop, which is employed as a key source of oil and plant protein globally. This study identified an EREBP-type transcription factor, GmESR1 (Enhance of Shot Regeneration). GmESR1 overexpression has been observed to significantly increase seed protein content. Furthermore, the molecular mechanism by which GmESR1 affects protein accumulation through transcriptome and metabolomics was also identified. The transcriptomic and metabolomic analyses identified 95 differentially expressed genes and 83 differentially abundant metabolites during the seed mid-maturity stage. Co-analysis strategies revealed that GmESR1 overexpression inhibited the biosynthesis of lignin, cellulose, hemicellulose, and pectin via the phenylpropane biosynthetic pathway, thereby redistributing biomass within cells. The key genes and metabolites impacted by this biochemical process included Gm4CL-like, GmCCR, Syringin, and Coniferin. Moreover, it was also found that GmESR1 binds to (AATATTATCATTAAGTACGGAC) during seed development and inhibits the transcription of GmCCR. GmESR1 overexpression also enhanced sucrose transporter gene expression during seed development and increased the sucrose transport rate. These results offer new insight into the molecular mechanisms whereby GmESR1 increases protein levels within soybean seeds, guiding future molecular-assisted breeding efforts aimed at establishing high-protein soybean varieties.

RhMYC2 controls petal size through synergistic regulation of jasmonic acid and cytokinin signaling in rose

Petal size is determined by cell division and cell expansion. Jasmonic acid (JA) has been reported to be associated with floral development, but its regulatory mechanism affecting petal size remains unclear. Here, we reveal the vital role of JA in regulating petal size and the duration of the cell division phase via the key JA signaling component RhMYC2. We show that RhMYC2 expression is induced by exogenous treatment with methyl jasmonate and decreases from stage 0 to stage 2 of flower organ development, corresponding to the cell division phase. Furthermore, silencing RhMYC2 shortened the duration of the cell division phase, ultimately accelerating flowering opening and resulting in smaller petals. In addition, we determined that RhMYC2 controls cytokinin homeostasis in rose petals by directly activating the expression of the cytokinin biosynthetic gene LONELY GUY3 (RhLOG3) and repressing that of the cytokinin catabolism gene CYTOKININ OXIDASE/DEHYDROGENASE6 (RhCKX6). Silencing RhLOG3 shortened the duration of the cell division period and produced smaller petals, similar to RhMYC2 silencing. Our results underscore the synergistic effects of JA and cytokinin in regulating floral development, especially for petal size in roses.

Genome-Wide Identification, Phylogenetic, and Expression Analysis of Jasmonate ZIM-Domain Gene Family in Medicago Sativa L

JASMONATE ZIM domain (JAZ) proteins, inhibitors of the jasmonic acid (JA) signaling pathway, are identified in different plants, such as rice and Arabidopsis. These proteins are crucial for growth, development, and abiotic stress responses. However, limited information is available regarding the JAZ family in alfalfa. This study identified 11 JAZ genes (MsJAZs) in the "Zhongmu No.1" reference genome of alfalfa. The physical and chemical properties, chromosome localization, phylogenetic relationships, gene structure, cis-acting elements, and collinearity of the 11 MsJAZ genes were subsequently analyzed. Tissue-specific analysis revealed distinct functions of different MsJAZ genes in growth and development. The expression patterns of MsJAZ genes under salt stress conditions were validated using qRT-PCR. All MsJAZ genes responded to salt stress, with varying levels of upregulation over time, highlighting their role in stress responses. Furthermore, heterogeneous expression of MsJAZ1 in Arabidopsis resulted in significantly lower seed germination and survival rates in OE-2 and OE-4 compared to the WT under 150 mM NaCl treatment. This study establishes a foundation for further exploration of the function of the JAZ family and provides significant insights into the genetic improvement of alfalfa.

