Agronomy

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18 pages, 5160 KiB

Open AccessArticle

A Soybean Pyrroline-5-Carboxylate Dehydrogenase GmP5CDH1 Modulates Plant Growth and Proline Sensitivity

by Shupeng Dong, Zhuozhuo Mao, Zhongyi Yang, Xiao Li, Dezhou Hu, Fei Wu, Deyue Yu and Fang Huang

Agronomy 2024, 14(10), 2411; https://doi.org/10.3390/agronomy14102411 - 18 Oct 2024

Viewed by 436

Abstract

Soybean [Glycine max (L.) Merr.], as a globally commercialized crop, is an important source of protein and oil for both humans and livestock. With more frequent extreme weather disasters, abiotic stress has become one of the critical factors restricting soybean production. Proline [...] Read more.

Soybean [Glycine max (L.) Merr.], as a globally commercialized crop, is an important source of protein and oil for both humans and livestock. With more frequent extreme weather disasters, abiotic stress has become one of the critical factors restricting soybean production. Proline (Pro) is a well-known substance in plants that responds to abiotic stress. To identify potential effector genes involved in soybean resistance to abiotic stress, we focused on the pyrroline-5-carboxylate dehydrogenase (P5CDH) which is a key enzyme in the degradation process of Pro. Through homologous sequence alignment, phylogenetic tree, and predicted expression, we chose GmP5CDH1 (Glyma.05G029200) for further research. Tissue-specific expression assay showed that GmP5CDH1 had higher expression levels in soybean seed and cotyledon development. Subcellular localization assay revealed that GmP5CDH1 was a nuclear-membrane-localized protein. As the result of the predicted cis-acting regulatory element indicates, the expression level of GmP5CDH1 was induced by low temperature, drought, salt stress, and ABA in soybean. Next, we constructed transgenic Arabidopsis overexpressing GmP5CDH1. The results showed that GmP5CDH1 also strongly responded to exogenous Pro, and overcame the toxicity of abiotic stress on plants by regulating the endogenous concentration of Pro. The interaction between GmP5CDH1 and GmSAM1 was validated through yeast two-hybrid, LUC fluorescence complementary, and BIFC. In conclusion, overexpression of a soybean pyrroline-5-carboxylate dehydrogenase GmP5CDH1 regulates the development of Arabidopsis thaliana by altering proline content dynamically under salt stress, especially improving the growth of plants under exogenous Pro. Full article

(This article belongs to the Special Issue Functional Genomics and Molecular Breeding of Soybeans)

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13 pages, 2756 KiB

Open AccessArticle

Resistance Analysis of a Soybean Cultivar, Nongqing 28 against Soybean Cyst Nematode, Heterodera glycines Ichinohe 1952

by Changjun Zhou, Yanfeng Hu, Yingpeng Han, Gang Chen, Bing Liu, Jidong Yu, Yaokun Wu, Jianying Li, Lan Ma and Jian Wei

Agronomy 2024, 14(9), 1964; https://doi.org/10.3390/agronomy14091964 - 30 Aug 2024

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Abstract

The soybean cyst nematode (SCN), Heterodera glycines Ichinohe, 1952, is one of the most destructive plant-parasitic nematodes in soybean production worldwide. The use of resistant soybean is the most effective alternative for its management. However, SCN-resistant soybean cultivars with increased yield and favorable [...] Read more.

The soybean cyst nematode (SCN), Heterodera glycines Ichinohe, 1952, is one of the most destructive plant-parasitic nematodes in soybean production worldwide. The use of resistant soybean is the most effective alternative for its management. However, SCN-resistant soybean cultivars with increased yield and favorable agronomic traits remain limited in the market. Here, we developed a new SCN-resistant soybean cultivar Nongqing 28 from the cross of the female parent cultivar An 02-318 and a male parent line F2 (Hei 99-980 × America Xiaoheidou). Resistance evaluation suggested that Nongqing 28 displayed stable resistance to SCN race 3 in pot assays and the 5-year field experiments, including inhibition of SCN development and reduction in female and cyst numbers. The average yields of Nongqing 28 were 2593 kg/ha and 2660 kg/ha in the 2-year regional trails and the 1-year production trials, with a yield increase of 6.2% and 8.1% compared with the local cultivar Nengfeng 18, respectively. The average seed fat contents in Nongqing 28 reached 21.26%. Additionally, RNA-seq analysis revealed that the resistance of Nongqing 28 to SCN infection is involved in pathogen perception and defense activation, such as reactive oxygen species burst, calcium-mediated defense signaling, hormonal signaling, the MAPK signaling cascade, and phenylpropanoid biosynthesis. In summary, this study provides a detailed characterization of a novel SCN-resistant soybean cultivar with high oil and yield potential. Full article

