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Agronomy
Special Issues
Functional Genomics Research of Crops
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Functional Genomics Research of Crops

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

Deadline for manuscript submissions: closed (25 May 2021) | Viewed by 21422

Special Issue Editors

Dr. Rafael A. Cañas

E-Mail Website
Guest Editor
Departamento Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos, E-29071 Málaga, Spain
Interests: genomics; transcriptomics; nitrogen uptake; nitrogen metabolism; maize, conifers
Dr. Javier Canales

E-Mail Website
Guest Editor
Institute of Biochemistry and Microbiology , Faculty of Science, Universidad Austral de Chile, Valdivia 5110566, Chile
Interests: plant nutrition; genomics; wheat; transcriptomics

Special Issue Information

Dear Colleagues,

In the past twenty years, our knowledge about whole genome sequences of plants has increased extraordinarily, and now, there are around 400 whole genome assemblies of seed plants in the NCBI databases. However, this information is only the first step toward understanding the life complexity at a molecular level. In this context, functional genomics has become fundamental in biological research. In a broad sense, it is a very extensive research area including from genome functional annotation to metabolome passing through to gene expression regulation. The omics techniques associated to this discipline are accelerating the pace with which we obtain new knowledge about crops and about to how improve them through biotechnological techniques.

The objective of this Special Issue is to present to the international research community a wide perspective about functional genomics in crops (including herbaceous and tree species). Submissions on the main topics are invited, but not excluding other related topics:

(1) Omics works in transcriptomics, proteomics and metabolomics but even in epigenomics and epitranscriptomics;

(2) Gene expression regulation, including transcription but also translation;

(3) Protein–protein and protein–nucleic acid interactions;

(4) Mutagenesis and gene edition (RNAi, CRISPR, etc.);

(5) Bioinformatic tools for functional genomics including genome annotation, direct RNA sequencing, etc.;

(6) Any work on functional genomics in crops.

Dr. Rafael A. Cañas
Dr. Javier Canales
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. 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

  • transcriptomics
  • proteomics
  • metabolomics
  • epigenomics and epitranscriptomics
  • gene expression regulation
  • protein interactions
  • protein-nucleic acid interactions
  • mutagenesis
  • gene/genome edition
  • bioinformatics

Published Papers (6 papers)

