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Polyploidy and Evolution in Plants
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Polyploidy and Evolution in Plants

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Molecular Biology".

Deadline for manuscript submissions: closed (15 June 2021) | Viewed by 16699

Special Issue Editor

Dr. Abdulqader Jighly

E-Mail Website
Guest Editor
Department of Jobs, Precincts and Regions, Agriculture Victoria, Bundoora 3083, VIC, Australia
Interests: evolution; genetic diversity; population and quantitative genetics; polyploidy; simulation; statistical genetics; synthetic hexaploid wheat

Special Issue Information

Dear Colleagues,

The evolution of new polyploid organisms differs from that in diploids because the former require only one generation in which a single genome is duplicated (autopolyploid) or multiple genomes are hybridized (allopolyploids). This sudden change is usually followed by quick cytological modifications and genomic rearrangements within the first few generations. The existence of multiple homologous chromosomes in autopolyploid or homoeologous chromosomes in allopolyploid organisms can further diverge polyploids from their ancestral diploids as they affect the cytogenetics, genomics, and population genetics characteristics of the newly emerged organisms. The rapid evolution of polyploids is usually associated with a sever bottleneck, which can be retrieved through time with the generation of new spontaneous mutations, spreading of successful polyploids in new environments or the occurrences of multiple independent polyploidization events. It is possible to reproduce polyploidization events in lab which is usually used to introduce new variation into the gene pool of commercially important crops such as wheat, canola, sugarcane, potato, and cotton. Despite the commercial importance of these polyploid crops, the evolution of polyploid organisms has received less attention compared to diploids. This research topic aims to improve the current understandings of polyploidization in plants and the practical implications in plant breeding, conservation and genetics.

Dr. Abdulqader Jighly
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. 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.

Keywords

  • allopolyploids
  • autopolyploid
  • diplodization
  • evolution
  • plant breeding
  • plant conservation
  • plant genetics
  • polyploidization

Published Papers (5 papers)

