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Advances in Research for Legume Genomics, Genetics, and Breeding

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (15 October 2023) | Viewed by 15337

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Dr. Naoufal Lakhssassi

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Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA
Interests: plant genetics; genomics; molecular biology; biochemistry; breeding
Special Issues, Collections and Topics in MDPI journals

Dr. Adnane Boualem

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Institute of Plant Sciences Paris-Saclay (IPS2), INRAE, CNRS, Université Evry, Université de Paris, Université Paris-Saclay, 91405 Orsay, France
Interests: plant genetics and genomics; development; specialized/secondary metabolites
Special Issues, Collections and Topics in MDPI journals

Dr. Gunvant B. Patil

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Department of Plant and Soil Sciences, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX 79409, USA
Interests: genome editing; genomic-assisted breeding; genetic engineering seed composition

Special Issue Information

Dear Colleagues,

Legumes provide food, feed grain, oil, and fiber for domestic consumption. Horticultural legumes are grown specifically for human diets and are useful in terms of enhancing the living environment. Legumes are an excellent source of protein and are low in fat and sodium and high in dietary fiber, iron, zinc, potassium, magnesium, vitamins, folate, etc.

The current issue of the International Journal of Molecular Sciences will focus on recent “Advances in Research for Legume Genomics, Genetics, and Breeding”. We encourage all kinds of efforts/work by the scientific community to accelerate legume improvement using genetic, genomic, and molecular breeding approaches. Works that bring new insights into biotic and abiotic stresses that affect legume production are also encouraged. Projects may include but are not limited to the improvement of nutraceutical and pharmaceutical compounds derived from legumes with extra human health benefits, seed composition (fatty acid, vitamins, oil, fiber, protein, carbohydrate, etc.), and diseases that affect cropping systems.

Dr. Naoufal Lakhssassi
Dr. Adnane Boualem
Dr. Gunvant B. Patil
Guest Editors

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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

legumes
genomics
plant breeding
seed composition
gene function
biotic and abiotic stress
legume pathogen resistance/mechanisms

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Advances in Research for Legume Genomics, Genetics, and Breeding 2.0 in International Journal of Molecular Sciences (1 article)

Published Papers (9 papers)

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Research

15 pages, 3132 KiB

Open AccessArticle

Deep Learning Model for Classifying and Evaluating Soybean Leaf Disease Damage

by Sandeep Goshika, Khalid Meksem, Khaled R. Ahmed and Naoufal Lakhssassi

Int. J. Mol. Sci. 2024, 25(1), 106; https://doi.org/10.3390/ijms25010106 - 20 Dec 2023

Viewed by 982

Abstract

Soybean (Glycine max (L.) Merr.) is a major source of oil and protein for human food and animal feed; however, soybean crops face diverse factors causing damage, including pathogen infections, environmental shifts, poor fertilization, and incorrect pesticide use, leading to reduced yields. Identifying the level of leaf damage aids yield projections, pesticide, and fertilizer decisions. Deep learning models (DLMs) and neural networks mastering tasks from abundant data have been used for binary healthy/unhealthy leaf classification. However, no DLM predicts and categorizes soybean leaf damage severity (five levels) for tailored pesticide use and yield forecasts. This paper introduces a novel DLM for accurate damage prediction and classification, trained on 2930 near-field soybean leaf images. The model quantifies damage severity, distinguishing healthy/unhealthy leaves and offering a comprehensive solution. Performance metrics include accuracy, precision, recall, and F1-score. This research presents a robust DLM for soybean damage assessment, supporting informed agricultural decisions based on specific damage levels and enhancing crop management and productivity. Full article

(This article belongs to the Special Issue Advances in Research for Legume Genomics, Genetics, and Breeding)

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18 pages, 7658 KiB

Open AccessArticle

Responsiveness of Candidate Genes on CoPv01^CDRK/PhgPv01^CD^RK Loci in Common Bean Challenged by Anthracnose and Angular Leaf Spot Pathogens

by Maike Lovatto, Maria Celeste Gonçalves-Vidigal, Mariana Vaz Bisneta, Alexandre Catto Calvi, Josmar Mazucheli, Pedro Soares Vidigal Filho, Eduardo Gomes Rosa Miranda and Maeli Melotto

