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Unraveling the Genetic Control of Sexual Reproduction in Wild Plants...
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Unraveling the Genetic Control of Sexual Reproduction in Wild Plants and Their Domesticated Cousins

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

Deadline for manuscript submissions: closed (30 June 2021) | Viewed by 18439

Special Issue Editor

Dr. Roberta Bergero

E-Mail Website
Guest Editor
Institue of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH8 9YL, UK
Interests: sex chromosomes; meiotic recombination; evolutionary genetics; plant breeding systems; plant domestication

Special Issue Information

Dear Colleagues,

The switch from vegetative to reproductive growth is a fundamental developmental feature of flowering plants. It ensures that meiotic recombination is accomplished, and from a practical point of view, it ends in the production of seeds and fruits in crop species.

Genomic analyses coupled with molecular experimental work is yielding new and exciting knowledge on the genetics underlying the switch from vegetative to reproductive growth, together with identifying key genes acting as master switches for maleness and femaleness in angiosperms. The use of wild plant species in such studies holds the key to unraveling the natural diversity of the genetic control at reproductive stages, together with finding common ancestral evolutionary and molecular pathways. This knowledge can be complemented with studies on domesticated plant species to identify the genetic basis of the evolution of their unique reproductive features and the accompanying adaptive changes occurring during plant domestication.

This Special Issue will focus on reporting new original research and review articles on the genes and genomic features underlying sexual reproduction in wild flowering plants and their domesticated relatives.

Dr. Roberta Bergero
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. 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

  • Genetics of flowering plant
  • Plant reproduction
  • Sex-determining genes
  • Molecular pathways of maleness
  • Molecular pathways of femaleness
  • Plant breeding systems
  • Evolution of reproductive traits
  • Domesticated plants
  • Wild relatives

Published Papers (5 papers)

