Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
5.2
3.7
Journals
Agronomy
Special Issues
Functional Genomics and Molecular Breeding of Soybeans
share announcement

Functional Genomics and Molecular Breeding of Soybeans

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Crop Breeding and Genetics".

Deadline for manuscript submissions: 31 October 2024 | Viewed by 6289

Special Issue Editors

Prof. Dr. Fang Huang

E-Mail Website
Guest Editor
National Center for Soybean Improvement, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
Interests: soybean molecualr biology; soybean molecular genetics and breeding for yield and quality
Prof. Dr. Lin Zhao

E-Mail Website
Guest Editor Assistant
Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
Interests: soybean molecualr biology; genetic improvement of soybean growth period
Prof. Dr. Xiaobo Wang

E-Mail Website
Guest Editor Assistant
School of Agronomy, Anhui Agricultural University, Hefei 230036, China
Interests: soybean molecular breeding; functional genomics; gene editing

Special Issue Information

Dear Colleagues,

Soybean (Glycine max (L.) Merr.) is one of the most important grain and oil crops. With the extensive exploitation of soybean gene resources, research on soybean functional genomics using genomic information and phenotypic group information has become increasingly important. With the continuous development of biotechnology, modern breeding techniques, such as whole genome selection breeding and genome editing breeding, are changing rapidly, and the selection of excellent soybean varieties has shifted towards soybean molecular design breeding. This Special Issue will collect cutting-edge research on soybean functional genomics and molecular breeding to further promote soybean molecular design and breeding.

Prof. Dr. Fang Huang
Guest Editor

Prof. Dr. Lin Zhao
Prof. Dr. Xiaobo Wang
Guest Editor Assistant

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Agronomy is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • soybean
  • functional genomics
  • molecular breeding

Published Papers (6 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

17 pages, 4630 KiB  
Article
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://0-doi-org.brum.beds.ac.uk/10.3390/agronomy14020332 - 06 Feb 2024
Viewed by 735
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)
►▼ Show Figures

Figure 1

21 pages, 4659 KiB  
Article
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://0-doi-org.brum.beds.ac.uk/10.3390/agronomy14010052 - 23 Dec 2023
Viewed by 1008
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)
►▼ Show Figures

Figure 1

12 pages, 1969 KiB  
Article
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://0-doi-org.brum.beds.ac.uk/10.3390/agronomy13112810 - 13 Nov 2023
Cited by 1 | Viewed by 959
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)
►▼ Show Figures

Figure 1

12 pages, 3075 KiB  
Communication
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://0-doi-org.brum.beds.ac.uk/10.3390/agronomy13112708 - 27 Oct 2023
Cited by 1 | Viewed by 946
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)
►▼ Show Figures

Figure 1

13 pages, 1875 KiB  
Article
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://0-doi-org.brum.beds.ac.uk/10.3390/agronomy13112680 - 25 Oct 2023
Viewed by 874
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)
►▼ Show Figures

Figure 1

15 pages, 7945 KiB  
Article
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://0-doi-org.brum.beds.ac.uk/10.3390/agronomy13102484 - 27 Sep 2023
Cited by 1 | Viewed by 1057
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)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-6

Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Title: Characterization analysis of GmTCP15 A key regulator of light signaling pathways in soybean
Author: Wu
Highlights: 1.GmTCP15 regulates soybean development by connecting light signals. 2.Prediction of GmTCP15 promoter regulatory elements reveals the mechanism of light and hormone signal regulation, advancing soybean research. 3.GmTCP15 gene expresses in all tissues at different developmental stages, with higher expression during the nutrient growth stage. 4.Genetic polymorphism analysis of GmTCP15 can identify high-quality soybean varieties.

Back to TopTop