Transcription factor OsbZIP10 modulates rice grain quality by regulating OsGIF1

Understanding and optimizing the process of grain filling helps the quest to maximize rice (Oryza sativa L.) seed yield and quality, yet the intricate mechanisms at play remain fragmented. Transcription factors (TFs) are major players in the gene networks underlying the grain filling process. Here, we employed grain incomplete filling (OsGIF1)/cell wall invertase 2, a key gene involved in grain filling, to explore its upstream TFs and identified a bZIP family TF, OsbZIP10, to be a transcriptional activator of OsGIF1. Rice grains of the knockouts of OsbZIP10 showed increased white-core rates but lower amylose content (AC), leading to better eating and cooking qualities in all genetic backgrounds investigated, though the impact of mutations in OsbZIP10 on grain weight depended on genetic background. Multi-omics analyses suggested that, in addition to OsGIF1, multiple genes involved in different biological processes contributing to grain filling were targeted by OsbZIP10, including OsAGPS1, a gene encoding the ADP-Glc pyrophosphorylase (AGPase) small subunit, and genes contributing to homeostasis of reactive oxygen species. Distinct genetic make-up was observed in OsbZIP10 between japonica and indica rice varieties, with the majority varieties of each subspecies belonging to two different haplotypes that were closely associated with AC. Overexpressing the haplotype linked to high-AC in the low-AC genetic background increased AC. Overall, this study sheds crucial light on the significance of the OsbZIP10-OsGIF1 module in the determination of rice grain quality, offering a potential avenue for genetic engineering of rice to produce seeds with tailored attributes.

PagJAZ5 regulates cambium activity through coordinately modulating cytokinin concentration and signaling in poplar

Wood is resulted from the radial growth paced by the division and differentiation of vascular cambium cells in woody plants, and phytohormones play important roles in cambium activity. Here, we identified that PagJAZ5, a key negative regulator of jasmonate (JA) signaling, plays important roles in enhancing cambium cell division and differentiation by mediating cytokinin signaling in poplar 84K (Populus alba × Populus glandulosa). PagJAZ5 is preferentially expressed in developing phloem and cambium, weakly in developing xylem cells. Overexpression (OE) of PagJAZ5m (insensitive to JA) increased cambium activity and xylem differentiation, while jaz mutants showed opposite results. Transcriptome analyses revealed that cytokinin oxidase/dehydrogenase (CKXs) and type-A response regulators (RRs) were downregulated in PagJAZ5m OE plants. The bioactive cytokinins were significantly increased in PagJAZ5m overexpressing plants and decreased in jaz5 mutants, compared with that in 84K plants. The PagJAZ5 directly interact with PagMYC2a/b and PagWOX4b. Further, we found that the PagRR5 is regulated by PagMYC2a and PagWOX4b and involved in the regulation of xylem development. Our results showed that PagJAZ5 can increase cambium activity and promote xylem differentiation through modulating cytokinin level and type-A RR during wood formation in poplar.

Exploration of GmDof11-lncRNA13082 Module Regulating Oil Synthesis in Plants

Soybean (Glycine max [Linn.] Merr.) is an important oilseed crop. Although transcription factors (TFs) can coordinate the expression of mRNA and lncRNA, their coordination in the soybean oil synthesis pathway remains unclear. This study examined the interaction between the TF GmDof11 and lncRNA13082 and found that overexpression of GmDof11 led to an increase in the number of Arabidopsis seeds, thousand seed weight, crude protein, hydrolysis amino acid, and soluble sugar. Additionally, it reduced the triglyceride and starch contents and affected the proportion of fatty acids, increasing the contents of palmitic acid, stearic acid, and linolenic acid. The yeast two-hybrid experiments revealed that GmDof11 interacts with GmBCCP1, GmLEC1b, and GmFAB2 proteins. In the RT-qPCR analysis of transgenic soybean roots, it was found that GmDof11 can activate the production of lncRNA13082 and work in conjunction with lncRNA13082 to oversee oil synthesis and nutrient storage. Our research provides robust theoretical evidence for a comprehensive resolution of TF-lncRNA regulation in the soybean oil synthesis network.

