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At least 19 recordsLinked to original sources
PubMed2026

A wild soybean MADS-box gene GsAGL62 improves seed weight by enhancing cytokinin signaling and cell proliferation.

Soybean seed weight is a key yield determinant, but the transcriptional mechanisms connecting hormone signaling to seed growth are poorly understood. Here, we identify GsAGL62, a wild soybean MADS-box transcription factor located within a previously mapped hundred-seed weight (HSW) locus and a domestication-associated selective sweep. Functional analyses show that overexpression of GsAGL62 in cultivated soybean significantly increases HSW, whereas ethyl methanesulfonate (EMS)-induced gmagl62 mutants reduce it. Integrated transcriptomic and metabolomic analyses reveal that GsAGL62 enhances cytokinin accumulation and signaling cytokinin-associated responses, accompanied by increased expression of genes involved in cell proliferation. Mechanistically, GsAGL62 directly binds to the promoter of the conserved growth inhibitor GmATPK2 and represses its transcription. Consistently, independent EMS-induced gmatpk2 mutants exhibit increased seed weight, supporting GmATPK2 as a downstream negative regulator of seed growth. Population genetic analyses further reveal strong differentiation of GsAGL62 promoter haplotypes during soybean domestication and improvement. These haplotypes show differential promoter activities and are associated with distinct agronomic performance, suggesting that cis-regulatory variation at GsAGL62 contributes to its selection during soybean improvement. Collectively, our findings establish a regulatory module linking GsAGL62 to cytokinin-associated responses, cell proliferation, and seed growth, and highlight GsAGL62 as a potential target for soybean yield improvement.

Cell proliferation↗
PubMed2025

The rice heat shock transcription factor OsHSFC1b increases seed weight, size, and vigor, but its function is disrupted by isoaspartyl modification.

Plant optimizes seed size, weight, vigor, and various other features during seed development, which are important not only for their successful propagation and establishment but also for effective agriculture. Despite several studies conducted, understanding how plants coordinate the regulatory mechanisms to achieve optimal seed size, weight, and vigor remains elusive. Here, our study reveals the role of rice heat shock transcription factor OsHSFC1b in modulating various seed attributes. We observe that OsHSFC1b expression increases during the later stage of seed development and is primarily localized in the embryo. We found that hsfc1b genome-edited lines exhibit compromised seed size, weight, and vigor, while overexpression lines exhibit increased seed size, weight, and vigor compared with the wild-type seeds. Our study further reveals that OsHSFC1b improves seed vigor by activating HSPs and RFO biosynthetic genes involved in protection mechanisms, while also mediating seed size and weight by modulating auxin biosynthesis, endosperm development, and seed filling. We found that upon ageing and stressful environments, OsHSFC1b undergoes isoaspartyl modification that negatively impacts its biological function in seeds. Our MS/MS analyses confirm that asparagine residues near the DNA-binding domain and nuclear localization sequence of OsHSFC1b undergo isoaspartyl modification that adversely affects OsHSFC1b's transactivation activity. However, PROTEIN L-ISOASPARTYL METHYLTRANSFERASE interacts and repairs this isoaspartate-mediated damage, and restores the function of OsHSFC1b. Taken together, our study uncovers how isoaspartyl modification affects the transactivation ability of OsHSFC1b, yet the intervention of PIMT not only repairs this damage but also elevates agronomically important seed traits.

Oryza↗
PubMed2026

Natural variation in GmSOP5 regulates seed oil and protein content during soybean domestication.

Seed oil content, protein content, and yield are agronomically important, correlated traits that determine the economic value of soybean (Glycine max). However, improving seed quality and yield simultaneously is challenging because gains in one breeding target often compromise the other, and the genetic basis of this trade-off is poorly understood. Here, we performed a genome-wide association study of 429 diverse soybean accessions and identified Seed Oil and Protein 5 (SOP5), which encodes a kinesin protein, as a key locus associated with seed oil and protein content. Knockout and overexpression experiments demonstrated that GmSOP5 positively affects seed oil content and 100-seed weight and negatively influences seed protein content. GmSOP5 is located in a selective sweep region, and the domestication-related GmSOP5H1 allele is nearly fixed in cultivated soybean, contributing to increased seed size, weight, and oil content and reduced protein content. Field trials demonstrated that neither loss-of-function GmSOP5-edited mutants, which have increased seed protein content, nor GmSOP5-overexpression lines, which have increased seed oil content, differed significantly in yield from wild-type plants, because changes in plant architecture were offset by changes in seed weight. Our results shed light on soybean domestication and suggest how pleiotropy can be harnessed in breeding to enhance seed quality without compromising yield.