(This article belongs to the Special Issue Functional Genomics and Molecular Breeding of Soybeans)

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17 pages, 4630 KiB

Open AccessEditor’s ChoiceArticle

Identifications of Seed Vigor-Related QTLs and Candidate Genes Combined Cultivated Soybean with Wild Soybean

by Shengnan Ma, Haojie Feng, Yiran Sun, Lin Yu, Chunshuang Tang, Yanqiang Zhao, Liansong Xue, Jinhui Wang, Chunyan Liu, Dawei Xin, Qingshan Chen and Mingliang Yang

Agronomy 2024, 14(2), 332; https://doi.org/10.3390/agronomy14020332 - 6 Feb 2024

Cited by 1 | Viewed by 1506

Abstract

Soybean (Glycine max) is an economically important cash crop and food source that serves as a key source of high-quality plant-derived protein and oil. Seed vigor is an important trait that influences the growth and development of soybean plants in an [...] Read more.

Soybean (Glycine max) is an economically important cash crop and food source that serves as a key source of high-quality plant-derived protein and oil. Seed vigor is an important trait that influences the growth and development of soybean plants in an agricultural setting, underscoring a need for research focused on identifying seed vigor-related genetic loci and candidate genes. In this study, a population consisting of 207 chromosome segment substitution lines (CSSLs) derived from the crossing and continuous backcrossing of the Suinong14 (improved cultivar, recurrent parent) and ZYD00006 (wild soybean, donor parent) soybean varieties was leveraged to identify quantitative trait loci (QTLs) related to seed vigor. The candidate genes detected using this approach were then validated through RNA-seq, whole-genome resequencing, and qPCR approaches, while the relationship between specific haplotypes and seed vigor was evaluated through haplotype analyses of candidate genes. Phenotypic characterization revealed that the seed vigor of Suinong14 was superior to that of ZYD00006, and 20 total QTLs were identified using the selected CSSLs. Glyma.03G256700 was also established as a seed vigor-related gene that was upregulated in high-vigor seeds during germination, with haplotypes for this candidate gene also remaining consistent with observed soybean seed vigor. The QTLs identified herein can serve as a foundation for future marker-assisted and convergent breeding efforts aimed at improving seed vigor. In addition, future molecular and functional research focused on Glyma.03G256700 has the potential to elucidate the signaling network and key regulatory mechanisms that govern seed germination in soybean plants. Full article

(This article belongs to the Special Issue Functional Genomics and Molecular Breeding of Soybeans)

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21 pages, 4659 KiB

Open AccessArticle

Genome-Wide Identification, Characterization, and Expression Analysis of the Amino Acid Permease Gene Family in Soybean

by Yuan Zhang, Le Wang, Bao-Hua Song, Dan Zhang and Hengyou Zhang

Agronomy 2024, 14(1), 52; https://doi.org/10.3390/agronomy14010052 - 23 Dec 2023

Viewed by 1610

Abstract

Amino acid permeases (AAPs) play important roles in transporting amino acids in plant species, leading to increased low-nitrogen tolerance, grain yield, or protein content. However, very few AAPs have been characterized in soybean (Glycine max). In this study, we scanned the [...] Read more.

Amino acid permeases (AAPs) play important roles in transporting amino acids in plant species, leading to increased low-nitrogen tolerance, grain yield, or protein content. However, very few AAPs have been characterized in soybean (Glycine max). In this study, we scanned the soybean reference genome and identified a total of 36 AAP genes (named GmAAP). The GmAAPs were phylogenetically divided into three evolutionary clades, with the genes in the same clades sharing similar gene structures and domain organization. We also showed that seventeen GmAAP genes on ten chromosomes were in collinearity, likely due to whole-genome duplication. Further analysis revealed a variety of cis-acting regulatory elements (such as hormone response elements (ABRE, ERE, GARE, P-box, and TGA-element), stress response elements (LTR, MBS, MYB-related components, TC-rich repeats, TCA-element, and WUN-motif), the tissue expression element (GCN4-motif), and the circadian regulatory element (circadian) present in the 2 kb region of the GmAAP promoter region, demonstrating functional diversity and expression specificity. RNA-Seq data and quantitative real-time PCR identified five GmAAPs showing differential expression under nitrogen limitation, including GmAAP3, GmAAP5, and GmAAP8 showing downregulation while GmAAP14, GmAAP29 showed upregulation, suggesting their involvement in low-nitrogen stress response. These results provide comprehensive information on soybean AAP genes in nitrogen stress, and provide putative candidates with possible roles in enhancing amino acid delivery to seeds for yield improvement. Full article

