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Plants
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Beyond Mendel's Laws
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Beyond Mendel's Laws

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: closed (20 December 2023) | Viewed by 10627

Special Issue Editors

Prof. Dr. Alex Troitsky

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Guest Editor
Department of Evolutionary Biochemistry, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
Interests: plant molecular phylogeny and systematics; genome evolution; biodiversity; phytoplanktonic metagenome
Special Issues, Collections and Topics in MDPI journals
Dr. Giorgio Perrella

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Guest Editor
Department of Biosciences, University of Milan, 20133 Milan, Italy
Interests: epigenetics; abiotic stress; light signaling; Arabidopsis and bio-refinery crops
Special Issues, Collections and Topics in MDPI journals
Dr. Francisco Fuentes

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Guest Editor
Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul. Casilla 306-22, Santiago, Chile
Interests: plant genetic improvement; plant genetic resources; integrated crop production systems; bioprospecting of natural products; nutrigenomic
Special Issues, Collections and Topics in MDPI journals
Dr. Sujan Mamidi

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Guest Editor
HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
Interests: genomics; diversity; population genomics; quantitative genomics; association mapping; resequencing; adaptation; domestication; QTL mapping
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Jan Dvorak

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Guest Editor
Department of Plant Sciences, University of California, Davis, CA 95616, USA
Interests: plant cytogenetics; genomics; molecular biology; evolution

Special Issue Information

Dear Colleagues,

The experiments of Gregor Mendel determined the formation and grandiose success of genetics in the 20th century. As this science developed with the use of new methods, evidence appeared that not all facts could be described on the frame of the patterns discovered by this scientist, and ideas about the so-called “non-Mendelian heredity” appeared. Science is an uninterrupted development of knowledge. Paying tribute to the inquisitive mind of Mendel, we present a Special Issue of the journal Plants devoted to the study of such phenomena. Since the main idea of the Issue is to present and discuss various aspects of non-Mendelian, non-canonical heredity and variability, articles including, but not limited to, the following topics will be welcome:

  • Mobile elements of plants as a factor of variability and evolution;
  • Cytoplasmic inheritance in plants;
  • Epigenetic variations and their role in plant adaptation and evolution;
  • Gene silencing;
  • Genome methylation;
  • Polyploidy and genome transformations in plants;
  • Supernumerary chromosomes;
  • Aspects of chromosomal and genomic evolution of plants;
  • Ontogenetic and genetic changes during vegetative hybridization;
  • Genetics of sex and its regulation;
  • Non-canonical measurements in cell culture and somatic hybridization;
  • Polygenic inheritance and environmental effects.

Prof. Dr. Alex Troitsky
Dr. Giorgio Perrella
Dr. Francisco Fuentes
Dr. Sujan Mamidi
Prof. Dr. Jan Dvorak
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. Plants is an international peer-reviewed open access semimonthly 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 2700 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.

Published Papers (5 papers)

