Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Genetic variation in a complex polyploid: unveiling the dynamic allelic features of sugarcane

View ORCID ProfileDanilo Augusto Sforça, Sonia Vautrin, Claudio Benicio Cardoso-Silva, Melina Cristina Mancini, María Victoria Romero da Cruz, Guilherme da Silva Pereira, Mônica Conte, Arnaud Bellec, Nair Dahmer, Joelle Fourment, Nathalie Rodde, Marie-Anne Van Sluys, Renato Vicentini, Antônio Augusto Franco Garcia, Eliana Regina Forni-Martins, Monalisa Sampaio Carneiro, Hermann Paulo Hoffmann, Luciana Rossini Pinto, Marcos Guimarães de Andrade Landell, Michel Vincentz, View ORCID ProfileHelene Berges, Anete Pereira Souza
doi: https://doi.org/10.1101/361089
Danilo Augusto Sforça
1Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Danilo Augusto Sforça
Sonia Vautrin
2Centre National de Ressources Genomiques Vegetales (CNRGV), Institut National de la Recherche Agronomique (INRA), Castanet Tolosan, France
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Claudio Benicio Cardoso-Silva
1Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Melina Cristina Mancini
1Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
María Victoria Romero da Cruz
1Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Guilherme da Silva Pereira
3Escola Superior de Agricultura Luiz de Queiroz (ESALQ), USP, Piracicaba, SP, Brazil
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Mônica Conte
1Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Arnaud Bellec
2Centre National de Ressources Genomiques Vegetales (CNRGV), Institut National de la Recherche Agronomique (INRA), Castanet Tolosan, France
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Nair Dahmer
1Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Joelle Fourment
2Centre National de Ressources Genomiques Vegetales (CNRGV), Institut National de la Recherche Agronomique (INRA), Castanet Tolosan, France
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Nathalie Rodde
2Centre National de Ressources Genomiques Vegetales (CNRGV), Institut National de la Recherche Agronomique (INRA), Castanet Tolosan, France
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Marie-Anne Van Sluys
4Universidade de São Paulo, USP, São Paulo, SP, Brazil
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Renato Vicentini
1Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Antônio Augusto Franco Garcia
3Escola Superior de Agricultura Luiz de Queiroz (ESALQ), USP, Piracicaba, SP, Brazil
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Eliana Regina Forni-Martins
1Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Monalisa Sampaio Carneiro
5Universidade Federal de São Carlos (UFSCAR), Araras, SP, Brazil
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Hermann Paulo Hoffmann
5Universidade Federal de São Carlos (UFSCAR), Araras, SP, Brazil
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Luciana Rossini Pinto
6Centro de Cana, Instituto Agronômico de Campinas, São Paulo, SP, Brazil
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Marcos Guimarães de Andrade Landell
6Centro de Cana, Instituto Agronômico de Campinas, São Paulo, SP, Brazil
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Michel Vincentz
1Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Helene Berges
2Centre National de Ressources Genomiques Vegetales (CNRGV), Institut National de la Recherche Agronomique (INRA), Castanet Tolosan, France
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Helene Berges
Anete Pereira Souza
1Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

Abstract

Background Sugarcane (Saccharum spp.) is highly polyploid and aneuploid. Modern cultivars are derived from hybridization between S. officinarum and S. spontaneum. This combination results in a genome exhibiting variable ploidy among different loci, a huge genome size (approximately 10 Gb) and a high content of repetitive regions. Gene expression mechanisms are poorly understood in these cultivars. An approach using genomic, transcriptomic and genetic mapping can improve our knowledge of the behavior of genetics in sugarcane.

Results The hypothetical HP600 and centromere protein C (CENP-C) genes from sugarcane were used to elucidate the allelic expression and genomic and genetic behavior of this complex polyploid. The genomically side-by-side genes HP600 and CENP-C were found in two different homeologous chromosome groups with ploidies of eight and ten. The first region (Region01) was a Sorghum bicolor ortholog with all haplotypes of HP600 and CENP- C expressed, but HP600 exhibited an unbalanced haplotype expression. The second region (Region02) was a scrambled sugarcane sequence formed from different noncollinear genes containing duplications of HP600 and CENP-C (paralogs). This duplication occurred before the Saccharum genus formation and after the separation of sorghum and sugarcane, resulting in a nonexpressed HP600 pseudogene and a recombined fusion version of CENP-C and orthologous gene Sobic.003G299500 with at least two chimerical gene haplotypes expressed. The genetic map construction supported the difficulty of mapping markers located in duplicated regions of complex polyploid genomes.