Genome-wide identification of JAZ gene family members in autotetraploid cultivated alfalfa (Medicago sativa subsp. sativa) and expression analysis under salt stress

BACKGROUND

Jasmonate ZIM-domain (JAZ) proteins, which act as negative regulators in the jasmonic acid (JA) signalling pathway, have significant implications for plant development and response to abiotic stress.

RESULTS

Through a comprehensive genome-wide analysis, a total of 20 members of the JAZ gene family specific to alfalfa were identified in its genome. Phylogenetic analysis divided these 20 MsJAZ genes into five subgroups. Gene structure analysis, protein motif analysis, and 3D protein structure analysis revealed that alfalfa JAZ genes in the same evolutionary branch share similar exon‒intron, motif, and 3D structure compositions. Eight segmental duplication events were identified among these 20 MsJAZ genes through collinearity analysis. Among the 32 chromosomes of the autotetraploid cultivated alfalfa, there were 20 MsJAZ genes distributed on 17 chromosomes. Extensive stress-related cis-acting elements were detected in the upstream sequences of MsJAZ genes, suggesting that their response to stress has an underlying function. Furthermore, the expression levels of MsJAZ genes were examined across various tissues and under the influence of salt stress conditions, revealing tissue-specific expression and regulation by salt stress. Through RT‒qPCR experiments, it was discovered that the relative expression levels of these six MsJAZ genes increased under salt stress.

CONCLUSIONS

In summary, our study represents the first comprehensive identification and analysis of the JAZ gene family in alfalfa. These results provide important information for exploring the mechanism of JAZ genes in alfalfa salt tolerance and identifying candidate genes for improving the salt tolerance of autotetraploid cultivated alfalfa via genetic engineering in the future.

Knockout of miR396 genes increases seed size and yield in soybean

Yield improvement has long been an important task for soybean breeding in the world in order to meet the increasing demand for food and animal feed. miR396 genes have been shown to negatively regulate grain size in rice, but whether miR396 family members may function in a similar manner in soybean is unknown. Here, we generated eight soybean mutants harboring different combinations of homozygous mutations in the six soybean miR396 genes through genome editing with clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated nuclease (Cas)12SF01 in the elite soybean cultivar Zhonghuang 302 (ZH302). Four triple mutants (mir396aci, mir396acd, mir396adf, and mir396cdf), two quadruple mutants (mir396abcd and mir396acfi), and two quintuple mutants (mir396abcdf and mir396bcdfi) were characterized. We found that plants of all the mir396 mutants produced larger seeds compared to ZH302 plants. Field tests showed that mir396adf and mir396cdf plants have significantly increased yield in growth zones with relatively high latitude which are suited for ZH302 and moderately increased yield in lower latitude. In contrast, mir396abcdf and mir396bcdfi plants have increased plant height and decreased yield in growth zones with relatively high latitude due to lodging issues, but they are suited for low latitude growth zones with increased yield without lodging problems. Taken together, our study demonstrated that loss-of-function of miR396 genes leads to significantly enlarged seed size and increased yield in soybean, providing valuable germplasms for breeding high-yield soybean.

A novel miR160a-GmARF16-GmMYC2 module determines soybean salt tolerance and adaptation

Salt stress is a major challenge that has a negative impact on soybean growth and productivity. Therefore, it is important to understand the regulatory mechanism of salt response to ensure soybean yield under such conditions. In this study, we identified and characterized a miR160a-GmARF16-GmMYC2 module and its regulation during the salt-stress response in soybean. miR160a promotes salt tolerance by cleaving GmARF16 transcripts, members of the Auxin Response Factor (ARF) family, which negatively regulates salt tolerance. In turn, GmARF16 activates GmMYC2, encoding a bHLH transcription factor that reduces salinity tolerance by down-regulating proline biosynthesis. Genomic analysis among wild and cultivated soybean accessions identified four distinct GmARF16 haplotypes. Among them, the GmARF16H3 haplotype is preferentially enriched in localities with relatively saline soils, suggesting GmARF16H3 was artificially selected to improve salt tolerance. Our findings therefore provide insights into the molecular mechanisms underlying salt response in soybean and provide valuable genetic targets for the molecular breeding of salt tolerance.