Int. J. Mol. Sci. 2023, 24(22), 16023; https://doi.org/10.3390/ijms242216023 - 07 Nov 2023

Viewed by 808

Abstract

Anthracnose (ANT) and angular leaf spot (ALS) are significant diseases in common bean, leading to considerable yield losses under specific environmental conditions. The California Dark Red Kidney (CDRK) bean cultivar is known for its resistance to multiple races of both pathogens. Previous studies have identified the CoPv01^CDRK/PhgPv01^CDRK resistance loci on chromosome Pv01. Here, we evaluated the expression levels of ten candidate genes near the CoPv01^CDRK/PhgPv01^CDRK loci and plant defense genes using quantitative real-time PCR in CDRK cultivar inoculated with races 73 of Colletotrichum lindemuthianum and 63-39 of Pseudocercospora griseola. Gene expression analysis revealed that the Phvul.001G246300 gene exhibited the most elevated levels, showing remarkable 7.8-fold and 8.5-fold increases for ANT and ALS, respectively. The Phvul.001G246300 gene encodes an abscisic acid (ABA) receptor with pyrabactin resistance, PYR1-like (PYL) protein, which plays a central role in the crosstalk between ABA and jasmonic acid responses. Interestingly, our results also showed that the other defense genes were initially activated. These findings provide critical insights into the molecular mechanisms underlying plant defense against these diseases and could contribute to the development of more effective disease management strategies in the future. Full article

(This article belongs to the Special Issue Advances in Research for Legume Genomics, Genetics, and Breeding)

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23 pages, 17959 KiB

Open AccessArticle

Effect of Triazole Fungicides Titul Duo and Vintage on the Development of Pea (Pisum sativum L.) Symbiotic Nodules

by Artemii P. Gorshkov, Pyotr G. Kusakin, Yaroslav G. Borisov, Anna V. Tsyganova and Viktor E. Tsyganov

Int. J. Mol. Sci. 2023, 24(10), 8646; https://doi.org/10.3390/ijms24108646 - 12 May 2023

Cited by 4 | Viewed by 1407

Abstract

Triazole fungicides are widely used in agricultural production for plant protection, including pea (Pisum sativum L.). The use of fungicides can negatively affect the legume-Rhizobium symbiosis. In this study, the effects of triazole fungicides Vintage and Titul Duo on nodule formation and, in particular, on nodule morphology, were studied. Both fungicides at the highest concentration decreased the nodule number and dry weight of the roots 20 days after inoculation. Transmission electron microscopy revealed the following ultrastructural changes in nodules: modifications in the cell walls (their clearing and thinning), thickening of the infection thread walls with the formation of outgrowths, accumulation of poly-β-hydroxybutyrates in bacteroids, expansion of the peribacteroid space, and fusion of symbiosomes. Fungicides Vintage and Titul Duo negatively affect the composition of cell walls, leading to a decrease in the activity of synthesis of cellulose microfibrils and an increase in the number of matrix polysaccharides of cell walls. The results obtained coincide well with the data of transcriptomic analysis, which revealed an increase in the expression levels of genes that control cell wall modification and defense reactions. The data obtained indicate the need for further research on the effects of pesticides on the legume-Rhizobium symbiosis in order to optimize their use. Full article

(This article belongs to the Special Issue Advances in Research for Legume Genomics, Genetics, and Breeding)

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15 pages, 2635 KiB

Open AccessArticle

Transcriptome Analysis of Differentially Expressed Genes Associated with Salt Stress in Cowpea (Vigna unguiculata L.) during the Early Vegetative Stage

by Byeong Hee Kang, Woon Ji Kim, Sreeparna Chowdhury, Chang Yeok Moon, Sehee Kang, Seong-Hoon Kim, Sung-Hwan Jo, Tae-Hwan Jun, Kyung Do Kim and Bo-Keun Ha

Int. J. Mol. Sci. 2023, 24(5), 4762; https://doi.org/10.3390/ijms24054762 - 01 Mar 2023

