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Genetics and Genomics of Polyploid Plants
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Genetics and Genomics of Polyploid Plants

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: 5 September 2024 | Viewed by 4582

Special Issue Editors

Dr. Carlo Fasano

E-Mail
Guest Editor
Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), TERIN-BBC-PBE, Trisaia Research Center, 75026 Rotondella, Matera, Italy
Interests: genetics; molecular biology; transcriptomics; polyploids; gene expression regulation
Dr. Nunzio D'Agostino

E-Mail Website
Guest Editor
Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
Interests: bioinformatics; computational biology; genomics; transcriptomics; population genomics; molecular breeding
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Polyploid is a heritable condition of the possession of more than two complete sets of chromosomes, and is particularly common in plants. Whole-genome polyploidization events are a key driving force in the evolutionary history of plants and have played an important role in the domestication of crops. By displaying novel phenotypes or exceeding the range of parental species, polyploids gain a fitness advantage. Polyploidy affects many traits, such as morphology, physiology, and resistance to stress. All possible allelic combinations produce hybrid proteins and protein diversity. Polyploids are classified into two types: autopolyploids, derived from an intra-species genome duplication; and allopolyploids, arising from inter-species hybridization along with genome doubling. Polyploidization is an acute shock that triggers genome reshuffling and modifies gene regulation, the epigenetic landscape, and the activity of transposable elements. This Special Issue aims to support readers with a collection of articles on the most recent and promising discoveries in polyploid plants, both auto- and allopolyploids. The focus will be on the multidisciplinary genetic and epigenetic study of polyploids and how polyploidization affects the morphology, physiology, biochemistry, and molecular biology of plants. Multi-omics approaches, including modelling and integrative analyses, are also welcome.

Dr. Carlo Fasano
Dr. Nunzio D'Agostino
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. Genes 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

  • autopolyploid
  • allopolyploid
  • genomics
  • transcriptomics
  • epigenetics
  • multi-omics integration

Published Papers (4 papers)

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Research

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12 pages, 1363 KiB  
Article
Genomic Prediction from Multi-Environment Trials of Wheat Breeding
by Guillermo García-Barrios, Leonardo Crespo-Herrera, Serafín Cruz-Izquierdo, Paolo Vitale, José Sergio Sandoval-Islas, Guillermo Sebastián Gerard, Víctor Heber Aguilar-Rincón, Tarsicio Corona-Torres, José Crossa and Rosa Angela Pacheco-Gil
Genes 2024, 15(4), 417; https://doi.org/10.3390/genes15040417 - 27 Mar 2024
Viewed by 686
Abstract
Genomic prediction relates a set of markers to variability in observed phenotypes of cultivars and allows for the prediction of phenotypes or breeding values of genotypes on unobserved individuals. Most genomic prediction approaches predict breeding values based solely on additive effects. However, the [...] Read more.
Genomic prediction relates a set of markers to variability in observed phenotypes of cultivars and allows for the prediction of phenotypes or breeding values of genotypes on unobserved individuals. Most genomic prediction approaches predict breeding values based solely on additive effects. However, the economic value of wheat lines is not only influenced by their additive component but also encompasses a non-additive part (e.g., additive × additive epistasis interaction). In this study, genomic prediction models were implemented in three target populations of environments (TPE) in South Asia. Four models that incorporate genotype × environment interaction (G × E) and genotype × genotype (GG) were tested: Factor Analytic (FA), FA with genomic relationship matrix (FA + G), FA with epistatic relationship matrix (FA + GG), and FA with both genomic and epistatic relationship matrices (FA + G + GG). Results show that the FA + G and FA + G + GG models displayed the best and a similar performance across all tests, leading us to infer that the FA + G model effectively captures certain epistatic effects. The wheat lines tested in sites in different TPE were predicted with different precisions depending on the cross-validation employed. In general, the best prediction accuracy was obtained when some lines were observed in some sites of particular TPEs and the worse genomic prediction was observed when wheat lines were never observed in any site of one TPE. Full article
(This article belongs to the Special Issue Genetics and Genomics of Polyploid Plants)
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14 pages, 1161 KiB  
Article
Modeling within and between Sub-Genomes Epistasis of Synthetic Hexaploid Wheat for Genome-Enabled Prediction of Diseases
by Jaime Cuevas, David González-Diéguez, Susanne Dreisigacker, Johannes W. R. Martini, Leo Crespo-Herrera, Nerida Lozano-Ramirez, Pawan K. Singh, Xinyao He, Julio Huerta and Jose Crossa
Genes 2024, 15(3), 262; https://doi.org/10.3390/genes15030262 - 20 Feb 2024
Viewed by 726
Abstract
Common wheat (Triticum aestivum) is a hexaploid crop comprising three diploid sub-genomes labeled A, B, and D. The objective of this study is to investigate whether there is a discernible influence pattern from the D sub-genome with epistasis in genomic models [...] Read more.
Common wheat (Triticum aestivum) is a hexaploid crop comprising three diploid sub-genomes labeled A, B, and D. The objective of this study is to investigate whether there is a discernible influence pattern from the D sub-genome with epistasis in genomic models for wheat diseases. Four genomic statistical models were employed; two models considered the linear genomic relationship of the lines. The first model (G) utilized all molecular markers, while the second model (ABD) utilized three matrices representing the A, B, and D sub-genomes. The remaining two models incorporated epistasis, one (GI) using all markers and the other (ABDI) considering markers in sub-genomes A, B, and D, including inter- and intra-sub-genome interactions. The data utilized pertained to three diseases: tan spot (TS), septoria nodorum blotch (SNB), and spot blotch (SB), for synthetic hexaploid wheat (SHW) lines. The results (variance components) indicate that epistasis makes a substantial contribution to explaining genomic variation, accounting for approximately 50% in SNB and SB and only 29% for TS. In this contribution of epistasis, the influence of intra- and inter-sub-genome interactions of the D sub-genome is crucial, being close to 50% in TS and higher in SNB (60%) and SB (60%). This increase in explaining genomic variation is reflected in an enhancement of predictive ability from the G model (additive) to the ABDI model (additive and epistasis) by 9%, 5%, and 1% for SNB, SB, and TS, respectively. These results, in line with other studies, underscore the significance of the D sub-genome in disease traits and suggest a potential application to be explored in the future regarding the selection of parental crosses based on sub-genomes. Full article
(This article belongs to the Special Issue Genetics and Genomics of Polyploid Plants)
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17 pages, 3936 KiB  
Article
Comparative Transcriptome Analysis Reveals the Effect of Lignin on Storage Roots Formation in Two Sweetpotato (Ipomoea batatas (L.) Lam.) Cultivars
by Taifeng Du, Zhen Qin, Yuanyuan Zhou, Lei Zhang, Qingmei Wang, Zongyun Li and Fuyun Hou
Genes 2023, 14(6), 1263; https://doi.org/10.3390/genes14061263 - 14 Jun 2023
Cited by 3 | Viewed by 1286
Abstract
Sweet potato (Ipomoea batatas (L.) Lam.) is one of the most important crops with high storage roots yield. The formation and expansion rate of storage root (SR) plays a crucial role in the production of sweet potato. Lignin affects the SR formation; [...] Read more.
Sweet potato (Ipomoea batatas (L.) Lam.) is one of the most important crops with high storage roots yield. The formation and expansion rate of storage root (SR) plays a crucial role in the production of sweet potato. Lignin affects the SR formation; however, the molecular mechanisms of lignin in SR development have been lacking. To reveal the problem, we performed transcriptome sequencing of SR harvested at 32, 46, and 67 days after planting (DAP) to analyze two sweet potato lines, Jishu25 and Jishu29, in which SR expansion of Jishu29 was early and had a higher yield. A total of 52,137 transcripts and 21,148 unigenes were obtained after corrected with Hiseq2500 sequencing. Through the comparative analysis, 9577 unigenes were found to be differently expressed in the different stages in two cultivars. In addition, phenotypic analysis of two cultivars, combined with analysis of GO, KEGG, and WGCNA showed the regulation of lignin synthesis and related transcription factors play a crucial role in the early expansion of SR. The four key genes swbp1, swpa7, IbERF061, and IbERF109 were proved as potential candidates for regulating lignin synthesis and SR expansion in sweet potato. The data from this study provides new insights into the molecular mechanisms underlying the impact of lignin synthesis on the formation and expansion of SR in sweet potatoes and proposes several candidate genes that may affect sweet potato yield. Full article
(This article belongs to the Special Issue Genetics and Genomics of Polyploid Plants)
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Review