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Research

16 pages, 3846 KiB  
Article
A Draft Genome of the Ginger Species Alpinia nigra and New Insights into the Genetic Basis of Flexistyly
by Surabhi Ranavat, Hannes Becher, Mark F. Newman, Vinita Gowda and Alex D. Twyford
Genes 2021, 12(9), 1297; https://doi.org/10.3390/genes12091297 - 24 Aug 2021
Cited by 6 | Viewed by 4118
Abstract
Angiosperms possess various strategies to ensure reproductive success, such as stylar polymorphisms that encourage outcrossing. Here, we investigate the genetic basis of one such dimorphism that combines both temporal and spatial separation of sexual function, termed flexistyly. It is a floral strategy characterised [...] Read more.
Angiosperms possess various strategies to ensure reproductive success, such as stylar polymorphisms that encourage outcrossing. Here, we investigate the genetic basis of one such dimorphism that combines both temporal and spatial separation of sexual function, termed flexistyly. It is a floral strategy characterised by the presence of two morphs that differ in the timing of stylar movement. We performed a de novo assembly of the genome of Alpinia nigra using high-depth genomic sequencing. We then used Pool-seq to identify candidate regions for flexistyly based on allele frequency or coverage differences between pools of anaflexistylous and cataflexistylous morphs. The final genome assembly size was 2 Gb, and showed no evidence of recent polyploidy. The Pool-seq did not reveal large regions with high FST values, suggesting large structural chromosomal polymorphisms are unlikely to underlie differences between morphs. Similarly, no region had a 1:2 mapping depth ratio which would be indicative of hemizygosity. We propose that flexistyly is governed by a small genomic region that might be difficult to detect with Pool-seq, or a complex genomic region that proved difficult to assemble. Our genome will be a valuable resource for future studies of gingers, and provides the first steps towards characterising this complex floral phenotype. Full article
(This article belongs to the Special Issue Unraveling the Genetic Control of Sexual Reproduction in Wild Plants and Their Domesticated Cousins)
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18 pages, 3149 KiB  
Article
Sexual Difference in the Optimum Environmental Conditions for Growth and Maturation of the Brown Alga Undaria pinnatifida in the Gametophyte Stage
by Yoichi Sato, Hikaru Endo, Hiroki Oikawa, Koichi Kanematsu, Hiroyuki Naka, Miho Mogamiya, Shigeyuki Kawano and Yusuke Kazama
Genes 2020, 11(8), 944; https://doi.org/10.3390/genes11080944 - 16 Aug 2020
Cited by 9 | Viewed by 4259
Abstract
Undaria pinnatifida is an annual brown kelp growing naturally in coastal areas as a major primary producer in temperate regions and is cultivated on an industrial scale. Kelps have a heteromorphic life cycle characterized by a macroscopic sporophyte and microscopic sexual gametophytes. The [...] Read more.
Undaria pinnatifida is an annual brown kelp growing naturally in coastal areas as a major primary producer in temperate regions and is cultivated on an industrial scale. Kelps have a heteromorphic life cycle characterized by a macroscopic sporophyte and microscopic sexual gametophytes. The sex-dependent effects of different environmental factors on the growth and maturation characteristics of the gametophyte stage were investigated using response surface methodology. Gametophytes were taken from three sites in Japan: Iwate Prefecture, Tokushima Prefecture, and Kagoshima Prefecture in order to confirm the sexual differences in three independent lines. Optimum temperature and light intensity were higher for males (20.7–20.9 °C and 28.6–33.7 µmol m−2 s−1, respectively) than females (16.5–19.8 °C and 26.9–32.5 µmol m−2 s−1), and maturity progressed more quickly in males than females. Optimum wavelengths of light for growth and maturation of the gametophytes were observed for both blue (400–500 nm, λmax 453 nm) and green (500–600 nm; λmax 525 nm) lights and were sex-independent. These characteristics were consistent among the three regional lines. Slower growth optima and progress of maturation could be important for female gametophytes to restrict fertilization and sporophyte germination to the lower water temperatures of autumn and winter, and suggest that the female gametophyte may be more sensitive to temperature than the male. The sexual differences in sensitivity to environmental factors improved the synchronicity of sporeling production. Full article
(This article belongs to the Special Issue Unraveling the Genetic Control of Sexual Reproduction in Wild Plants and Their Domesticated Cousins)
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20 pages, 3237 KiB  
Article
Sequencing and Analysis of the Sex Determination Region of Populus trichocarpa
by Ran Zhou, David Macaya-Sanz, Jeremy Schmutz, Jerry W. Jenkins, Gerald A. Tuskan and Stephen P. DiFazio
Genes 2020, 11(8), 843; https://doi.org/10.3390/genes11080843 - 24 Jul 2020
Cited by 20 | Viewed by 3940
Abstract
The ages and sizes of a sex-determination region (SDR) are difficult to determine in non-model species. Due to the lack of recombination and enrichment of repetitive elements in SDRs, the quality of assembly with short sequencing reads is universally low. Unique features present [...] Read more.