Cited by 4 | Viewed by 1817

Abstract

Cowpea (Vigna unguiculata (L.), 2n = 22) is a tropical crop grown in arid and semiarid regions that is tolerant to abiotic stresses such as heat and drought. However, in these regions, salt in the soil is generally not eluted by rainwater, leading to salt stress for a variety of plant species. This study was conducted to identify genes related to salt stress using the comparative transcriptome analysis of cowpea germplasms with contrasting salt tolerance. Using the Illumina Novaseq 6000 platform, 1.1 billion high-quality short reads, with a total length of over 98.6 billion bp, were obtained from four cowpea germplasms. Of the differentially expressed genes identified for each salt tolerance type following RNA sequencing, 27 were shown to exhibit significant expression levels. These candidate genes were subsequently narrowed down using reference-sequencing analysis, and two salt stress-related genes (Vigun_02G076100 and Vigun_08G125100) with single-nucleotide polymorphism (SNP) variation were selected. Of the five SNPs identified in Vigun_02G076100, one that caused significant amino acid variation was identified, while all nucleotide variations in Vigun_08G125100 was classified as missing in the salt-resistant germplasms. The candidate genes and their variation, identified in this study provide, useful information for the development of molecular markers for cowpea breeding programs. Full article

(This article belongs to the Special Issue Advances in Research for Legume Genomics, Genetics, and Breeding)

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14 pages, 2118 KiB

Open AccessArticle

NAC Transcription Factor GmNAC12 Improved Drought Stress Tolerance in Soybean

by Chengfeng Yang, Yanzhong Huang, Peiyun Lv, Augustine Antwi-Boasiako, Naheeda Begum, Tuanjie Zhao and Jinming Zhao

Int. J. Mol. Sci. 2022, 23(19), 12029; https://doi.org/10.3390/ijms231912029 - 10 Oct 2022

Cited by 6 | Viewed by 2364

Abstract

NAC transcription factors (TFs) could regulate drought stresses in plants; however, the function of NAC TFs in soybeans remains unclear. To unravel NAC TF function, we established that GmNAC12, a NAC TF from soybean (Glycine max), was involved in the manipulation of stress tolerance. The expression of GmNAC12 was significantly upregulated more than 10-fold under drought stress and more than threefold under abscisic acid (ABA) and ethylene (ETH) treatment. In order to determine the function of GmNAC12 under drought stress conditions, we generated GmNAC12 overexpression and knockout lines. The present findings showed that under drought stress, the survival rate of GmNAC12 overexpression lines increased by more than 57% compared with wild-type plants, while the survival rate of GmNAC12 knockout lines decreased by at least 46%. Furthermore, a subcellular localisation analysis showed that the GmNAC12 protein is concentrated in the nucleus of the tobacco cell. In addition, we used a yeast two-hybrid assay to identify 185 proteins that interact with GmNAC12. Gene ontology (GO) and KEGG analysis showed that GmNAC12 interaction proteins are related to chitin, chlorophyll, ubiquitin–protein transferase, and peroxidase activity. Hence, we have inferred that GmNAC12, as a key gene, could positively regulate soybean tolerance to drought stress. Full article

(This article belongs to the Special Issue Advances in Research for Legume Genomics, Genetics, and Breeding)

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14 pages, 7629 KiB

Open AccessArticle

Molecular Characterizations of the er1 Alleles Conferring Resistance to Erysiphe pisi in Three Chinese Pea (Pisum sativum L.) Landraces

by Suli Sun, Dong Deng, Wenqi Wu, Yuhua He, Gaoling Luo, Chengzhang Du, Canxing Duan and Zhendong Zhu

Int. J. Mol. Sci. 2022, 23(19), 12016; https://doi.org/10.3390/ijms231912016 - 10 Oct 2022