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.

Protoplast transient expression-based RNA-sequencing: A simple method to screen transcriptional regulation in plants

Protoplast transient expression-based RNA-sequencing identifies Opaque2 targets supported by molecular evidence and expression quantitative trait loci.

Regulation of seed traits in soybean

Soybean (Glycine max) is an essential economic crop that provides vegetative oil and protein for humans, worldwide. Increasing soybean yield as well as improving seed quality is of great importance. Seed weight/size, oil and protein content are the three major traits determining seed quality, and seed weight also influences soybean yield. In recent years, the availability of soybean omics data and the development of related techniques have paved the way for better research on soybean functional genomics, providing a comprehensive understanding of gene functions. This review summarizes the regulatory genes that influence seed size/weight, oil content and protein content in soybean. We also provided a general overview of the pleiotropic effect for the genes in controlling seed traits and environmental stresses. Ultimately, it is expected that this review will be beneficial in breeding improved traits in soybean.

Global analysis of seed transcriptomes reveals a novel PLATZ regulator for seed size and weight control in soybean

Seed size and weight are important factors that influence soybean yield. Combining the weighted gene co-expression network analysis (WGCNA) of 45 soybean accessions and gene dynamic changes in seeds at seven developmental stages, we identified candidate genes that may control the seed size/weight. Among these, a PLATZ-type regulator overlapping with 10 seed weight QTLs was further investigated. This zinc-finger transcriptional regulator, named as GmPLATZ, is required for the promotion of seed size and weight in soybean. The GmPLATZ may exert its functions through direct binding to the promoters and activation of the expression of cyclin genes and GmGA20OX for cell proliferation. Overexpression of the GmGA20OX enhanced seed size/weight in soybean. We further found that the GmPLATZ binds to a 32-bp sequence containing a core palindromic element AATGCGCATT. Spacing of the flanking sequences beyond the core element facilitated GmPLATZ binding. An elite haplotype Hap3 was also identified to have higher promoter activity and correlated with higher gene expression and higher seed weight. Orthologues of the GmPLATZ from rice and Arabidopsis play similar roles in seeds. Our study reveals a novel module of GmPLATZ-GmGA20OX/cyclins in regulating seed size and weight and provides valuable targets for breeding of crops with desirable agronomic traits.

Genome-wide association study and RNA-seq identifies GmWRI1-like transcription factor related to the seed weight in soybean

The cultivated soybean (Glycine max (L.) Merrill) is domesticated from wild soybean (Glycine soja) and has heavier seeds with a higher oil content than the wild soybean. In this study, we identified a novel candidate gene associated with SW using a genome-wide association study (GWAS). The candidate gene GmWRI14-like was detected by GWAS analysis in three consecutive years. By constructing transgenic soybeans overexpressing the GmWRI14-like gene and gmwri14-like soybean mutants, we found that overexpression of GmWRI14-like increased the SW and increased total fatty acid content. We then used RNA-seq and qRT-PCR to identify the target genes directly or indirectly regulated by GmWRI14-like. Transgenic soyabeans overexpressing GmWRI14-like showed increased accumulation of GmCYP78A50 and GmCYP78A69 than non-transgenic soybean lines. Interestingly, we also found that GmWRI14-like proteins could interact with GmCYP78A69/GmCYP78A50 using yeast two-hybrid and bimolecular fluorescence complementation. Our results not only shed light on the genetic architecture of cultivated soybean SW, but also lays a theoretical foundation for improving the SW and oil content of soybeans.