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Research

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18 pages, 3644 KiB  
Article
Estimation of Genome Size in the Endemic Species Reseda pentagyna and the Locally Rare Species Reseda lutea Using comparative Analyses of Flow Cytometry and K-Mer Approaches
by Fahad Al-Qurainy, Abdel-Rhman Z. Gaafar, Salim Khan, Mohammad Nadeem, Aref M. Alshameri, Mohamed Tarroum, Saleh Alansi, Naser B. Almarri and Norah S. Alfarraj
Plants 2021, 10(7), 1362; https://doi.org/10.3390/plants10071362 - 03 Jul 2021
Cited by 8 | Viewed by 4716
Abstract
Genome size is one of the fundamental cytogenetic features of a species, which is critical for the design and initiation of any genome sequencing projects and can provide essential insights in studying taxonomy, cytogenetics, phylogenesis, and evolutionary studies. However, this key cytogenetic information [...] Read more.
Genome size is one of the fundamental cytogenetic features of a species, which is critical for the design and initiation of any genome sequencing projects and can provide essential insights in studying taxonomy, cytogenetics, phylogenesis, and evolutionary studies. However, this key cytogenetic information is almost lacking in the endemic species Reseda pentagyna and the locally rare species Reseda lutea in Saudi Arabia. Therefore, genome size was analyzed by propidium iodide PI flow cytometry and compared to k-mer analysis methods. The standard method for genome size measures (flow cytometry) estimated the genome size of R. lutea and R. pentagyna with nuclei isolation MB01 buffer were found to be 1.91 ± 0.02 and 2.09 ± 0.03 pg/2 °C, respectively, which corresponded approximately to a haploid genome size of 934 and 1.022 Mbp, respectively. For validation, K-mer analysis was performed on both species’ Illumina paired-end sequencing data from both species. Five k-mer analysis approaches were examined for biocomputational estimation of genome size: A general formula and four well-known programs (CovEST, Kmergenie, FindGSE, and GenomeScope). The parameter preferences had a significant impact on GenomeScope and Kmergenie estimates. While the general formula estimations did not differ considerably, with an average genome size of 867.7 and 896. Mbp. The differences across flow cytometry and biocomputational predictions may be due to the high repeat content, particularly long repetitive regions in both genomes, 71% and 57%, which interfered with k-mer analysis. GenomeScope allowed quantification of high heterozygosity levels (1.04 and 1.37%) of R. lutea and R. pentagyna genomes, respectively. Based on our observations, R. lutea may have a tetraploid genome or higher. Our results revealed fundamental cytogenetic information for R. lutea and R. pentagyna, which should be used in future taxonomic studies and whole-genome sequencing. Full article
(This article belongs to the Special Issue Polyploidy and Evolution in Plants)
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17 pages, 4115 KiB  
Article
Evolutionary Divergence and Biased Expression of NAC Transcription Factors in Hexaploid Bread Wheat (Triticum aestivum L.)
by Jianhui Ma, Meng Yuan, Bo Sun, Daijing Zhang, Jie Zhang, Chunxi Li, Yun Shao, Wei Liu and Lina Jiang
Plants 2021, 10(2), 382; https://doi.org/10.3390/plants10020382 - 17 Feb 2021
Cited by 9 | Viewed by 2167
Abstract
The NAC genes, a large plant-specific family of transcription factors, regulate a wide range of pathways involved in development and response to biotic and abiotic stress. In this study, the NAC transcription factors were identified in 27 green plants, and the results showed [...] Read more.
The NAC genes, a large plant-specific family of transcription factors, regulate a wide range of pathways involved in development and response to biotic and abiotic stress. In this study, the NAC transcription factors were identified in 27 green plants, and the results showed that NAC transcription factors in plants undergo an appearance stage from water to land and a number expansion stage from gymnosperm to angiosperm. Investigating the evolutionary process of the NAC transcription factors from diploid species to hexaploid wheat revealed that tandem replications during the polyploidization process is an important event for increasing the number of NAC transcription factors in wheat. Then, the molecular characteristics, phylogenetic relationships, and expression patterns of 462 NAC transcription factors of hexaploid wheat (TaNACs) were analyzed. The protein structure results showed that TaNAC was relatively conservative at the N-terminal that contains five subdomains. All these TaNACs were divided into Group I and Group II by phylogenetic analysis, and the TaNACs in Group I should undergo strong artificial selection based on single nucleotide polymorphism (SNP) analysis. Through genome synteny and phylogenetic analysis, these TaNACs were classified into 88 groups and 9 clusters. The biased expression results of these TaNACs showed that there are 24 groups and 67 groups of neofunctionalization genes under biotic and abiotic stress, respectively, and 16 groups and 59 groups of subfunctionalization genes. This shows that neofunctionalization plays an important role in coping with different stresses. Our study provides new insights into the evolution of NAC transcription factors in hexaploid wheat. Full article
(This article belongs to the Special Issue Polyploidy and Evolution in Plants)
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12 pages, 2624 KiB  
Article
Sampling Variation of RAD-Seq Data from Diploid and Tetraploid Potato (Solanum tuberosum L.)
by Zhenyu Dang, Jixuan Yang, Lin Wang, Qin Tao, Fengjun Zhang, Yuxin Zhang and Zewei Luo
Plants 2021, 10(2), 319; https://doi.org/10.3390/plants10020319 - 07 Feb 2021
Cited by 2 | Viewed by 2197
Abstract
The new sequencing technology enables identification of genome-wide sequence-based variants at a population level and a competitively low cost. The sequence variant-based molecular markers have motivated enormous interest in population and quantitative genetic analyses. Generation of the sequence data involves a sophisticated experimental [...] Read more.
The new sequencing technology enables identification of genome-wide sequence-based variants at a population level and a competitively low cost. The sequence variant-based molecular markers have motivated enormous interest in population and quantitative genetic analyses. Generation of the sequence data involves a sophisticated experimental process embedded with rich non-biological variation. Statistically, the sequencing process indeed involves sampling DNA fragments from an individual sequence. Adequate knowledge of sampling variation of the sequence data generation is one of the key statistical properties for any downstream analysis of the data and for implementing statistically appropriate methods. This paper reports a thorough investigation on modeling the sampling variation of the sequence data from the optimized RAD-seq (Restriction sit associated DNA sequencing) experiments with two parents and their offspring of diploid and autotetraploid potato (Solanum tuberosum L.). The analysis shows significant dispersion in sampling variation of the sequence data over that expected under multinomial distribution as widely assumed in the literature and provides statistical methods for modeling the variation and calculating the model parameters, which may be easily implemented in real sequence datasets. The optimized design of RAD-seq experiments enabled effective control of presentation of undesirable chloroplast DNA and RNA genes in the sequence data generated. Full article
(This article belongs to the Special Issue Polyploidy and Evolution in Plants)
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18 pages, 3938 KiB  
Article
Characterization and Stress Response of the JmjC Domain-Containing Histone Demethylase Gene Family in the Allotetraploid Cotton Species Gossypium hirsutum
by Jie Zhang, Junping Feng, Wei Liu, Zhongying Ren, Junjie Zhao, Xiaoyu Pei, Yangai Liu, Daigang Yang and Xiongfeng Ma
Plants 2020, 9(11), 1617; https://doi.org/10.3390/plants9111617 - 20 Nov 2020
Cited by 7 | Viewed by 2686
Abstract
Histone modification is an important epigenetic modification that controls gene transcriptional regulation in eukaryotes. Histone methylation is accomplished by histone methyltransferase and can occur on two amino acid residues, arginine and lysine. JumonjiC (JmjC) domain-containing histone demethylase regulates gene transcription and chromatin structure [...] Read more.
Histone modification is an important epigenetic modification that controls gene transcriptional regulation in eukaryotes. Histone methylation is accomplished by histone methyltransferase and can occur on two amino acid residues, arginine and lysine. JumonjiC (JmjC) domain-containing histone demethylase regulates gene transcription and chromatin structure by changing the methylation state of the lysine residue site and plays an important role in plant growth and development. In this study, we carried out genome-wide identification and comprehensive analysis of JmjC genes in the allotetraploid cotton species Gossypium hirsutum. In total, 50 JmjC genes were identified and in G. hirsutum, and 25 JmjC genes were identified in its two diploid progenitors, G. arboreum and G. raimondii, respectively. Phylogenetic analysis divided these JmjC genes into five subfamilies. A collinearity analysis of the two subgenomes of G. hirsutum and the genomes of G. arboreum and G. raimondii uncovered a one-to-one relationship between homologous genes of the JmjC gene family. Most homologs in the JmjC gene family between A and D subgenomes of G. hirsutum have similar exon-intron structures, which indicated that JmjC family genes were conserved after the polyploidization. All G. hirsutumJmjC genes were found to have a typical JmjC domain, and some genes also possess other special domains important for their function. Analysis of promoter regions revealed that cis-acting elements, such as those related to hormone and abiotic stress response, were enriched in G. hirsutum JmjC genes. According to a reverse transcription-quantitative polymerase chain reaction (RT-qPCR) analysis, most G. hirsutumJmjC genes had high abundance expression at developmental stages of fibers, suggesting that they might participate in cotton fiber development. In addition, some G. hirsutumJmjC genes were found to have different degrees of response to cold or osmotic stress, thus indicating their potential role in these types of abiotic stress response. Our results provide useful information for understanding the evolutionary history and biological function of JmjC genes in cotton. Full article
(This article belongs to the Special Issue Polyploidy and Evolution in Plants)
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Review