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Research

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11 pages, 2029 KiB  
Article
The Role of Chromatin Modifications in the Evolution of Giant Plant Genomes
by Andrew R. Leitch, Lu Ma, Steven Dodsworth, Jörg Fuchs, Andreas Houben and Ilia J. Leitch
Plants 2023, 12(11), 2159; https://doi.org/10.3390/plants12112159 - 30 May 2023
Cited by 1 | Viewed by 1444
Abstract
Angiosperm genome sizes (GS) range ~2400-fold and comprise genes and their regulatory regions, repeats, semi-degraded repeats, and ‘dark matter’. The latter represents repeats so degraded that they can no longer be recognised as repetitive. In exploring whether the histone modifications associated with chromatin [...] Read more.
Angiosperm genome sizes (GS) range ~2400-fold and comprise genes and their regulatory regions, repeats, semi-degraded repeats, and ‘dark matter’. The latter represents repeats so degraded that they can no longer be recognised as repetitive. In exploring whether the histone modifications associated with chromatin packaging of these contrasting genomic components are conserved across the diversity of GS in angiosperms, we compared immunocytochemistry data for two species whose GS differ ~286-fold. We compared published data for Arabidopsis thaliana with a small genome (GS = 157 Mbp/1C) with newly generated data from Fritillaria imperialis, which has a giant genome (GS = 45,000 Mbp/1C). We compared the distributions of the following histone marks: H3K4me1, H3K4me2, H3K9me1, H3K9me2, H3K9me3, H3K27me1, H3K27me2, and H3K27me3. Assuming these histone marks are associated with the same genomic features across all species, irrespective of GS, our comparative analysis enables us to suggest that while H3K4me1 and H3K4me2 methylation identifies genic DNA, H3K9me3 and H3K27me3 marks are associated with ‘dark matter’, H3K9me1 and H3K27me1 mark highly homogeneous repeats, and H3K9me2 and H3K27me2 mark semi-degraded repeats. The results have implications for our understanding of epigenetic profiles, chromatin packaging and the divergence of genomes, and highlight contrasting organizations of the chromatin within the nucleus depending on GS itself. Full article
(This article belongs to the Special Issue Beyond Mendel's Laws)
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12 pages, 2653 KiB  
Article
Epigenetic Modifications Related to Potato Skin Russeting
by Pawan Kumar, Yulia Kaplan, Jeffrey B. Endelman and Idit Ginzberg
Plants 2023, 12(10), 2057; https://doi.org/10.3390/plants12102057 - 22 May 2023
Viewed by 1787
Abstract
Potato tuber skin is a protective corky tissue consisting of suberized phellem cells. Smooth-skinned varieties are characterized by a clean, shiny appearance compared to the darker hue of russeted potatoes. The rough skin of russeted cultivars is a desired, genetically inherited characteristic; however, [...] Read more.
Potato tuber skin is a protective corky tissue consisting of suberized phellem cells. Smooth-skinned varieties are characterized by a clean, shiny appearance compared to the darker hue of russeted potatoes. The rough skin of russeted cultivars is a desired, genetically inherited characteristic; however, unwanted russeting of smooth-skinned cultivars often occurs under suboptimal growth conditions. The involvement of epigenetic modifiers in regulating the smooth skin russeting disorder was tested. We used smooth-skin commercial cultivars with and without the russeting disorder and three lines from a breeding population segregating for russeting. Anatomically, the russet skin showed similar characteristics, whether the cause was environmentally triggered or genetically determined. The old outer layers of the corky phellem remain attached to the newly formed phellem layers instead of being sloughed off. Global DNA methylation analysis indicated a significant reduction in the percentage of 5-methylcytosine in mature vs. immature skin and russet vs. smooth skin. This was true for both the smooth-skin commercial cultivars and the russeted lines. The expression level of selected DNA methyltransferases was reduced in accordance. DNA demethylase expression did not change between the skin types and age. Hence, the reduced DNA methylation in mature and russet skin is more likely to be achieved through passive DNA demethylation and loss of methyltransferase activity. Full article
(This article belongs to the Special Issue Beyond Mendel's Laws)
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18 pages, 26783 KiB  
Article
Festuca pratensis-like Subgenome Reassembly from a “Chromosomal Cocktail” in the Intergeneric Festulolium (Poaceae) Hybrid: A Rare Chromoanagenesis Event in Grasses
by Izolda Pašakinskienė
Plants 2023, 12(5), 984; https://doi.org/10.3390/plants12050984 - 21 Feb 2023
Cited by 1 | Viewed by 1259
Abstract
Festuca and Lolium grass species are used for Festulolium hybrid variety production where they display trait complementarities. However, at the genome level, they show antagonisms and a broad scale of rearrangements. A rare case of an unstable hybrid, a donor plant manifesting pronounced [...] Read more.
Festuca and Lolium grass species are used for Festulolium hybrid variety production where they display trait complementarities. However, at the genome level, they show antagonisms and a broad scale of rearrangements. A rare case of an unstable hybrid, a donor plant manifesting pronounced variability of its clonal parts, was discovered in the F2 group of 682 plants of Lolium multiflorum × Festuca arundinacea (2n = 6x = 42). Five phenotypically distinct clonal plants were determined to be diploids, having only 14 chromosomes out of the 42 in the donor. GISH defined the diploids as having the basic genome from F. pratensis (2n = 2x = 14), one of the progenitors of F. arundinacea (2n = 6x = 42), with minor components from L. multiflorum and another subgenome, F. glaucescens. The 45S rDNA position on two chromosomes also corresponded to the variant of F. pratensis in the F. arundinacea parent. In the highly unbalanced donor genome, F. pratensis was the least represented, but the most involved in numerous recombinant chromosomes. Specifically, FISH highlighted 45S rDNA-containing clusters involved in the formation of unusual chromosomal associations in the donor plant, suggesting their active role in karyotype realignment. The results of this study show that F. pratensis chromosomes have a particular fundamental drive for restructuring, which prompts the disassembly/reassembly processes. The finding of F. pratensis “escaping” and rebuilding itself from the chaotic “chromosomal cocktail” of the donor plant points to a rare chromoanagenesis event and extends the view of plant genome plasticity. Full article
(This article belongs to the Special Issue Beyond Mendel's Laws)
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11 pages, 495 KiB  
Article
Sex Determination in Dioscorea dumetorum: Evidence of Heteromorphic Sex Chromosomes and Sex-Linked NORs
by Florence Ngo Ngwe and Sonja Siljak-Yakovlev
Plants 2023, 12(2), 228; https://doi.org/10.3390/plants12020228 - 4 Jan 2023
Viewed by 1542
Abstract
Yams (Dioscorea spp.) are a pantropical genus located worldwide that constitute an important source of nutrients and pharmaceutical substances. Some Dioscorea crop species are widely grown in West Africa. One species that is mainly cultivated in Cameroon is Dioscorea dumetorum. This is [...] Read more.
Yams (Dioscorea spp.) are a pantropical genus located worldwide that constitute an important source of nutrients and pharmaceutical substances. Some Dioscorea crop species are widely grown in West Africa. One species that is mainly cultivated in Cameroon is Dioscorea dumetorum. This is a dioecious root crop whose sex-determining system was unknown until now. To address the possible presence of sex chromosomes in D. dumetorum, we performed a karyotype characterization of male and female individuals using classical and molecular cytogenetic approaches. It was determined that 2n = 40 was the most common number of chromosomes in all of the investigated samples. One chromosome pair was longer than the others in the chromosome set and was a heteromorph in male and homomorph in female individuals. This pair corresponded to sex chromosomes, and we also confirmed this with molecular cytogenetic experiments. The results of chromomycin banding revealed the presence of strong positive signals on this chromosome pair. The signals, corresponding to GC-rich DNA regions, were similar in size on the chromosomes of the female individuals, whereas they were different in size in the male individuals. This size difference in the GC-rich heterochromatin regions was also apparent in the interphase nuclei as one small and one large fluorescent spot. The results of the in situ hybridization experiment showed that these chromomycin positive signals on the sex chromosomes also corresponded to the 35S rDNA cluster. The mean 2C DNA value (genome size) obtained for D. dumentorum was 0.71 pg (±0.012), which represents a small genome size. We found no difference in the genome size between the male and female individuals. The results of this study contribute to increasing our knowledge of sex determination in D. dumetorum (standard sex-determining XX/XY system) and may have some agronomic applications. Full article
(This article belongs to the Special Issue Beyond Mendel's Laws)
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Review