Cited by 1 | Viewed by 1461

Abstract

Powdery mildew caused by Erysiphe pisi DC. is a major disease affecting pea worldwide. This study aimed to confirm the resistance genes contained in three powdery mildew-resistant Chinese pea landraces (Suoshadabaiwan, Dabaiwandou, and Guiwan 1) and to develop the functional markers of the novel resistance genes. The resistance genes were identified by genetic mapping and PsMLO1 gene sequence identification. To confirm the inheritance of powdery mildew resistance in the three Landraces, the susceptible cultivars Bawan 6, Longwan 1, and Chengwan 8 were crossed with Suoshadabaiwan, Dabaiwandou, and Guiwan 1 to produce F₁, F₂, and F_2:3 populations, respectively. All F₁ plants were susceptible to E. pisi, and phenotypic segregation patterns in all the F₂ and F_2:3 populations fit the 3:1 (susceptible: resistant) and 1:2:1 (susceptible homozygotes: heterozygotes: resistant homozygotes) ratios, respectively, indicating powdery mildew resistance in the three Landraces were controlled by a single recessive gene, respectively. The analysis of er1-linked markers and genetic mapping in the F₂ populations suggested that the recessive resistance genes in three landraces could be er1 alleles. The cDNA sequences of 10 homologous PsMLO1 cDNA clones from the contrasting parents were obtained. A known er1 allele, er1-4, was identified in Suoshadabaiwan. Two novel er1 alleles were identified in Dabaiwandou and Guiwan 1, which were designated as er1-13 and er1-14, respectively. Both novel alleles were characterized with a 1-bp deletion (T) in positions 32 (exon 1) and 277 (exon 3), respectively, which caused a frame-shift mutation to result in premature termination of translation of PsMLO1 protein. The co-dominant functional markers specific for er1-13 and er1-14, KASPar-er1-13, and KASPar-er1-14 were developed and effectively validated in populations and pea germplasms. Here, two novel er1 alleles were characterized and their functional markers were validated. These results provide powerful tools for marker-assisted selection in pea breeding. Full article

(This article belongs to the Special Issue Advances in Research for Legume Genomics, Genetics, and Breeding)

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21 pages, 3631 KiB

Open AccessArticle

Proteomic, Transcriptomic, Mutational, and Functional Assays Reveal the Involvement of Both THF and PLP Sites at the GmSHMT08 in Resistance to Soybean Cyst Nematode

by Naoufal Lakhssassi, Dounya Knizia, Abdelhalim El Baze, Aicha Lakhssassi, Jonas Meksem and Khalid Meksem

Int. J. Mol. Sci. 2022, 23(19), 11278; https://doi.org/10.3390/ijms231911278 - 24 Sep 2022

Cited by 1 | Viewed by 1576

Abstract

The serine hydroxymethyltransferase (SHMT; E.C. 2.1.2.1) is involved in the interconversion of serine/glycine and tetrahydrofolate (THF)/5,10-methylene THF, playing a key role in one-carbon metabolism, the de novo purine pathway, cellular methylation reactions, redox homeostasis maintenance, and methionine and thymidylate synthesis. GmSHMT08 is the soybean gene underlying soybean cyst nematode (SCN) resistance at the Rhg4 locus. GmSHMT08 protein contains four tetrahydrofolate (THF) cofactor binding sites (L129, L135, F284, N374) and six pyridoxal phosphate (PLP) cofactor binding/catalysis sites (Y59, G106, G107, H134, S190A, H218). In the current study, proteomic analysis of a data set of protein complex immunoprecipitated using GmSHMT08 antibodies under SCN infected soybean roots reveals the presence of enriched pathways that mainly use glycine/serine as a substrate (glyoxylate cycle, redox homeostasis, glycolysis, and heme biosynthesis). Root and leaf transcriptomic analysis of differentially expressed genes under SCN infection supported the proteomic data, pointing directly to the involvement of the interconversion reaction carried out by the serine hydroxymethyltransferase enzyme. Direct site mutagenesis revealed that all mutated THF and PLP sites at the GmSHMT08 resulted in increased SCN resistance. We have shown the involvement of PLP sites in SCN resistance. Specially, the effect of the two Y59 and S190 PLP sites was more drastic than the tested THF sites. This unprecedented finding will help us to identify the biological outcomes of THF and PLP residues at the GmSHMT08 and to understand SCN resistance mechanisms. Full article

(This article belongs to the Special Issue Advances in Research for Legume Genomics, Genetics, and Breeding)

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16 pages, 34022 KiB

Open AccessArticle

Systematic Characterization of the OSCA Family Members in Soybean and Validation of Their Functions in Osmotic Stress

by Congge Liu, Hong Wang, Yu Zhang, Haijing Cheng, Zhangli Hu, Zhen-Ming Pei and Qing Li

Int. J. Mol. Sci. 2022, 23(18), 10570; https://doi.org/10.3390/ijms231810570 - 12 Sep 2022