(This article belongs to the Special Issue Functional Genomics and Molecular Breeding of Soybeans)

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12 pages, 1969 KiB

Open AccessArticle

Soybean LEAFY COTYLEDON 1: A Key Target for Genetic Enhancement of Oil Biosynthesis

by Sehrish Manan, Khulood Fahad Alabbosh, Abeer Al-Andal, Waqas Ahmad, Khalid Ali Khan and Jian Zhao

Agronomy 2023, 13(11), 2810; https://doi.org/10.3390/agronomy13112810 - 13 Nov 2023

Cited by 2 | Viewed by 1611

Abstract

Soybean is an important oilseed crop that is used as a feed for livestock and has several industrial uses. Lipid biosynthesis and accumulation primarily occur during seed development in plants. This process is regulated by several transcription factors and interconnected biochemical pathways. This [...] Read more.

Soybean is an important oilseed crop that is used as a feed for livestock and has several industrial uses. Lipid biosynthesis and accumulation primarily occur during seed development in plants. This process is regulated by several transcription factors and interconnected biochemical pathways. This study investigated the role of glycine max LEAFY COTYLEDON 1 (GmLEC1) in soybean seed development and the accumulation of storage reserves. The overexpression of GmLEC1 significantly increased the amount of triacylglycerol (TAG) in transgenic Arabidopsis seeds compared to the wild-type and an atlec1 mutant. Similarly, the high expression of GmLEC1 led to a 12% increase in TAG content in transgenic soybean hairy roots compared to the control. GmLEC1 also altered the fatty acid composition in transgenic Arabidopsis seeds and soybean hairy roots. Additionally, the overexpression of GmLEC1 resulted in a reduction in starch accumulation in seeds and vegetative tissues, as well as changes in cotyledon and seed morphology. The cotyledons of the atlec1 mutant displayed abnormal trichome development, and the seeds were smaller and less tolerant to desiccation. A complementation assay in Arabidopsis restored normal cotyledon phenotype and seed size. The main downstream targets of LEC1 are GL2 and WRI1, which were found to participate in fatty acid biosynthesis and trichome formation through the regulation of phytohormones and various transcription factors involved in seed development and maturation. The findings of this study suggest that GmLEC1 controls seed development and regulates the accumulation of seed storage compounds. Furthermore, these results demonstrate that GmLEC1 could be a reliable target for the genetic improvement of oil biosynthesis in soybean. Full article

(This article belongs to the Special Issue Functional Genomics and Molecular Breeding of Soybeans)

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12 pages, 3075 KiB

Open AccessCommunication

Development of a Set of Polymorphic DNA Markers for Soybean (Glycine max L.) Applications

by Man-Wah Li, Xin Wang, Ching-Ching Sze, Wai-Shing Yung, Fuk-Ling Wong, Guohong Zhang, Gyuhwa Chung, Ting-Fung Chan and Hon-Ming Lam

Agronomy 2023, 13(11), 2708; https://doi.org/10.3390/agronomy13112708 - 27 Oct 2023

Cited by 1 | Viewed by 1756

Abstract

Soybean (Glycine max L.) is gaining in importance due to its many uses, including as a food crop and a source of industrial products, among others. Increasing efforts are made to accelerate soybean research and develop new soybean varieties to meet global [...] Read more.

Soybean (Glycine max L.) is gaining in importance due to its many uses, including as a food crop and a source of industrial products, among others. Increasing efforts are made to accelerate soybean research and develop new soybean varieties to meet global demands. Soybean research, breeding, identification, and variety protection all rely on precise genomic information. While DNA markers are invaluable tools for these purposes, the older generations, especially those developed before the advent of genome sequencing, lack precision and specificity. Thankfully, advancements in genome sequencing technologies have generated vast amounts of sequence data over the past decade, allowing precise and high-resolution analyses. However, making sense of the genomic information requires a certain level of professional training and computational power, which are not universally available to researchers. To address this, we generated a set of PCR-based DNA markers out of the existing genomic data from 228 popular soybean varieties that offer precise, unambiguous genomic information and can be easily adapted in various applications. A standard operating procedure (SOP) was also designed for these markers and validated on diverse soybean varieties to ensure their reproducibility. This user-friendly universal panel of DNA markers, along with the SOP, will facilitate soybean research and breeding programs through simple applications. Full article

(This article belongs to the Special Issue Functional Genomics and Molecular Breeding of Soybeans)

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13 pages, 1875 KiB

Open AccessArticle

Increased Accumulation of Recombinant Proteins in Soybean Seeds via the Combination Strategy of Polypeptide Fusion and Suppression of Endogenous Storage Proteins

by Jing Yang, Yuanyu Zhang, Guojie Xing, Jia Wei, Lu Niu, Qianqian Zhao, Qinan Cai, Xiaofang Zhong and Xiangdong Yang

Agronomy 2023, 13(11), 2680; https://doi.org/10.3390/agronomy13112680 - 25 Oct 2023

Viewed by 1459

Abstract

Soybean seeds show great potential as a safe and cost-effective host for the large-scale production of biopharmaceuticals and industrially important macromolecules. However, the yields of desired recombinant proteins in soybean seeds are usually lower than the economic threshold for their potential commercialization. Our [...] Read more.