GWAS↗
PubMed2025

Yield and yield component trait analysis with DArT genotyping for GWAS in soybean grown in drought conditions of Kazakhstan.

Development of drought tolerant cultivars of soybean is the single best way to address the challenge of global climate change and very limited water resources for crop irrigation in Central Asia including Kazakhstan. A set of 188 soybean cultivars with diverse origins was assessed for genome-wide association study (GWAS) for yield and eight yield-related traits in both irrigated (well-watered, WW) and non-irrigated (drought) conditions during 2 years in field trials in South-Eastern Kazakhstan. The 295K Diversity array technology (DArT) analysis was applied, and 16K filtered DArT markers were used for genotyping of 183 soybean accessions. In the results, 41 quantitative trait nucleotides (QTN) were identified as significantly associated with nine studied traits. To verify these results, bulk segregant analysis (BSA) was carried out in six breeding lines originating from two crosses between high-yielding under drought cvs, Sponsor and Zen, with drought sensitive cv Lastochka. The evaluation of combined results revealed 10 most significant QTN and eight most promising putative candidate genes, which were selected and tested for their gene expression using RT-qPCR under drought compared with WW controls. Among them, glucose-6-phosphate isomerase (G6PI), pentatricopeptide repeats (PPR) protein, and ABC transporter, associated with seed yield, seed weight per plant, and plant height, were highly upregulated in drought tolerant genotypes. In contrast, two other genes, Rab-GDP dissociation inhibitor (Rab-GDI) and Transducin with WD40 repeats, associated with seed yield, showed repression in the same genotypes. These verified genes involved in the control of yield and yield-related traits can be used for marker-assisted selection to develop novel genotypes and new soybean cultivars tolerant to strong drought in Kazakhstan and in other countries with similar conditions.

Diversity array technology (DArT)↗
PubMed2025

Large-scale screening of genes responsible for silique length and seed size in Brassica Napus via pooled CRISPR library.

BACKGROUND: Enhancing rapeseed (Brassica napus, B. napus) yield is critical for ensuring global vegetable oil security. However, yield is heavily influenced by silique development and seed size, the enhancement of which is limited by scarce genetic resources. The CRISPR/Cas9 system has emerged as a powerful tool for constructing genome-wide mutant libraries, even in polyploid crops with complex genomes. RESULTS: The transcriptome-wide association study (TWAS) data, tissue-specific expression profiles data and reported genes were integrated to identify candidate genes regulating silique development and seed size. We constructed a sgRNA library targeting these genes and generated a CRISPR/Cas9 editing mutant library through genetic transformation. Specifically, 6124 sgRNAs were designed for 1739 candidate genes with ≦ 4 orthologues. 681 T0 plants were obtained through genetic transformation, which harbor 453 sgRNAs. Of 408 T0 plants analyzed, 151 (37.00%) exhibited successful gene editing events, targeting 84 candidate genes. Ten homozygous mutant plants were isolated and preliminary phenotypic analysis was performed in mutants targeting the BnaHRDs. The results suggest that mutations in BnaHRD.A03 and BnaHRD.C03 may modulate plant height (PH), main inflorescence length (MIL), silique length (SL), effective silique number per plant (ENS), seed number per silique (SNPS), and thousand-seed weight (TSW). CONCLUSIONS: This study harnessed the CRISPR/Cas9 technology to establish a preliminary library of gene-edited mutants in B. napus, thereby laying a robust foundation for the future screening of candidate genes pertaining to silique development and seed size. Furthermore, this study provides a methodological framework for rapid functional gene discovery in B. napus through CRISPR-based approaches.

Brassica napus↗
PubMed2025

From bottleneck to boom: Polyploidy, genetic instability and response to artificial selection resolve the peanut paradox.