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Research

26 pages, 3030 KiB  
Article
Integrative Transcriptomic and Metabolomic Analysis at Organ Scale Reveals Gene Modules Involved in the Responses to Suboptimal Nitrogen Supply in Tomato
by Begoña Renau-Morata, Rosa-Victoria Molina, Eugenio G. Minguet, Jaime Cebolla-Cornejo, Laura Carrillo, Raúl Martí, Víctor García-Carpintero, Eva Jiménez-Benavente, Lu Yang, Joaquín Cañizares, Javier Canales, Joaquín Medina and Sergio G. Nebauer
Agronomy 2021, 11(7), 1320; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy11071320 - 29 Jun 2021
Cited by 5 | Viewed by 4079
Abstract
The development of high nitrogen use efficiency (NUE) cultivars under low N inputs is required for sustainable agriculture. To this end, in this study, we analyzed the impact of long-term suboptimal N conditions on the metabolome and transcriptome of tomato to identify specific [...] Read more.
The development of high nitrogen use efficiency (NUE) cultivars under low N inputs is required for sustainable agriculture. To this end, in this study, we analyzed the impact of long-term suboptimal N conditions on the metabolome and transcriptome of tomato to identify specific molecular processes and regulators at the organ scale. Physiological and metabolic analysis revealed specific responses to maintain glutamate, asparagine, and sucrose synthesis in leaves for partition to sustain growth, while assimilated C surplus is stored in the roots. The transcriptomic analyses allowed us to identify root and leaf sets of genes whose expression depends on N availability. GO analyses of the identified genes revealed conserved biological functions involved in C and N metabolism and remobilization as well as other specifics such as the mitochondrial alternative respiration and chloroplastic cyclic electron flux. In addition, integrative analyses uncovered N regulated genes in root and leaf clusters, which are positively correlated with changes in the levels of different metabolites such as organic acids, amino acids, and formate. Interestingly, we identified transcription factors with high identity to TGA4, ARF8, HAT22, NF-YA5, and NLP9, which play key roles in N responses in Arabidopsis. Together, this study provides a set of nitrogen-responsive genes in tomato and new putative targets for tomato NUE and fruit quality improvement under limited N supply. Full article
(This article belongs to the Special Issue Functional Genomics Research of Crops)
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21 pages, 1850 KiB  
Article
Genome-Wide Analysis of Somatic Embryogenesis-Related Transcription Factors in Cultivated Strawberry (Fragaria × ananassa) and Evolutionary Relationships among Rosaceae Species
by Adrián Garrido-Bigotes, Herman Silva and Rodrigo Hasbún
Agronomy 2021, 11(2), 356; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy11020356 - 17 Feb 2021
Cited by 1 | Viewed by 2490
Abstract
Somatic embryogenesis is a plant regeneration method commonly used in tissue culture. Its molecular mechanisms are well-known in model plants such as Arabidopsis thaliana L. LEAFY COTYLEDON1 (LEC1), LEAFY COTYLEDON2 (LEC2), FUSCA3 (FUS3), ABSCISIC ACID INSENSITIVE3 ( [...] Read more.
Somatic embryogenesis is a plant regeneration method commonly used in tissue culture. Its molecular mechanisms are well-known in model plants such as Arabidopsis thaliana L. LEAFY COTYLEDON1 (LEC1), LEAFY COTYLEDON2 (LEC2), FUSCA3 (FUS3), ABSCISIC ACID INSENSITIVE3 (ABI3), and BABYBOOM (BBM) genes are considered master regulators in the induction, growth, and maturation of somatic embryos. However, the study of these transcription factors in fruit crops with high agronomic and economic value such as cultivated strawberry (Fragaria × ananassa Duch.) and other Rosaceae species is scarce. The purpose of this study was the in silico characterization of LEC1, ABI3, FUS3, LEC2, and BBM(LAFL-B) genes from F. × ananassa genome and the study of the evolutionary relationships within the Rosaceae family. Synteny analyses and molecular evolutionary rates were performed to analyze the evolution of each transcription factor within the Rosaceae family. Synteny was conserved between F. × ananassa and other Rosaceae genomes, and paralogous genes were selected through negative selection. Additionally, the exon–intron organization and multiple alignments showed that gene structure and DNA-binding domains were conserved in F. × ananassa transcription factors. Finally, phylogenetic trees showed close evolutionary relationships between F. × ananassa and its orthologous proteins in the Rosoideae subfamily. Overall, this research revealed novel insights in the LAFL-B network in F. × ananassa and other species of the Rosaceae family. These results provide useful in silico information and new resources for the establishment of more efficient propagation systems or the study of ploidy effects on somatic embryogenesis. Full article
(This article belongs to the Special Issue Functional Genomics Research of Crops)
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19 pages, 4768 KiB  
Communication
