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Functional Genomics for Plant Breeding 3.0
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Functional Genomics for Plant Breeding 3.0

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

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 10798

Special Issue Editor

Dr. Fatemeh Maghuly

E-Mail Website
Guest Editor
Institute of Molecular Biotechnology, Department of Biotechnology, VIBT, University of Natural Resources and Life Sciences, 1180 Vienna, Austria
Interests: plant functional genomics; plant breeding; plant physiology; population genetics; omic strategies and molecular biology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Next-generation genome sequencing technology in plants has accelerated the generation of multi-omic data at the DNA, RNA, protein, and metabolite levels, leading to a new era of “big data”. This can provide us with an integrative view and opens up new possibilities to draw attention to the importance of recording and analyzing large-scale omics data obtained in different systems and their relationship to phenotypes, and also for understanding how the exploration of these relationships can be used for management intervention and agricultural innovation in breeding programs.

Large-scale sequence-based markers and precise phenotypic data provide a crucial basis for the application of GWAS and QTL-mapping analysis. Further, genomic research has facilitated and accelerated the breeding process and offers applications for genetic improvement such as GS, MAS, and gene pyramiding.

On the other hand, it is not just the sequence of plant DNA that matters: how are some genes activated, and why are others silenced? How can genomics facilitate the study of complex traits in plant breeding? These are questions of widespread interest, and genome editing has been shown to be a crucial tool for functional genomic research that could be utilized as a precision-breeding approach for any programs seeking to improve traits of interest.

Often, the traits of interest cannot be evaluated with traditional tools, but the entrance of targeted metabolomics such as the type and content of small molecules (such as antioxidants and sugars), or macromolecules (such as lignin, non-structural polysaccharides, or protein) facilitates the evaluation of plant metabolisms and biomarkers from a commercial perspective.

Given the success of the two previous Special Issues, we are pleased to announce the launch of “Functional Genomics for Plant Breeding 3.0”. It will cover a selection of research topics and review articles regarding the recent development of genomics, epigenomics, epitranscriptomics, and metabolomics, that can enhance breeding strategies to shorten the time and efficiency of development of new crop cultivars.

Dr. Jose Manuel Cruz Rubio (jose.cruz-rubio@boku.ac.at) is serving as a research assistant and will assist Dr. Fatemeh Maghuly in managing this issue.

Dr. Fatemeh Maghuly
Guest Editor

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.

Published Papers (6 papers)

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Editorial

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2 pages, 169 KiB  
Editorial
Functional Genomics for Plant Breeding 3.0
by Fatemeh Maghuly and José Manuel Cruz-Rubio
Int. J. Mol. Sci. 2024, 25(4), 2131; https://doi.org/10.3390/ijms25042131 - 9 Feb 2024
Viewed by 602
Abstract
Functional genomics, as a scientific discipline, has significantly transformed the landscape of plant breeding in recent years [...] Full article
(This article belongs to the Special Issue Functional Genomics for Plant Breeding 3.0)