This study, the second in a three-part series, shows how peanut's polyploid origin enabled rapid diversification and enhanced domestication potential. Building on the knowledge that cultivated peanut (Arachis hypogaea) originated from a narrow hybridization between Arachis duranensis and Arachis ipaënsis less than 10 000 years ago, we are confronted with a paradox: how did such a narrow origin give rise to so much diversity-two subspecies, six botanical varieties, and thousands of landraces differing in growth habit, seed size, and pod morphology? Although several diploid Arachis species were cultivated earlier, only the allotetraploid became fully domesticated and widely adopted. The global success of peanut, despite its narrow genetic origin, suggests that polyploidization itself facilitated domestication. To test this hypothesis, we investigated how the two diploid progenitors and neoallotetraploids derived from a single hybridization and polyploidization event responded under artificial selection. In a pollinator-free greenhouse, we advanced lineages of the neoallotetraploid and its diploid parents over 6 years, selecting for divergent seed weights. The neoallotetraploid showed a much stronger response to artificial selection than its diploid parents, while also spontaneously generating diverse phenotypic variation-including flower color, pod reticulation, and chlorophyll content-traits that distinguish A. hypogaea subspecies and landraces. These traits mirrored directional shifts in parental genome dosage caused by homoeologous exchange, supporting a causal connection with phenotype. These findings offer a compelling rationale for a domestication advantage in polyploid peanut, and provide a living demonstration of how a single ancestral tetraploid, despite an extreme genetic bottleneck, generates a phenotypic boom.

Arachis↗
PubMed2026

Transgenic overexpression of GmAPC7-CT improves seed yield and reduces susceptibility to soybean mosaic virus and Meloidogyne incognita in soybean.

Stable transgenic soybean lines overexpressing the GmAPC7-CT gene have demonstrated increased seed yield and reduced susceptibility to the soybean mosaic virus and Meloidogyne incognita. The Anaphase-Promoting Complex subunit 7 (APC7) is a core structural component of the anaphase-promoting complex or cyclosome (APC/C). The terminal region of this AtAPC7 gene has been shown in Arabidopsis thaliana to accumulate more transcripts than the full-length gene. The AtAPC7-CT gene (terminal region of the AtAPC7) encodes a protein with significant homology to a tobacco viral replication inhibitor (IVR). Its stable overexpression in transgenic A. thaliana lines resulted in notable improvements in biomass, seed yield, earliness of vegetative-reproductive transitions, and reduced susceptibility to viruses. In this study, we generated stable transgenic soybean lines overexpressing the GmAPC7-CT gene (terminal region or 3' portion of Glyma.15G096000, corresponding to the AtAPC7-CT) and evaluated seed yield and susceptibility of these lines to soybean mosaic virus and Meloidogyne incognita. The GmAPC7-CT gene is 624 nucleotides long and encodes a 207-amino acid protein with two tetratricopeptide repeat (TPR) domains. GmAPC7-CT showed 100% amino acid identity with full-length GmAPC7, 81.16% identity with AtAPC7-CT, and 87.94% identity with tobacco IVR. Stable transgenic lines demonstrated significant advancements in plant development and seed yield, with the top three lines producing up to 43% more pods, 44% more seeds, and a 16% increase in seed weight. Furthermore, these soybean lines showed up to a 70% reduction in susceptibility to soybean mosaic virus and M. incognita, reflected by decreased viral RNA load and nematode reproduction factor. Collectively, these results support a conserved role of GmAPC7-CT in soybean and AtAPC7-CT in A. thaliana, acting similarly to the tobacco IVR. Thus, our findings underscore the strong biotechnological potential of the GmAPC7-CT gene to improve key agronomic traits in soybean through genetic engineering approaches, including conventional breeding, transgenesis, and genome editing.

Glycine max↗
PubMed2026

Generational variation and stabilization in resynthesized allotetraploid Brassica juncea derived from diploid progenitors B. rapa and B. nigra.