Identification of microRNAs and Their Expression in Leaf Tissues of Guava (Psidium guajava L.) under Salinity Stress
by Ashutosh Sharma, Luis M. Ruiz-Manriquez, Francisco I. Serrano-Cano, Paula Roxana Reyes-Pérez, Cynthia Karina Tovar Alfaro, Yulissa Esmeralda Barrón Andrade, Ana Karen Hernández Aros, Aashish Srivastava and Sujay Paul
Agronomy 2020, 10(12), 1920; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy10121920 - 07 Dec 2020
Cited by 20 | Viewed by 4063
Abstract
Superfruit guava (Psidium guajava L.) is one of the healthiest fruits due to its high antioxidant dietary fiber and vitamin content. However, the growth and development of this plant are severely affected by salinity stress, mostly at the seedling stage. MicroRNAs (miRNAs) [...] Read more.
Superfruit guava (Psidium guajava L.) is one of the healthiest fruits due to its high antioxidant dietary fiber and vitamin content. However, the growth and development of this plant are severely affected by salinity stress, mostly at the seedling stage. MicroRNAs (miRNAs) are small, noncoding, endogenous, highly conserved RNA molecules that play key regulatory roles in plant development, organ morphogenesis, and stress response signaling. In this study, applying computational approaches and following high stringent filtering criteria, a total of 40 potential microRNAs belonging to 19 families were characterized from guava. The identified miRNA precursors formed stable stem-loop structures and exhibited high sequence conservation among diverse and evolutionarily distant plant species. Differential expression pattern of seven selected guava miRNAs (pgu-miR156f-5p, pgu-miR160c-5p, pgu-miR162-3p, pgu-miR164b-5p, pgu-miR166t, pgu-miR167a-5p, and pgu-miR390b-5p) were recorded under salinity stress and pgu-miR162-3p, pgu-miR164b-5p as well as pgu-miR166t were found to be the most affected ones. Using the psRNATarget tool, a total of 49 potential target transcripts of the characterized guava miRNAs were identified in this study which are mostly involved in metabolic pathways, cellular development, and stress response signaling. A biological network has also been constructed to understand the miRNA mediated gene regulation using the minimum free energy (MFE) values of the miRNA-target interaction. To the best of our knowledge, this is the first report of guava miRNAs and their targets. Full article
(This article belongs to the Special Issue Functional Genomics Research of Crops)
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15 pages, 1428 KiB  
Communication
Interactions of JAZ Repressors with Anthocyanin Biosynthesis-Related Transcription Factors of Fragaria × ananassa
by Adrián Garrido-Bigotes, Marcela Torrejón, Roberto Solano and Carlos R. Figueroa
Agronomy 2020, 10(10), 1586; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy10101586 - 16 Oct 2020
Cited by 11 | Viewed by 2673
Abstract
Strawberry fruits are rich in flavonoids like proanthocyanidins and anthocyanins. Their biosynthesis and accumulation are controlled by the MYB-bHLH-WD40 (MBW) transcriptional complex, which is mainly formed by basic helix-loop-helix (bHLH) and MYB transcription factors (TFs). In Arabidopsis thaliana both bHLH and MYB TFs [...] Read more.
Strawberry fruits are rich in flavonoids like proanthocyanidins and anthocyanins. Their biosynthesis and accumulation are controlled by the MYB-bHLH-WD40 (MBW) transcriptional complex, which is mainly formed by basic helix-loop-helix (bHLH) and MYB transcription factors (TFs). In Arabidopsis thaliana both bHLH and MYB TFs are repressed by JASMONATE ZIM-DOMAIN (JAZ) proteins, the key repressors of the jasmonate-signaling pathway. The aim of this research was the characterization of the FaJAZ1/8.1/9/10 proteins and molecular targets of signaling components and anthocyanin biosynthesis-related TFs of Fragaria × ananassa by protein–protein interactions. For this, domain compositions were studied by multiple alignments and phylogenetic analyses, while interactions were analyzed by yeast two-hybrid (Y2H) assays. We detected high conservation of FaJAZ proteins and jasmonate-signaling components, as well as FabHLHs and FaMYB10 TFs. Moreover, we report the F. × ananassa YABBY1 (FaYAB1) TF, which is related to anthocyanin biosynthesis in Arabidopsis, showed high conservation of functional domains. We demonstrated that FaJAZ repressors interacted with F. × ananassa NOVEL INTERACTOR OF JAZ (FaNINJA), FaMYC2, and JASMONATE ASSOCIATED MYC2-LIKE (FaJAM) proteins. Besides, transcription factors of MBW-complex like FabHLH3, FabHLH33, and FaMYB10, together with FaYAB1, were molecular targets of FaJAZ repressors, exhibiting specificity or redundancy of interaction depending on particular FaJAZ protein. Overall, these results suggest that interactions of jasmonate-signaling components are fully conserved, and anthocyanin biosynthesis might be regulated by JAZ repressors in F. × ananassa. Full article
(This article belongs to the Special Issue Functional Genomics Research of Crops)
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29 pages, 3372 KiB  
Article
Transcriptomic Analysis of L. japonicus Symbiosis Reveals New Candidate Genes for Local and Systemic Regulation of Nodule Function
