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At least 19 recordsLinked to original sources
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↗
PubMed1976

Physico-chemical studies on the 11S globulin in soybean seeds: size and shape determination of the molecule.

The molecular shape of the 11S globulin, the major storage protein of soybean seeds, was estimated to be an oblate ellipsoid with a revolution axial ratio of 8.11-8.38 with or without scarce hydration according to the procedure of Simha & Perrin by measuring the partial specific volume, diffusion coefficient, molecular weight and volume fraction intrinsic viscosity. The length of the major axis of the molecule is 178-180 A and that of the minor axis 22 A. Subsequently, the shape factor beta, and the hydrodynamically effective volume, Ve, of the protein were calculated by the procedure of Scheraga & Mandelkern. Consequently, the 11S globulin molecule was also an oblate ellipsoid from beta. Ve was found to be equal to MV/N, the anhydrous volume of protein. It was therefore concluded that the protein existed in a rigid and nearly anhydrous state in solution.

Globulins↗
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↗
PubMed2025

Functional analysis of a GWAS pleiotropic hotspot suggests an auxin biosynthesis gene (AhPDS1), regulating pod development in peanut (Arachis hypogaea L.).

Peanut productivity and quality improvement rely on understanding the genetic factors influencing pod and seed size. This study aims to identify genetic factors and regulatory mechanisms influencing pod and seed size in peanuts. Herein, a genome-wide association study (GWAS) was conducted using 390 accessions from 15 peanut growing regions to analyze pod and seed traits across multiple planting seasons. A significant phenotypic variation was observed, with broad-sense heritability ranging from 53.6 to 85.4%. Strong correlations between pod and seed traits further suggest potential for co-selection in breeding efforts. A pleiotropic hotspot on chromosome B06 was strongly associated with six pod and seed traits. A peanut pod size regulator AhPDS1 (PODSIZE-1, Ahy_B06g085516) homolog of Arabidopsis thaliana YUCCA4 (AtYUC4, AT5G11320), involved in auxin biosynthesis, was selected as a candidate regulating pod and seed size. Quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) confirmed higher AhPDS1 expression in large pod as compared with the small pod genotypes. Subcellular localization showed AhPDS1 to be predominantly cytoplasmic, and GUS reporter assays indicated widespread expression in roots, stems, leaves, flowers, and pods, suggesting a broad functional role. Further overexpression of AhPDS1 in Arabidopsis and rice enhanced pod, seed, and grain sizes via the indole-3-pyruvic acid pathway in transgene lines. These findings highlight AhPDS1 as a potential target for peanut molecular breeding, offering opportunities to enhance pod size via auxin biosynthesis and support sustainable crop improvement.

Arachis↗
PubMed1985

Grasping in the pigeon (Columba livia): final common path mechanisms.

A combination of cinematographic and denervation procedures were used to analyse the mechanisms involved in the adjustment of gape size during grasping in the pigeon. Gape size was found to vary directly with seed size and to reflect the operation of two variables, jaw opening velocity and jaw opening duration. Effects upon duration are mediated, indirectly, by the effect of seed size upon head height, which, in turn, controls the velocity of head descent. The data suggest that the control of gape during grasping may involve two different effector systems (jaw muscles, neck muscles). Analysis of the displacement of individual jaws (maxilla, mandible) during grasping indicates that both opener muscles take part in the control of gape. Denervation experiments (motor nerve section) identified these opener motoneurons as contributors to the final common path for the opening phase of grasping. A comparison of the kinematics of pecking/grasping in pigeons and reaching/grasping in humans reveals a number of similarities in the topography and spatiotemporal organization of these behaviors.

Animals↗
PubMed2026

Natural variation in Miniature5 determines mitochondrial nad1 splicing and seed development in maize.