BACKGROUND: Polyploidy is a major driver of plant evolution and crop improvement, generating novel variation in morphology, physiology, and agronomic traits. Brassica juncea (AABB, 2n = 36), a natural allotetraploid derived from B. rapa (AA) and B. nigra (BB), is an important oilseed and vegetable crop; however, its narrow genetic base limits further breeding gains. Resynthesized B. juncea (RBJ), developed from known progenitors, provides a tractable system to investigate polyploid stabilization, trait diversification, and generational variation. This study evaluated RBJ across nine generations (F1-S8) to elucidate generational variation in morphological, molecular, cytological, and oil content traits during progressive stabilization. RESULTS: Substantial variation was observed for key yield-related traits, including siliqua length, seeds per siliqua, and thousand-seed weight. High estimates of heritability, genotypic variance, and genetic advance indicated their potential utility in selection based improvement. Comparative analyses revealed a clear generational progression, characterized by relatively enhanced performance in early generations, increased recombination-driven variability in intermediate generations, and the partial stabilization of several traits in later generations. Generation mean analysis suggested the involvement of additive, dominance, and epistatic gene effects in trait inheritance. Molecular analysis using SSR markers confirmed the amphidiploid origin and genomic integrity of RBJ generations. Cytological assessments, pollen viability assays, and flow cytometric analysis collectively demonstrated stable chromosome numbers, improved fertility, and maintenance of ploidy stability across successive generations. CONCLUSIONS: The study provides valuable insights into the generational variation and stabilization of morphological, molecular, and oil content traits in resynthesized B. juncea. The findings suggest that variability arising from polyploidization and interspecific hybridization undergoes gradual reorganization across successive generations, leading to increased trait stabilization and more consistent expression of selected agronomic characteristics. Collectively, these results contribute to the understanding of early stabilization processes in RBJ, highlighting resynthesized polyploids as useful systems for studying variation and stabilization in allopolyploid crops.

Mustard Plant↗
PubMed2025

Surprisingly frequent chromosomal instability in cultivated peanut.

This study, the third in a three-part series, investigates whether chromosomal instability persists in cultivated peanut. The allotetraploid peanut (Arachis hypogaea; genome type AABB) originated from the hybridization and polyploidization of A. duranensis (AA) and A. ipaënsis (BB). Our first study established that this was an extremely narrow genetic origin, likely from a single hybridization event. This raised a paradox: how did such narrow genetics give rise to the phenotypic diversity seen in cultivated peanut? The second study addressed this, showing that a single neoallotetraploid spontaneously generates striking diversity, and that homoeologous exchanges-abundant in early generations following polyploidy-are a key mechanism in creating this diversity. In contrast to this early-generation instability, cultivated peanut is generally considered to be genetically stable, presumably due to selection. This third study tests whether residual instability still occurs in modern peanut. From a single plant of the highly selfed 'genome stock' of the cultivar 'Tifrunner', we advanced lineages through seven generations in a pollinator-free greenhouse. Among 233 plants, we identified three new large-scale chromosomal instability events: a large deletion on chromosome B01, associated with reduced pod width and seed weight, and two ABBB compositions involving chromosomes A02/B02 and A05/B05. With these observations in hand, we reinterpreted previously published data from two recombinant inbred populations. Together, these results indicate that at least 1% of pure pedigree A. hypogaea plants exhibit spontaneous large-scale chromosomal changes-a surprising frequency of instability that likely contributes to peanut's long-term adaptability and evolution.

Arachis↗
PubMed2026

Branching plasticity and candidate gene-hormone networks associated with shade responses in soybean under relay strip intercropping.

BACKGROUND: Branching is a key determinant of high-yield plant architecture in soybean, particularly in maize- soybean relay strip intercropping where plants experience an "initially shaded-then fully illuminated" light regime. However, the genetic regulation of branching responses to shading remains poorly understood. METHODS: We evaluated 11 branching-related traits across 202 soybean accessions grown under monoculture (SS) and relay strip intercropping (RI). Branch number (BN), branching incidence (BI), and total branch length (TBL) were assessed together with stress tolerance indices (STI) and relative distance plasticity index (RDPI). Genome-wide association studies (GWAS) using mixed linear model (MLM) and three-variance-component MLM (3VmrMLM) were combined with haplotype and protein structural analyses to refine candidate genes. RESULTS: Based on Pearson correlation analysis of all 11 traits, BN, BI, and TBL measured before maize harvest showed the strongest and most consistent associations with branch seed weight within the corresponding cropping system (BSW_SS under SS and BSW_RI under RI), whereas other traits showed weaker or environment-dependent associations. Higher STI values calculated from these traits during the co-growth phase were negatively associated with BSW_RI, suggesting weaker compensatory recovery after light restoration in genotypes with more stable early branching patterns between SS and RI. In contrast, mediation analysis indicated that RDPI was positively associated with BSW_RI mainly through improved mature branching architecture (MB_index), which accounted for approximately 70% of the total positive effect. GWAS identified 57 and 74 significant QTNs using MLM and 3VmrMLM, respectively, and LD-window genes were filtered for exonic nonsynonymous or premature stop-codon variants, yielding 883 genes with putative functional variants. Two high-confidence genes emerged: Glyma.02G058600 (PP2C55), exhibiting shading-specific haplotype effects likely linked to GA-mediated branch-stem balance, and Glyma.02G059900 (DA1-related protein), showing stable effects across environments and implicated in ABA-mediated suppression of axillary meristems. CONCLUSIONS: These results provide insight into the genetic and physiological basis of soybean branching responses under relay strip intercropping, clarify that branching plasticity and relative shade tolerance represent distinct response dimensions in this system, and identify putative loci that may be useful for breeding soybean cultivars with improved shade adaptation and yield stability.