by Carmen M. Pérez-Delgado, Margarita García-Calderón, María Dolores Monje-Rueda, Antonio J. Márquez and Marco Betti
Agronomy 2020, 10(6), 819; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy10060819 - 09 Jun 2020
Cited by 3 | Viewed by 2864
Abstract
Several aspects of the legume–rhizobia symbiosis are far from being completely understood, such as the transport of compounds through the symbiosome membrane and the molecular actors (receptors, transcription factors and hormones) involved in the systemic regulation of nodulation. In this work, the transcriptomes [...] Read more.
Several aspects of the legume–rhizobia symbiosis are far from being completely understood, such as the transport of compounds through the symbiosome membrane and the molecular actors (receptors, transcription factors and hormones) involved in the systemic regulation of nodulation. In this work, the transcriptomes of L. japonicus plants growing under symbiotic or non-symbiotic conditions were studied in roots and shoots, in order to look for new genes involved in nodule function and regulation both at the local and systemic levels. Several of the genes differentially expressed in roots were well-known nodulins; however, other genes with unknown function were also discovered that showed univocal nodule-specific expression profiles. Transporters of the Nitrate Transporter1/Peptide Transporter Family family, putative oligopeptide transporters, as well as other uncharacterized transporters were upregulated in nodulated roots. Five transcription factors, as well as receptors/kinases and an f-box domain containing protein, all of unknown function, were also more upregulated in nodulated roots. In the shoots of nodulated plants, genes involved in jasmonic acid and indole-3-acetic acid metabolism were differentially expressed. Moreover, three genes encoding for different glutaredoxins, proteins that were recently involved in the systemic signaling of the Arabidopsis nitrogen status, were highly downregulated in the leaves of nodulated plants. Protein–protein interaction network analysis identified nitrate reductase as a central hub in nitrogen metabolism, and a putative protein of the NADH-ubiquinone complex was highly connected to several SWEET transporters. Clustering analysis of the differentially expressed genes also suggested a possible role for a previously uncharacterized ethylene-responsive transcription factor and for LBD38 homologs in L. japonicus nodule function. The new genes identified in this study represent a promising target for the understating and manipulation of symbiotic nitrogen fixation, with the aim of improving crop legumes’ productivity. Full article
(This article belongs to the Special Issue Functional Genomics Research of Crops)
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13 pages, 1164 KiB  
Article
The Analysis of Pinus pinaster SnRKs Reveals Clues of the Evolution of This Family and a New Set of Abiotic Stress Resistance Biomarkers
by Francisco Javier Colina, María Carbó, Ana Álvarez, Luis Valledor and María Jesús Cañal
Agronomy 2020, 10(2), 295; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy10020295 - 19 Feb 2020
Cited by 3 | Viewed by 4124
Abstract
Climate change is increasing the intensity and incidence of environmental stressors, reducing the biomass yields of forestry species as Pinus pinaster. Selection of new stress-tolerant varieties is thus required. Many genes related to plant stress signaling pathways have proven useful for this [...] Read more.
Climate change is increasing the intensity and incidence of environmental stressors, reducing the biomass yields of forestry species as Pinus pinaster. Selection of new stress-tolerant varieties is thus required. Many genes related to plant stress signaling pathways have proven useful for this purpose with sucrose non-fermenting related kinases (SnRK), conserved across plant evolution and connected to different phosphorylation cascades within ABA- and Ca2+-mediated signaling pathways, as a good example. The modulation of SnRKs and/or the selection of specific SnRK alleles have proven successful strategies to increase plant stress resistance. Despite this, SnRKs have been barely studied in gymnosperms. In this work P. pinaster SnRK sequences (PpiSnRK) were identified through a homology- and domain-based sequence analysis using Arabidopsis SnRK sequences as query. Moreover, PpiSnRKs links to the gymnosperm stress response were modeled out of the known interactions of PpiSnRKs orthologs from other species with different signaling complexity. This approach successfully identified the pine SnRK family and predicted their central role into the gymnosperm stress response, linking them to ABA, Ca2+, sugar/energy and possibly ethylene signaling. These links made the gymnosperm kinases promising candidates into the search for new stress resistance-related biomarkers, which would be useful into future breeding strategies. Full article
(This article belongs to the Special Issue Functional Genomics Research of Crops)
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