Research

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16 pages, 3253 KiB  
Article
Hormonal Regulation and Stimulation Response of Jatropha curcas L. Homolog Overexpression on Tobacco Leaf Growth by Transcriptome Analysis
by Qiuhong Wu, Dongchao Zheng, Na Lian, Xuli Zhu and Jun Wu
Int. J. Mol. Sci. 2023, 24(17), 13183; https://doi.org/10.3390/ijms241713183 - 24 Aug 2023
Cited by 1 | Viewed by 924
Abstract
The Flowering locus T (FT) gene encodes the florigen protein, which primarily regulates the flowering time in plants. Recent studies have shown that FT genes also significantly affect plant growth and development. The FT gene overexpression in plants promotes flowering and [...] Read more.
The Flowering locus T (FT) gene encodes the florigen protein, which primarily regulates the flowering time in plants. Recent studies have shown that FT genes also significantly affect plant growth and development. The FT gene overexpression in plants promotes flowering and suppresses leaf and stem development. This study aimed to conduct a transcriptome analysis to investigate the multiple effects of Jatropha curcas L. homolog (JcFT) overexpression on leaf growth in tobacco plants. The findings revealed that JcFT overexpression affected various biological processes during leaf development, including plant hormone levels and signal transduction, lipid oxidation metabolism, terpenoid metabolism, and the jasmonic-acid-mediated signaling pathway. These results suggested that the effects of FT overexpression in plants were complex and multifaceted, and the combination of these factors might contribute to a reduction in the leaf size. This study comprehensively analyzed the effects of JcFT on leaf development at the transcriptome level and provided new insights into the function of FT and its homologous genes. Full article
(This article belongs to the Special Issue Functional Genomics for Plant Breeding 3.0)
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14 pages, 6711 KiB  
Article
A Single Nucleotide Variation of CRS2 Affected the Establishment of Photosynthetic System in Rice
by Hongwei Chen, Qi Wang, Mingqian Fan, Xijuan Zhang, Pulin Feng, Lin Zhu, Jiayi Wu, Xiaoyi Cheng and Jiayu Wang
Int. J. Mol. Sci. 2023, 24(6), 5796; https://doi.org/10.3390/ijms24065796 - 18 Mar 2023
Cited by 1 | Viewed by 1410
Abstract
Chloroplasts are essential sites for plant photosynthesis, and the biogenesis of the photosynthetic complexes involves the interaction of nuclear genes and chloroplast genes. In this study, we identified a rice pale green leaf mutant, crs2. The crs2 mutant showed different degrees of [...] Read more.
Chloroplasts are essential sites for plant photosynthesis, and the biogenesis of the photosynthetic complexes involves the interaction of nuclear genes and chloroplast genes. In this study, we identified a rice pale green leaf mutant, crs2. The crs2 mutant showed different degrees of low chlorophyll phenotypes at different growth stages, especially at the seedling stage. Fine mapping and DNA sequencing of crs2 revealed a single nucleotide substitution (G4120A) in the eighth exons of CRS2, causing a G-to-R mutation of the 229th amino acid of CRS2 (G229R). The results of complementation experiments confirmed that this single-base mutation in crs2 is responsible for the phenotype of the crs2 mutant. CRS2 encodes a chloroplast RNA splicing 2 protein localized in the chloroplast. Western blot results revealed an abnormality in the abundance of the photosynthesis-related protein in crs2. However, the mutation of CRS2 leads to the enhancement of antioxidant enzyme activity, which could reduce ROS levels. Meanwhile, with the release of Rubisco activity, the photosynthetic performance of crs2 was improved. In summary, the G229R mutation in CRS2 causes chloroplast protein abnormalities and affects photosystem performance in rice; the above findings facilitate the elucidation of the physiological mechanism of chloroplast proteins affecting photosynthesis. Full article
(This article belongs to the Special Issue Functional Genomics for Plant Breeding 3.0)
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13 pages, 3800 KiB  
Article
Cloning of an Albino Mutation of Arabidopsis thaliana Using Mapping-by-Sequencing
by Eva Rodríguez-Alcocer, Erundina Ruiz-Pérez, Ricardo Parreño, César Martínez-Guardiola, José Marcos Berna, Ayça Çakmak Pehlivanlı, Sara Jover-Gil and Héctor Candela
Int. J. Mol. Sci. 2023, 24(4), 4196; https://doi.org/10.3390/ijms24044196 - 20 Feb 2023
Cited by 1 | Viewed by 2518
Abstract
We report the molecular characterization of an ethyl methanesulfonate (EMS)-induced mutation that causes albinism and lethality at the seedling stage in Arabidopsis thaliana. We identified the mutation using a mapping-by-sequencing approach that uses Fisher’s exact tests to detect changes in allele frequencies [...] Read more.
We report the molecular characterization of an ethyl methanesulfonate (EMS)-induced mutation that causes albinism and lethality at the seedling stage in Arabidopsis thaliana. We identified the mutation using a mapping-by-sequencing approach that uses Fisher’s exact tests to detect changes in allele frequencies among the seedlings of an F2 mapping population, which had been pooled according to their phenotypes (wild-type or mutant). After purifying genomic DNA from the plants of both pools, the two samples were sequenced using the Illumina HiSeq 2500 next-generation sequencing platform. The bioinformatic analysis allowed us to identify a point mutation that damages a conserved residue at the acceptor site of an intron of the At2g04030 gene, which encodes the chloroplast-localized AtHsp90.5 protein, a member of the HSP90 family of heat shock proteins. Our RNA-seq analysis demonstrates that the new allele alters the splicing of At2g04030 transcripts in multiple ways, leading to massive deregulation of genes encoding plastid-localized proteins. A search for protein–protein interactions using the yeast two-hybrid method allowed us to identify two members of the GrpE superfamily as potential interactors of AtHsp90.5, as has previously been reported for green algae. Full article