Glycine max↗
PubMed2026

Genomic early growth mechanisms of two endangered Mexican spruces.

This study elucidated the genomic basis of family-level growth variance in the critically endangered endemic Mexican spruces Picea martinezii and P. mexicana by: (i) analyzing family- and population-level variations in seedling basal diameter and height after 12 months of growth under common garden conditions and seed weight as maternal provisioning trait; and (ii) identifying genomic loci (SNPs) associated with these traits. Despite limited sample sizes (77 and 74 families representing all known populations of both species), 32 and 10 outlier SNPs were identified yielding 17 and six annotated candidate genes in P. martinezii and P. mexicana, respectively. These genes showed contrasting multivariate associations suggesting species-specific hypothesized growth strategies at the family level: defense-oriented framework in P. martinezii and plasticity-driven response in P. mexicana. Notably, several candidate genes encode key components of growth hormone pathways, including a gibberellin-regulated protein, a cytokinin hydroxylase and the AP2-like transcription factor ANT, providing valuable insights into how maternal genetic variation corresponds to the hormonal pathways that govern cell proliferation and organ size in the progeny. Integration of these findings with the contrasting demographic histories of both species revealed that population bottlenecks enhance the detectability of growth-associated variants by reducing background genetic variation. These genomic resources provide actionable information for prioritizing conservation measures, implementing assisted gene flow to maintain adaptive potential under climate change and designing future breeding programs. With 80.9-99.6% sequence identity to conserved Picea abies homologs, these findings may extend across the genus.

Picea↗
PubMed1975

Peanut alkaline lipase.

Peanut alkaline lipase, (glycerol ester hydrolase EC 3.1.1.3), pH optimum 8.5, was isolated from acetone powders prepared from developing and germinated peanut seed (arachis hypogaea L. var. NC-2). Enzyme activity/seed increased in successive developmental stages. The course of the hydrolytic reaction was linear with regard to enzyme concentration and all times tested up to periods exceeding 60 min. Km for the reaction was determined to be 2.6 times 10-4M. Molecular weight of peanut lipase, as estimated by Sephadex gel filtration and sodium dodecyl sulfate gel electrophoresis, was ca. 55,000.

Ammonium Sulfate↗
PubMed1978

alpha-Galactosidases II, III and IV from seeds of Trifolium repens. Purification, physicochemical properties and mode of galactomannan hydrolysis in vitro.

Five alpha-galactosidases (alpha-D-galactoside galactohydrolase, EC 3.2.1.22) were identified by chromatography and by their different electrophoretic mobilities, in the germinated seeds of Trifolium repens (white clover). alpha-Galactosidases II, III and IV were purified to homogeneity, with increases in specific activity of approx. 4600-, 4900- and 2800-fold respectively. The enzymes were purified by a procedure that included (NH4)2SO4 precipitation, hydroxyapatite, Sephadex G-75 and DEAE-cellulose chromatography, and preparative polyacrylamide-gel disc electrophoresis. The purified enzymes showed a single protein band, corresponding to the alpha-galactosidase activity, when examined by polyacrylamide-gel electrophoresis. The pH optimum was determined with o-nitrophenyl alpha-D-galactoside and the galactomannan of T. repens To as substrate. All three enzymes are highly thermolabile. Hydrolysis of oligosaccharides and galactomannans was examined, including two galactomannans from the germinated seed of T. repens (T24 and T36). By sodium dodecyl sulphate/polyacrylamide-gel electrophoresis the mol.wts. of the multiple forms of enzyme were found to be identical (41 000).