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0 pages, 4544 KiB  
Review
Allelic Variations in Vernalization (Vrn) Genes in Triticum spp.
by Sanaz Afshari-Behbahanizadeh, Damiano Puglisi, Salvatore Esposito and Pasquale De Vita
Genes 2024, 15(2), 251; https://doi.org/10.3390/genes15020251 - 17 Feb 2024
Viewed by 1127
Abstract
Rapid climate changes, with higher warming rates during winter and spring seasons, dramatically affect the vernalization requirements, one of the most critical processes for the induction of wheat reproductive growth, with severe consequences on flowering time, grain filling, and grain yield. Specifically, the [...] Read more.
Rapid climate changes, with higher warming rates during winter and spring seasons, dramatically affect the vernalization requirements, one of the most critical processes for the induction of wheat reproductive growth, with severe consequences on flowering time, grain filling, and grain yield. Specifically, the Vrn genes play a major role in the transition from vegetative to reproductive growth in wheat. Recent advances in wheat genomics have significantly improved the understanding of the molecular mechanisms of Vrn genes (Vrn-1, Vrn-2, Vrn-3, and Vrn-4), unveiling a diverse array of natural allelic variations. In this review, we have examined the current knowledge of Vrn genes from a functional and structural point of view, considering the studies conducted on Vrn alleles at different ploidy levels (diploid, tetraploid, and hexaploid). The molecular characterization of Vrn-1 alleles has been a focal point, revealing a diverse array of allelic forms with implications for flowering time. We have highlighted the structural complexity of the different allelic forms and the problems linked to the different nomenclature of some Vrn alleles. Addressing these issues will be crucial for harmonizing research efforts and enhancing our understanding of Vrn gene function and evolution. The increasing availability of genome and transcriptome sequences, along with the improvements in bioinformatics and computational biology, offers a versatile range of possibilities for enriching genomic regions surrounding the target sites of Vrn genes, paving the way for innovative approaches to manipulate flowering time and improve wheat productivity. Full article
(This article belongs to the Special Issue Genetics and Genomics of Polyploid Plants)
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