Cited by 8 | Viewed by 1895

Abstract

Since we discovered OSCA1, a hyperosmolarity-gated calcium-permeable channel that acted as an osmosensor in Arabidopsis, the OSCA family has been identified genome-wide in several crops, but only a few OSCA members’ functions have been experimentally demonstrated. Osmotic stress seriously restricts the yield and quality of soybean. Therefore, it is essential to decipher the molecular mechanism of how soybean responds to osmotic stress. Here, we first systematically studied and experimentally demonstrated the role of OSCA family members in the osmotic sensing of soybean. Phylogenetic relationships, gene structures, protein domains and structures analysis revealed that 20 GmOSCA members were divided into four clades, of which members in the same cluster may have more similar functions. In addition, GmOSCA members in clusters III and IV may be functionally redundant and diverged from those in clusters I and II. Based on the spatiotemporal expression patterns, GmOSCA1.6, GmOSCA2.1, GmOSCA2.6, and GmOSCA4.1 were extremely low expressed or possible pseudogenes. The remaining 16 GmOSCA genes were heterologously overexpressed in an Arabidopsis osca1 mutant, to explore their functions. Subcellular localization showed that most GmOSCA members could localize to the plasma membrane (PM). Among 16 GmOSCA genes, only overexpressing GmOSCA1.1, GmOSCA1.2, GmOSCA1.3, GmOSCA1.4, and GmOSCA1.5 in cluster I could fully complement the reduced hyperosmolality-induced [Ca²⁺]_i increase (OICI) in osca1. The expression profiles of GmOSCA genes against osmotic stress demonstrated that most GmOSCA genes, especially GmOSCA1.1, GmOSCA1.2, GmOSCA1.3, GmOSCA1.4, GmOSCA1.5, GmOSCA3.1, and GmOSCA3.2, strongly responded to osmotic stress. Moreover, overexpression of GmOSCA1.1, GmOSCA1.2, GmOSCA1.3, GmOSCA1.4, GmOSCA1.5, GmOSCA3.1, and GmOSCA3.2 rescued the drought-hypersensitive phenotype of osca1. Our findings provide important clues for further studies of GmOSCA-mediated calcium signaling in the osmotic sensing of soybean and contribute to improving soybean drought tolerance through genetic engineering and molecular breeding. Full article

(This article belongs to the Special Issue Advances in Research for Legume Genomics, Genetics, and Breeding)

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24 pages, 14610 KiB

Open AccessArticle

Uncovering a Phenomenon of Active Hormone Transcriptional Regulation during Early Somatic Embryogenesis in Medicago sativa

by Jianbo Yuan, Yuehui Chao and Liebao Han

Int. J. Mol. Sci. 2022, 23(15), 8633; https://doi.org/10.3390/ijms23158633 - 03 Aug 2022

Cited by 6 | Viewed by 1687

Abstract

Somatic embryogenesis (SE) is a developmental process in which somatic cells undergo dedifferentiation to become plant stem cells, and redifferentiation to become a whole embryo. SE is a prerequisite for molecular breeding and is an excellent platform to study cell development in the majority of plant species. However, the molecular mechanism involved in M. sativa somatic embryonic induction, embryonic and maturation is unclear. This study was designed to examine the differentially expressed genes (DEGs) and miRNA roles during somatic embryonic induction, embryonic and maturation. The cut cotyledon (ICE), non-embryogenic callus (NEC), embryogenic callus (EC) and cotyledon embryo (CE) were selected for transcriptome and small RNA sequencing. The results showed that 17,251 DEGs, and 177 known and 110 novel miRNAs families were involved in embryonic induction (ICE to NEC), embryonic (NEC to EC), and maturation (EC to CE). Expression patterns and functional classification analysis showed several novel genes and miRNAs involved in SE. Moreover, embryonic induction is an active process of molecular regulation, and hormonal signal transduction related to pathways involved in the whole SE. Finally, a miRNA–target interaction network was proposed during M. sativa SE. This study provides novel perspectives to comprehend the molecular mechanisms in M. sativa SE. Full article

(This article belongs to the Special Issue Advances in Research for Legume Genomics, Genetics, and Breeding)

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