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20 pages, 2542 KiB  
Review
Unveiling the Mysteries of Non-Mendelian Heredity in Plant Breeding
by Mohsen Yoosefzadeh Najafabadi, Mohsen Hesami and Istvan Rajcan
Plants 2023, 12(10), 1956; https://doi.org/10.3390/plants12101956 - 11 May 2023
Cited by 2 | Viewed by 3449
Abstract
Mendelian heredity is the cornerstone of plant breeding and has been used to develop new varieties of plants since the 19th century. However, there are several breeding cases, such as cytoplasmic inheritance, methylation, epigenetics, hybrid vigor, and loss of heterozygosity (LOH), where Mendelian [...] Read more.
Mendelian heredity is the cornerstone of plant breeding and has been used to develop new varieties of plants since the 19th century. However, there are several breeding cases, such as cytoplasmic inheritance, methylation, epigenetics, hybrid vigor, and loss of heterozygosity (LOH), where Mendelian heredity is not applicable, known as non-Mendelian heredity. This type of inheritance can be influenced by several factors besides the genetic architecture of the plant and its breeding potential. Therefore, exploring various non-Mendelian heredity mechanisms, their prevalence in plants, and the implications for plant breeding is of paramount importance to accelerate the pace of crop improvement. In this review, we examine the current understanding of non-Mendelian heredity in plants, including the mechanisms, inheritance patterns, and applications in plant breeding, provide an overview of the various forms of non-Mendelian inheritance (including epigenetic inheritance, cytoplasmic inheritance, hybrid vigor, and LOH), explore insight into the implications of non-Mendelian heredity in plant breeding, and the potential it holds for future research. Full article
(This article belongs to the Special Issue Beyond Mendel's Laws)
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