Seed size is a key determinant of cereal grain yield, but natural variations in defective-kernel genes have rarely been applied in maize breeding. Here, we report the positional cloning of maize Miniature5 (Mn5), which encodes a mitochondrial-targeted P-class pentatricopeptide repeat (PPR) protein. Further analysis shows that a missense mutation of Mn5, Mn5Val109, presents in maize populations and correlates with reduced seed size. The Mn5Val109 variant exhibits compromised function in the miniature5 (mn5-ref) mutant, failing to trans-splice mitochondrial nad1 intron1, drastically reducing the abundance and activity of respiratory complex I, accompanied by disorganized mitochondrial cristae. Mn5 directly binds to domain IV of the pre-nad1.1 transcript. Notably, this binding site is located downstream of the previously presumed 3'-terminus bound by MITOCHONDRIA STABILITY/PROCESSING PPR FACTOR1 (MSP1), thus redefining the 3'-end of the nad1.1 pre-RNA. Furthermore, Mn5 physically interacts with the maturases ZmnMAT1 and ZmnMAT3, as well as the PPR proteins PPR-SMR1 and SPR2, which are broadly involved in organellar group II intron splicing. Together, our results suggest that Mn5 recruits maturases and PPR proteins to form spliceosomal complexes responsible for the trans-splicing of nad1 intron1. Importantly, natural variations in Mn5 confer differences in seed size control, offering potential for breeding high-yield maize varieties.

Zea mays↗
PubMed2025

CRISPR-Cas9-mediated knockout of OsKCS11 in rice reveals potential crosstalk between very-long-chain fatty acids and cytokinin.

Very-long-chain fatty acids (VLCFAs) play crucial roles in various physiological processes in plants. Through our investigation using a CRISPR-Cas9 knockout mutant library in rice, we identified a semi-dwarf rice mutant named CRISPR-Cas-based dwarf-1 (csd-1). This mutant displayed multiple developmental defects, such as decreased plant height, panicle length, seed size, and seed-setting rate. Whole-genome resequencing analysis revealed that a T-nucleotide insertion in β-ketoacyl-CoA synthase 11 (KCS11), responsible for the initial step in fatty acid elongation, was responsible for the observed defects in csd-1. The identity of csd-1 was confirmed through genetic complementation and CRISPR-Cas9-mediated knockout. Expression analysis indicated that OsKCS11 was present in various tissues, with differential abundance observed through RT-qPCR and promoter GUS staining, and strong localization at the node position by RNA in situ hybridization; furthermore, OsKCS11 protein was confirmed to be in the endoplasmic reticulum. Furthermore, csd-1 exhibited significantly reduced levels of linolenic acid (18:3), C24:0-OH, C28:0-alkanes, C29:0-alkanes, alpha-tocopherol, and C33:0-alkanes, while trans-nonadecenoic acid and behenic acid levels were increased. Cytokinin analysis revealed significant increases in isopentenyladenine (IPA) and cis-zeatin (cZ) levels in csd-1. Molecular investigations indicated upregulation of genes involved in cytokinin biosynthesis or signaling, suggesting a potential link between VLCFAs and cytokinin synthesis through acetyl-CoA. This study not only proposed an alternative gene mapping method based on whole-genome resequencing but also elucidated the mechanism by which VLCFAs influence cytokinin synthesis and signaling.

Oryza↗
PubMed2026

Assessment of genomic prediction and genetic gain in multi‑population half-sib families in the perennial grass crop intermediate wheatgrass.

The University of Minnesota has been domesticating the perennial forage intermediate wheatgrass (IWG) since 2011 using a combination of conventional methods and modern breeding tools such as genomic selection. Globally, most IWG selection nurseries are spaced-planted individuals of several hundred genotypes whereas commercial fields established for grain production are row-planted panmictic populations. This study evaluated genomic prediction models and estimated genetic gain in yield and agronomic performance of row-planted IWG half-sib families assessed over 3 years and 2 locations, Lamberton and St. Paul, MN, USA. The strongest trait correlation was negative (r = -0.49) between 2023 St. Paul height and 2022 St. Paul seed size. The three St. Paul environments were more similar for plant height and seed size and so were the Lamberton environments yet no specific trend was observed for grain yield. Evaluation of different univariate and multivariate genomic prediction models showed that multivariate models outperformed the best univariate models by 23 percentage points, yet no single multivariate model was the best predictor of all traits. Cross-environment predictions were the best among St. Paul environments and no single environment was the best predictor of the remaining environments. Genetic gain estimates indicated a 20 kg ha-1 increase in grain yield and 3 cm reduction in plant height per breeding cycle. While no single model predicted all traits with high accuracy, results obtained in this study suggest that evaluating IWG sibs in row plots followed by genomic trait predictions could lead to desired breeding progress for desired traits.