Galactans↗
PubMed1979

Albumins, glyoxysomal enzymes and globulins in dry seeds of cucumis sativus: qualitative and quantitative analysis.

1) Albumins and globulins were prepared from dry seeds of cucumbers (Cucumis sativus) by differential extraction. The globulin fraction was analyzed by gel electrophoresis under denaturing conditions in the presence and absence of mercaptoethanol. The subunit (Mr = 54000) of the tetramer (Mr = 240000) was shown to be composed of two different peptides. Microheterogeneity rendered the exact interpretation of the analysis difficult. 2) Glyoxysomal proteins were already present in dry seeds: malate synthase, isocitrate lyase, citrate synthase, malate dehydrogenase, catalase and crotonase could be detected unequivocally. It was demonstrated that the enzymatic and immunological properties of malate synthase and isocitrate lyase were not distinguishable from that of enzymes assigned to glyoxysomes of fully developed cotyledons. 3) Homogenates prepared from seeds by cautious cell disintegration were subjected to sucrose density gradient centrifugation and yielded microbody and protein body fractions, among other things.

Albumins↗
PubMed1978

Purification and properties of beta-mannanases I and II from the germinated seeds of Trifolium repens. Mode of galactomannan degradation in vitro.

Two beta-mannanases (beta-mannosidases, EC 3.2.1.25) purified from the germinated seeds of Trifolium repens by a procedure that included chromatography on hydroxyapatite, gel filtration on acrylamide/agarose (Ultragel 5/4) and preparative polyacrylamide-gel-electrophoresis. The final purification step completely resolved two beta-mannanases with distinct specificities, which were termed beta-mannanase I and beta-mannanase II. beta-Mannanase I was purified 1400-fold and beta-mannanase II 1000-fold. The purified enzymes showed a single protein band when examined by polyacrylamide-gel disc electrophoresis. beta-Mannanase I, apparent mol.wt. 43 000, accounted for 49% of the total activity recovered from the final step of purification. beta-Mannanase II, apparent mol.wt. 38 000, accounted for the remaining 51% of activity. Molecular-weight determinations were by sodium dodecyl sulphate/polyacrylamide-gel electrophoresis and by the electrophoretic method of Hendrick & Smith [(1968) Arch. Biochem. Biophys. 126, 155-164]. The substrate specificities of both enzymes were examined with the galactomannans of T. repens and of Medicago sativa, as well as with manno-oligosaccharides. The pH optimum was between pH 5.1 and 5.6 for both enzymes.

Enzyme Activation↗
PubMed1977

Purification and properties of an alpha-D-galactoside galactohydrolase from the seeds of Trifolium repens (white clover).

Five alpha-D-galactosidases (alpha-D-galactoside galactohydrolase; EC 3.2.1.22) have been identified by chromatography and polyacrylamide-disc-gel electrophoresis in the germinated seeds of Trifolium repens (white clover). alpha-Galactosidase I has been purified to homogeneity with an approx. 2000-fold increase in specific activity. The enzyme was purified by a procedure which included precipitation by dialysis against citrate/phosphate buffer, pH3.5; (NH4)2SO4 precipitation; hydroxyapatite, DEAE-cellulose and ECTEOLA-cellulose column chromatography. Each stage of purification was controlled by polyacrylamide-disc-gel electrophoresis; the purified enzyme showed a single protein band that corresponded to the alpha-D-galactosidic activity. The pH optimum was found to be between pH 3.8 and 4.2; the enzyme is highly thermolabile. Hydrolysis of oligosaccharides and galactomannans has been examined, and it has been found that alpha-galactosidase I exhibits two enzymic activities, namely alpha-D-galactoside galactohydrolase and galactosyltransferase. By the polyacrylamide-gel-electrophoresis method of Hendrick & Smith (1968), and by sodium dodecyl sulphate/polyacrylamide-gel electrophoresis, the mol.wt. has been estimated to be 43 000 and 41 000 respectively. These results indicate that alpha-galactosidase I is a monomeric protein and that both enzymic activities associated with the enzyme reside on the same polypeptide chain.

Chromatography↗