The ages and sizes of a sex-determination region (SDR) are difficult to determine in non-model species. Due to the lack of recombination and enrichment of repetitive elements in SDRs, the quality of assembly with short sequencing reads is universally low. Unique features present in the SDRs help provide clues about how SDRs are established and how they evolve in the absence of recombination. Several Populus species have been reported with a male heterogametic configuration of sex (XX/XY system) mapped on chromosome 19, but the exact location of the SDR has been inconsistent among species, and thus far, none of these SDRs has been fully assembled in a genomic context. Here we identify the Y-SDR from a Y-linked contig directly from a long-read PacBio assembly of a Populus trichocarpa male individual. We also identified homologous gene sequences in the SDR of P. trichocarpa and the SDR of the W chromosome in Salix purpurea. We show that inverted repeats (IRs) found in the Y-SDR and the W-SDR are lineage-specific. We hypothesize that, although the two IRs are derived from the same orthologous gene within each species, they likely have independent evolutionary histories. Furthermore, the truncated inverted repeats in P. trichocarpa may code for small RNAs that target the homologous gene for RNA-directed DNA methylation. These findings support the hypothesis that diverse sex-determining systems may be achieved through similar evolutionary pathways, thereby providing a possible mechanism to explain the lability of sex-determination systems in plants in general. Full article
(This article belongs to the Special Issue Unraveling the Genetic Control of Sexual Reproduction in Wild Plants and Their Domesticated Cousins)
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18 pages, 2574 KiB  
Article
Evidence for Dosage Compensation in Coccinia grandis, a Plant with a Highly Heteromorphic XY System
by Cécile Fruchard, Hélène Badouin, David Latrasse, Ravi S. Devani, Aline Muyle, Bénédicte Rhoné, Susanne S. Renner, Anjan K. Banerjee, Abdelhafid Bendahmane and Gabriel A. B. Marais
Genes 2020, 11(7), 787; https://doi.org/10.3390/genes11070787 - 13 Jul 2020
Cited by 10 | Viewed by 3490
Abstract
About 15,000 angiosperms are dioecious, but the mechanisms of sex determination in plants remain poorly understood. In particular, how Y chromosomes evolve and degenerate, and whether dosage compensation evolves as a response, are matters of debate. Here, we focus on Coccinia grandis, [...] Read more.
About 15,000 angiosperms are dioecious, but the mechanisms of sex determination in plants remain poorly understood. In particular, how Y chromosomes evolve and degenerate, and whether dosage compensation evolves as a response, are matters of debate. Here, we focus on Coccinia grandis, a dioecious cucurbit with the highest level of X/Y heteromorphy recorded so far. We identified sex-linked genes using RNA sequences from a cross and a model-based method termed SEX-DETector. Parents and F1 individuals were genotyped, and the transmission patterns of SNPs were then analyzed. In the >1300 sex-linked genes studied, maximum X-Y divergence was 0.13–0.17, and substantial Y degeneration is implied by an average Y/X expression ratio of 0.63 and an inferred gene loss on the Y of ~40%. We also found reduced Y gene expression being compensated by elevated expression of corresponding genes on the X and an excess of sex-biased genes on the sex chromosomes. Molecular evolution of sex-linked genes in C. grandis is thus comparable to that in Silene latifolia, another dioecious plant with a strongly heteromorphic XY system, and cucurbits are the fourth plant family in which dosage compensation is described, suggesting it might be common in plants. Full article
(This article belongs to the Special Issue Unraveling the Genetic Control of Sexual Reproduction in Wild Plants and Their Domesticated Cousins)
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14 pages, 637 KiB  
Article
The Location of the Pseudoautosomal Boundary in Silene latifolia
by Marc Krasovec, Yu Zhang and Dmitry A. Filatov
Genes 2020, 11(6), 610; https://doi.org/10.3390/genes11060610 - 31 May 2020
Cited by 7 | Viewed by 2012
Abstract
Y-chromosomes contain a non-recombining region (NRY), and in many organisms it was shown that the NRY expanded over time. How and why the NRY expands remains unclear. Young sex chromosomes, where NRY expansion occurred recently or is on-going, offer an opportunity to study [...] Read more.
Y-chromosomes contain a non-recombining region (NRY), and in many organisms it was shown that the NRY expanded over time. How and why the NRY expands remains unclear. Young sex chromosomes, where NRY expansion occurred recently or is on-going, offer an opportunity to study the causes of this process. Here, we used the plant Silene latifolia, where sex chromosomes evolved ~11 million years ago, to study the location of the boundary between the NRY and the recombining pseudoautosomal region (PAR). The previous work devoted to the NRY/PAR boundary in S. latifolia was based on a handful of genes with locations approximately known from the genetic map. Here, we report the analysis of 86 pseudoautosomal and sex-linked genes adjacent to the S. latifolia NRY/PAR boundary to establish the location of the boundary more precisely. We take advantage of the dense genetic map and polymorphism data from wild populations to identify 20 partially sex-linked genes located in the “fuzzy boundary”, that rarely recombines in male meiosis. Genes proximal to this fuzzy boundary show no evidence of recombination in males, while the genes distal to this partially-sex-linked region are actively recombining in males. Our results provide a more accurate location for the PAR boundary in S. latifolia, which will help to elucidate the causes of PAR boundary shifts leading to NRY expansion over time. Full article
(This article belongs to the Special Issue Unraveling the Genetic Control of Sexual Reproduction in Wild Plants and Their Domesticated Cousins)
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