Poaceae↗
PubMed1985

Sunflower seed protein: size and charge heterogeneity in subunits of the globulin fraction.

The subunit heterogeneity of the globulin fraction of sunflower seeds was investigated by two dimensional electrophoresis, using isoelectric focusing in the first dimension and sodium dodecyl sulphate polyacrylamide gel electrophoresis in the second dimension. Under non reducing conditions, intermediary subunits B, C and D (molecular weight 54 000, 48 000 and 40 000, respectively) were focused within a pI range 5.4-6.0 but intermediary subunits A (molecular weight 60 000) focused within a pI range 6.3-6.8. Under reducing conditions the electrophoretic patterns show that intermediary subunits consist in large "acidic" and small "basic" subunits linked by disulphide bonds. The large subunits of B species are more acidic and less heterogeneous than the corresponding subunits of the A species. These results confirm that helianthinin had a "legumin-type" structure.

2S Albumins, Plant↗
PubMed2026

Dissecting genetic architecture of growth and yield traits in horsegram using GWAS.

Horsegram (Macrotyloma uniflorum), a member of the Fabaceae family, is a nutritious and low-cost legume used for both grain and fodder. This study employed a genome-wide association approach to identify loci linked to key agronomic traits in horsegram. Plant height, seed size, and shoot fresh weight were evaluated in a panel of 96 diverse genotypes. GBS was performed using the Illumina HiSeq platform, yielding 20,241 high-quality SNPs after filtering at a 5% minor allele frequency. Population structure analysis classified genotypes into three admixed subgroups. Phenotyping was conducted over three consecutive years at two locations in Himachal Pradesh (Palampur and Bajaura) using a randomized block design with two replications. GWAS analyses using GLM, MLM, FarmCPU, and BLINK models identified eight markers for plant height, three for seed size, and five for shoot fresh weight across different chromosomes. These markers provide valuable tools for accelerating trait improvement in future horsegram breeding programs.

Genome-Wide Association Study↗
PubMed1992

[Physical, technological, and protein characteristics of wild and cultivated beans (Phaseolus vulgaris L.)].

The main purpose of this work was to observe and compare some physical, technological and proteinic characteristics of four bean seed cultivars developed in Mexico, eight wild bean seed accessions collected in Mexico and four wild bean seed accessions collected in South America. All of them belong to the species Phaseolus vulgaris L. In the South American materials the seed size was very similar (mean = 10.4 g/100 seeds). Nevertheless the water absorption was variable 36-64%, the percentages of seed coat and solids were statistically alike, the protein content range varied from 23.8 to 27.2% d.b. In the Mexican wild beans were found the smallest seeds (2.8 g/100 seeds) and those in which the water absorption percentage was very small. These two variables were correlated (r = 0.83**); they have the biggest amount of seed coat and during cooking lose a small quantity of solids. The protein content range was 21.3-24.6%. The lysine quantity was low. The cultivated material had the best physical and technological characteristics, but the average protein content of the group (X = 22.3%) was the lowest, the lysine and tryptophan amounts were 1.14 and 0.36%, respectively. The linear regression coefficient between cooking time and the percentage of cooked seeds was different in the members of each group. After 200 minutes only 85% of the South American accessions were cooked, whereas in the wild Mexican accession 153 only 40% was cooked; accessions 147, 148, 153 and 175 represented a group with long and irregular cooking time; accessions 631, 882, 900 and 939, likewise the cultivated materials Bayomex and Negro Puebla were 100% cooked in 140 minutes. Jamapa needed only 100 minutes in order to be completely cooked.

Absorption↗
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↗
PubMed1988

Preliminary study of the factors that determine nutrient composition of bean-cooking broth.