Soybean seeds show great potential as a safe and cost-effective host for the large-scale production of biopharmaceuticals and industrially important macromolecules. However, the yields of desired recombinant proteins in soybean seeds are usually lower than the economic threshold for their potential commercialization. Our previous study demonstrated that polypeptide fusion such as maize γ-zein or elastin-like polypeptide (ELP) could significantly increase the accumulation of foreign proteins. In the present study, a recombination strategy of polypeptide fusions (γ-zein or ELP) and suppression of intrinsic storage proteins (glycinin or conglycinin) via RNA interference was further exploited to improve the yield of the target protein in soybean seeds. Transgenic soybean plants harboring both polypeptide-fused green fluorescent protein (GFP) and glycinin/conglycinin RNAi expression cassettes were generated and confirmed by molecular analysis. The results showed that on both the glycinin and conglycinin suppression backgrounds, the average accumulation levels of recombinant zein-GFP and GFP-ELP proteins were significantly increased as compared to that of their counterparts without such suppressions in our previous study. Moreover, zein-GFP and GFP-ELP accumulation was also remarkably higher than unfused GFP on the glycinin suppression background. However, no significant differences were detected in the glycinin or conglycinin suppression backgrounds for the same polypeptide fusion constructs, though suppression of one of the storage proteins in soybean seeds led to a significant increase in the other. Additionally, the increases in the recombinant protein yield did not affect the total protein content and the protein/oil ratio in soybean seeds. Taken together, the results indicate that both the fusion of the foreign protein with polypeptide tags together with the depletion of endogenous storage proteins contributed to a higher accumulation of the recombinant proteins without affecting the total protein content or the protein/oil ratio in soybean seeds. Full article

(This article belongs to the Special Issue Functional Genomics and Molecular Breeding of Soybeans)

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15 pages, 7945 KiB

Open AccessArticle

Genome-Wide Identification of the Phytocyanin Gene Family and Its Potential Function in Salt Stress in Soybean (Glycine max (L.) Merr.)

by Li Wang, Jinyu Zhang, Huici Li, Gongzhan Zhang, Dandan Hu, Dan Zhang, Xinjuan Xu, Yuming Yang and Zhongwen Huang

Agronomy 2023, 13(10), 2484; https://doi.org/10.3390/agronomy13102484 - 27 Sep 2023

Cited by 2 | Viewed by 1534

Abstract

Phytocyanins (PCs), plant-specific blue copper proteins, are crucial for various biological processes during plant development. However, a comprehensive characterization of the soybean PC gene family (GmPC) is lacking. In this study, we performed genome-wide screening of soybean PC genes, and 90 [...] Read more.

Phytocyanins (PCs), plant-specific blue copper proteins, are crucial for various biological processes during plant development. However, a comprehensive characterization of the soybean PC gene family (GmPC) is lacking. In this study, we performed genome-wide screening of soybean PC genes, and 90 PC genes were identified in the soybean genome. Further analysis revealed that the GmPC family was categorized into four subfamilies (stellacyanins, GmSCs; uclacyanins, GmUCs; plantacyanins, GmPLCs; and early nodulin-like proteins, GmENODLs). In-depth analysis revealed that each specific GmPC subfamily exhibited similar characteristics, with segmental duplications playing a major role in expanding the members of GmPC. Additionally, synteny and evolutionary constraint analyses suggested that GmPCs have undergone strong selective pressure for purification during the evolution of soybeans. The promoter cis-regulatory elements analysis of GmPCs suggested that GmPCs might play a crucial role in various stress responses. The expression patterns of GmPCs exhibited tissue-specific variations. Moreover, 23 of the GmPCs may be involved in soybean’s response to salt stress. In all, our study presents a systematic overview of GmPC, which not only provides a valuable foundation for further functional investigations of GmPCs, but also offers new insights into the mechanism of soybean salt tolerance. Full article

(This article belongs to the Special Issue Functional Genomics and Molecular Breeding of Soybeans)

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