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14 pages, 297 KiB  
Review
A New Way of Rice Breeding: Polyploid Rice Breeding
by Rongrong Chen, Ziyi Feng, Xianhua Zhang, Zhaojian Song and Detian Cai
Plants 2021, 10(3), 422; https://doi.org/10.3390/plants10030422 - 24 Feb 2021
Cited by 25 | Viewed by 3770
Abstract
Polyploid rice, first discovered by Japanese scientist Eiiti Nakamori in 1933, has a history of nearly 90 years. In the following years, polyploid rice studies have mainly focused on innovations in breeding theory, induction technology and the creation of new germplasm, the analysis [...] Read more.
Polyploid rice, first discovered by Japanese scientist Eiiti Nakamori in 1933, has a history of nearly 90 years. In the following years, polyploid rice studies have mainly focused on innovations in breeding theory, induction technology and the creation of new germplasm, the analysis of agronomic traits and nutritional components, the study of gametophyte development and reproduction characteristics, DNA methylation modification and gene expression regulation, distant hybridization and utilization among subspecies, species and genomes. In recent years, PMeS lines and neo-tetraploid rice lines with stable high seed setting rate characteristics have been successively selected, breaking through the bottleneck of low seed setting rate of polyploid rice. Following, a series of theoretical and applied studies on high seed setting rate tetraploid rice were carried out. This has pushed research on polyploid rice to a new stage, opening new prospects for polyploid rice breeding. Full article
(This article belongs to the Special Issue Polyploidy and Evolution in Plants)
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