Genetic regulatory networks of soybean seed size, oil and protein contents

Duan, Zongbiao; Li, Qing; Wang, Hong; He, Xuemei; Zhang, Min

doi:10.3389/fpls.2023.1160418

Cited by 15 publications

(14 citation statements)

References 123 publications

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“…Soybeans are one of the world’s most important crops, covering 6% of global arable land and supplying 60% of oilseed production [ 1 , 2 ]. Soybean seeds are rich in protein, oil, micronutrients, flavonoids, and saponins, have become vital crops for human and livestock consumption, and have extensive industrial applications [ 3 ].…”

Section: Introductionmentioning

confidence: 99%

Rationally Designed Novel Antimicrobial Peptides Targeting Chitin Synthase for Combating Soybean Phytophthora Blight

Ran,

Shehzadi,

Liang

et al. 2024

IJMS

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Soybean phytophthora blight is a severe menace to global agriculture, causing annual losses surpassing USD 1 billion. Present crop loss mitigation strategies primarily rely on chemical pesticides and disease-resistant breeding, frequently surpassed by the pathogens’ quick adaptive evolution. In this urgent scenario, our research delves into innovative antimicrobial peptides characterized by low drug resistance and environmental friendliness. Inhibiting chitin synthase gene activity in Phytophthora sojae impairs vital functions such as growth and sporulation, presenting an effective method to reduce its pathogenic impact. In our study, we screened 16 previously tested peptides to evaluate their antimicrobial effects against Phytophthora using structure-guided drug design, which involves molecular docking, saturation mutagenesis, molecular dynamics, and toxicity prediction. The in silico analysis identified AMP_04 with potential inhibitory activity against Phytophthora sojae’s chitin synthase. Through three rounds of saturation mutagenesis, we pin-pointed the most effective triple mutant, TP (D10K, G11I, S14L). Molecular dynamic simulations revealed TP’s stability in the chitin synthase-TP complex and its transmembrane mechanism, employing an all-atom force field. Our findings demonstrate the efficacy of TP in occupying the substrate-binding pocket and translocation catalytic channel. Effective inhibition of the chitin synthase enzyme can be achieved. Specifically, the triple mutant demonstrates enhanced antimicrobial potency and decreased toxicity relative to the wild-type AMP_04, utilizing a mechanism akin to the barrel-stave model during membrane translocation. Collectively, our study provides a new strategy that could be used as a potent antimicrobial agent in combatting soybean blight, contributing to sustainable agricultural practices.

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Section: Introductionmentioning

confidence: 99%

Rationally Designed Novel Antimicrobial Peptides Targeting Chitin Synthase for Combating Soybean Phytophthora Blight

Ran,

Shehzadi,

Liang

et al. 2024

IJMS

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show abstract

“…Soybeans [Glycine max (L.) Merrill] are grown worldwide mainly for their high values in oil and protein, yielding over 360 million metric tons in 2020 [1]. The need for soybean production continues increasing as it is essential in feeding humans, animals, and the industries for producing biofuel, ethanol, among others [2][3][4].…”

Section: Introductionmentioning

confidence: 99%

Identification and Genetic Dissection of Resistance to Red Crown Rot Disease in a Diverse Soybean Germplasm Population

Antwi-Boasiako,

Jia,

Liu

et al. 2024

Plants

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Red crown rot (RCR) disease caused by Calonectria ilicicola negatively impacts soybean yield and quality. Unfortunately, the knowledge of the genetic architecture of RCR resistance in soybeans is limited. In this study, 299 diverse soybean accessions were used to explore their genetic diversity and resistance to RCR, and to mine for candidate genes via emergence rate (ER), survival rate (SR), and disease severity (DS) by a multi-locus random-SNP-effect mixed linear model of GWAS. All accessions had brown necrotic lesions on the primary root, with five genotypes identified as resistant. Nine single-nucleotide polymorphism (SNP) markers were detected to underlie RCR response (ER, SR, and DS). Two SNPs colocalized with at least two traits to form a haplotype block which possessed nine genes. Based on their annotation and the qRT-PCR, three genes, namely Glyma.08G074600, Glyma.08G074700, and Glyma.12G043600, are suggested to modulate soybean resistance to RCR. The findings from this study could serve as the foundation for breeding RCR-tolerant soybean varieties, and the candidate genes could be validated to deepen our understanding of soybean response to RCR.

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“…By interfering with well-established gene networks upstream and downstream, classical gene knock-out can lead to unintended pleiotropic effects, consistent with these notions. Scientists have advanced our understanding by revealing that plant systems biology, including seed development and maturation, involves complex and intricate gene networks (Duan et al, 2023). Although the regulatory network controlling SSPs in developing seeds is being elucidated, loss-of-function mutations in master regulators of seed maturation give rise to unwanted seed phenotypes, including a significant reduction of SSPs (Tang et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

Seed storage allergens tackled via next-generation research assistant

Evangelista,

Amoroso,

Nitride

et al. 2024

Front. Food. Sci. Technol.

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The expanding consumption of plant proteins in the diet to overcome the environmental issues associated with animal proteins is increasing the incidence of food-induced allergic reactions. One of the 21st-century research drivers in agriculture sciences is the development and validation of concrete approaches for modulating the expression of allergenic proteins in crops before harvesting. The increasing incidence of plant food allergies is primarily induced by seed storage proteins that clinicians are experiencing recently because of the more predominant use of plant-derived proteins in the food industry. Increased availability of high-throughput technologies has generated an ever-growing number of omics data, allowing us to have better structural knowledge of SSPs and molecular properties that can inform the allergenicity assessment. The recent systems for targeted genome engineering, without double-strand DNA breaks, allow the introduction of precise modifications directly into commercial plant species. Artificial intelligence is significantly transforming scientific research across every stage, assisting scientists, processing large-scale data, making predictions, automating tasks. During this epochal change, marked by the encounter between artificial intelligence and synthetic biology, a next-generation research assistant (NGA) is coming alive. Here, we propose a new conceptual vision to facilitate and speed up the editing of cross-reactivity sites to obtain hypoallergenic cultivars and avoid pleiotropic effects. Finally, we discuss the potential applications of this new way to conceive the research. NGA may be undoubtedly capable of managing the evolution of SPP allergies through the prediction of novel epitopes, as well as the prediction of immunological response mechanisms.

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Genetic regulatory networks of soybean seed size, oil and protein contents

Cited by 15 publications

References 123 publications

Rationally Designed Novel Antimicrobial Peptides Targeting Chitin Synthase for Combating Soybean Phytophthora Blight

Rationally Designed Novel Antimicrobial Peptides Targeting Chitin Synthase for Combating Soybean Phytophthora Blight

Identification and Genetic Dissection of Resistance to Red Crown Rot Disease in a Diverse Soybean Germplasm Population

Seed storage allergens tackled via next-generation research assistant

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