Bean cooking broth or liquor is a food preparation that results from cooking beans under a number of circumstances. This preparation is the first bean-derived food provided by mothers to their children as young as two months of age. Because of this, bean cooking plays an important nutritional role that must be evaluated. The present study attempted to evaluate, through a number of experiments, the significance of cultivars, method of cooking--either under atmospheric or vapor pressure--cooking time, salt addition, soaking and grain size on bean broth content. This was established mainly by solid content, and also by protein, ash and tannin content in different experiments. The results indicated that cultivars, but mainly cooking and soaking time, cooking method, and seed size were all important factors in determining brean-broth composition, mainly of total solids. Protein and ash contents were less affected. Prolonged cooking of the bean-broth resulted in a decrease in polyphenolic content. The relative nutritional importance of the above factors should be studied further.

Cooking↗
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

Analysis of deep-resequencing data of 984 soybean accessions reveals structural variations underlying agronomic traits.

Genomic structural variants (SVs) are major sources of genetic variation and have profound impacts on phenotypic traits. However, their functional effects remain largely unexplored in soybean. Here, we resequence 940 soybean accessions. Together with 44 publicly available datasets, we identify 602,281 SVs. Using a graph-based genome, we detect an additional 58,760 presence/absence variations (PAVs) that broadly affect gene expression. Population genomic analyses reveal that SVs serve as a core driving force for soybean domestication and improvement. Integrating SVs with QTLs for oil and protein content, and performing GWAS on 27 traits, we identify key functional SVs. These include transposable element insertions altering seed coat color, multiple insertions within a cytochrome P450 gene modifying flower and hypocotyl color, and a GmMATE1 deletion enhancing seed size. Together, our study establishes a comprehensive SV map of soybean, offering a valuable resource for dissecting the genetic basis of complex traits to accelerate molecular breeding.

Glycine max↗
PubMed1986

Cooperative polymerization reactions. Analytical approximations, numerical examples, and experimental strategy.

How does one obtain kinetic rate constants from the time course of a reversible and cooperative polymerization reaction? We examine a simple version of the homogeneous nucleation-elongation model with both analytical and numerical techniques to test some common assumptions and develop an experimental strategy. The assumption of irreversible polymer formation is found to be a useful and adequate approximation for the numerical determination of monomer disappearance. The assumption of early "pre-equilibrium" between monomer and seed, however, is shown numerically and analytically to produce significant errors over a wide range of parameters, particularly for small seed lengths. We exhibit numerical solutions for many different parameters, and also discuss analytical techniques that allow approximate solutions for several conditions: the high-concentration limit; the long-time limit; and the long-seed-length, lows concentration limit. The overall reaction simplifies when the monomer concentration is large. An experimental strategy for elucidating the seed size and the rate constants for polymerization and depolymerization is presented.

Biopolymers↗
PubMed1985

Salmonella isolation with Rappaport-Vassiliadis enrichment medium seeded with different sized inocula of pre-enrichment cultures of meat products and sewage polluted water.

A total of 574 samples, of seven different types, were examined for the presence of salmonellas. All the specimens were pre-enriched in buffered peptone water and enriched in Rappaport-Vassiliadis medium (RV medium). In one trial 0.1 ml of pre-enrichment culture of 497 samples (79 chicken carcasses, 228 specimens of minced meat, 100 pork sausages, 19 samples of dried powdered chicken meat, 11 specimens of faeces of healthy pigs and 60 samples of sewage polluted natural sea water) was seeded to 10 ml as well as to 100 ml of RV medium. With the first inoculum (ratio 0.1:10), 111 samples were found to contain salmonellas, while with the second inoculum (ratio 0.1:100), only 102 positive samples were detected. This difference is marginally significant (P less than 0.05). In another trial, 0.1 ml, 0.2 ml and 0.5 ml of pre-enrichment culture of 162 specimens (71 chicken carcasses, 40 samples of sewage polluted sea water and 51 samples of sewage polluted river water) were in turn introduced to 10 ml of RV medium. With the 0.1 ml inoculum 93 positive samples were detected, while with the 0.2 and 0.5 ml inocula 93 and 88 positive samples were found. The differences are not statistically significant. In these trials the growth of competing organisms was minimal with ratios of inocula 0.1:10 or 0.1:100.

Animals↗