(This article belongs to the Special Issue Functional Genomics for Plant Breeding 3.0)
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12 pages, 3287 KiB  
Article
Isolation of a Novel QTL, qSCM4, Associated with Strong Culm Affects Lodging Resistance and Panicle Branch Number in Rice
by Xianli Yang, Yongcai Lai, Lizhi Wang, Minghui Zhao, Jiayu Wang, Mingxian Li, Liyong Chi, Guoyi Lv, Youhong Liu, Zhibo Cui, Rui Li, Liren Wu, Bing Sun, Xijuan Zhang and Shukun Jiang
Int. J. Mol. Sci. 2023, 24(1), 812; https://doi.org/10.3390/ijms24010812 - 3 Jan 2023
Cited by 5 | Viewed by 2084
Abstract
Rice breeders are now developing new varieties with semi-high or even high plant height to further increase the grain yield, and the problem of lodging has re-appeared. We identified a major quantitative trait locus (QTL), qSCM4, for resistance to lodging by using an [...] Read more.
Rice breeders are now developing new varieties with semi-high or even high plant height to further increase the grain yield, and the problem of lodging has re-appeared. We identified a major quantitative trait locus (QTL), qSCM4, for resistance to lodging by using an F2 segregant population and a recombinant self-incompatible line population from the cross between Shennong265 (SN265) and Lijiangxintuanheigu (LTH) after multiple years and multiple environments. Then, the residual heterozygous derived segregant population which consisted of 1781 individual plants, and the BC3F2 segregant population which consisted of 3216 individual plants, were used to shorten the physical interval of qSCM4 to 58.5 kb including 11 genes. DNA sequencing revealed the most likely candidate gene for qSCM4 was Os04g0615000, which encoded a functional protein with structural domains of serine and cysteine. There were 13 DNA sequence changes in LTH compared to SN265 in this gene, including a fragment deletion, two base changes in the 3′ UTR region, six base changes in the exons, and four base changes in the introns. A near-isogenic line carrying qSCM4 showed that it improved the lodging resistance through increasing stem thickness by 25.3% and increasing stem folding resistance by 20.3%. Furthermore, it was also discovered that qSCM4 enhanced the primary branch per panicle by 16.7%, secondary branch by per panicle 9.9%, and grain number per panicle by 14.7%. All the above results will give us a valuable genetic resource for concurrently boosting culm strength and lodging resistance, and they will also provide a basis for further research on the lodging resistance mechanism of rice. Full article
(This article belongs to the Special Issue Functional Genomics for Plant Breeding 3.0)
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22 pages, 9332 KiB  
Article
Genome Wide Identification and Annotation of NGATHA Transcription Factor Family in Crop Plants
by Hymavathi Salava, Sravankumar Thula, Adrià Sans Sánchez, Tomasz Nodzyński and Fatemeh Maghuly
Int. J. Mol. Sci. 2022, 23(13), 7063; https://doi.org/10.3390/ijms23137063 - 25 Jun 2022
Cited by 5 | Viewed by 2094
Abstract
The NGATHA (NGA) transcription factor (TF) belongs to the ABI3/VP1 (RAV) transcriptional subfamily, a subgroup of the B3 superfamily, which is relatively well-studied in Arabidopsis. However, limited data are available on the contributions of NGA TF in other plant species. In this study, [...] Read more.
The NGATHA (NGA) transcription factor (TF) belongs to the ABI3/VP1 (RAV) transcriptional subfamily, a subgroup of the B3 superfamily, which is relatively well-studied in Arabidopsis. However, limited data are available on the contributions of NGA TF in other plant species. In this study, 207 NGA gene family members were identified from a genome-wide search against Arabidopsis thaliana in the genome data of 18 dicots and seven monocots. The phylogenetic and sequence alignment analyses divided NGA genes into different clusters and revealed that the numbers of genes varied depending on the species. The phylogeny was followed by the characterization of the Solanaceae (tomato, potato, capsicum, tobacco) and Poaceae (Brachypodium distachyon, Oryza sativa L. japonica, and Sorghum bicolor) family members in comparison with A. thaliana. The gene and protein structures revealed a similar pattern for NGA and NGA-like sequences, suggesting that both are conserved during evolution. Promoter cis-element analysis showed that phytohormones such as abscisic acid, auxin, and gibberellins play a crucial role in regulating the NGA gene family. Gene ontology analysis revealed that the NGA gene family participates in diverse biological processes such as flower development, leaf morphogenesis, and the regulation of transcription. The gene duplication analysis indicates that most of the genes are evolved due to segmental duplications and have undergone purifying selection pressure. Finally, the gene expression analysis implicated that the NGA genes are abundantly expressed in lateral organs and flowers. This analysis has presented a detailed and comprehensive study of the NGA gene family, providing basic knowledge of the gene, protein structure, function, and evolution. These results will lay the foundation for further understanding of the role of the NGA gene family in various plant developmental processes. Full article
(This article belongs to the Special Issue Functional Genomics for Plant Breeding 3.0)
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