Conclusion All these findings describe a low synteny region in sugarcane, formed by events occurring in all members of the Saccharum genus. Additionally, evidence of duplicated and truncate gene expression and the behavior of genetic markers in a duplicated region was found. Thus, we describe the complexity involved in sugarcane genetics and genomics and allelic dynamics, which can be useful for understanding the complex polyploid genome.

  • List of abbreviations

    ºC
    Celsius degrees
    BACs
    Bacterial Artificial Chromosomes
    BES
    BAC ends sequencing
    Bp
    base pairs
    BRIX
    Soluble solid content
    CDS
    Coding DNA sequence
    CenH3
    histone H3
    CENP-C
    Centromere protein C
    CMA
    A3 Chromomycin
    DAPI
    4’,6-diamidino-2-phenylindole
    DNA
    Deoxyribonucleic acid
    EST
    Expressed Sequence Tag
    FISH
    Fluorescent in situ hybridization
    Gb
    Giga-base pairs
    GBS
    Genotyping by sequencing
    HMW
    High-molecular-weight
    Kb
    Kilo-base pairs
    QTL
    Quantitative Trait Loci
    LTR
    Long Terminal Repeat
    Min
    Minutes
    Mya
    Millions Years Ago
    PCR
    Polymerase chain reaction
    PFGE
    Pulsed Field Gel Electrophoresis
    RNA
    Ribonucleic acid
    RNAseq
    RNA sequencing
    Sec
    Seconds
    SNP
    Single Nucleotide Polymorphism
    TEs
    Transposable Elements
  • Copyright 
    The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
    Back to top
    PreviousNext
    Posted August 21, 2018.
    Download PDF

    Supplementary Material

    Email

    Thank you for your interest in spreading the word about bioRxiv.

    NOTE: Your email address is requested solely to identify you as the sender of this article.

    Enter multiple addresses on separate lines or separate them with commas.
    Genetic variation in a complex polyploid: unveiling the dynamic allelic features of sugarcane
    (Your Name) has forwarded a page to you from bioRxiv
    (Your Name) thought you would like to see this page from the bioRxiv website.
    CAPTCHA
    This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
    Share
    Genetic variation in a complex polyploid: unveiling the dynamic allelic features of sugarcane
    Danilo Augusto Sforça, Sonia Vautrin, Claudio Benicio Cardoso-Silva, Melina Cristina Mancini, María Victoria Romero da Cruz, Guilherme da Silva Pereira, Mônica Conte, Arnaud Bellec, Nair Dahmer, Joelle Fourment, Nathalie Rodde, Marie-Anne Van Sluys, Renato Vicentini, Antônio Augusto Franco Garcia, Eliana Regina Forni-Martins, Monalisa Sampaio Carneiro, Hermann Paulo Hoffmann, Luciana Rossini Pinto, Marcos Guimarães de Andrade Landell, Michel Vincentz, Helene Berges, Anete Pereira Souza
    bioRxiv 361089; doi: https://doi.org/10.1101/361089
    Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
    Citation Tools
    Genetic variation in a complex polyploid: unveiling the dynamic allelic features of sugarcane
    Danilo Augusto Sforça, Sonia Vautrin, Claudio Benicio Cardoso-Silva, Melina Cristina Mancini, María Victoria Romero da Cruz, Guilherme da Silva Pereira, Mônica Conte, Arnaud Bellec, Nair Dahmer, Joelle Fourment, Nathalie Rodde, Marie-Anne Van Sluys, Renato Vicentini, Antônio Augusto Franco Garcia, Eliana Regina Forni-Martins, Monalisa Sampaio Carneiro, Hermann Paulo Hoffmann, Luciana Rossini Pinto, Marcos Guimarães de Andrade Landell, Michel Vincentz, Helene Berges, Anete Pereira Souza
    bioRxiv 361089; doi: https://doi.org/10.1101/361089

    Citation Manager Formats

    • BibTeX
    • Bookends
    • EasyBib
    • EndNote (tagged)
    • EndNote 8 (xml)
    • Medlars
    • Mendeley
    • Papers
    • RefWorks Tagged
    • Ref Manager
    • RIS
    • Zotero
    • Tweet Widget
    • Facebook Like
    • Google Plus One

    Subject Area

    • Plant Biology
    Subject Areas
    All Articles
    • Animal Behavior and Cognition (3592)
    • Biochemistry (7562)
    • Bioengineering (5508)
    • Bioinformatics (20762)
    • Biophysics (10309)
    • Cancer Biology (7967)
    • Cell Biology (11627)
    • Clinical Trials (138)
    • Developmental Biology (6602)
    • Ecology (10190)
    • Epidemiology (2065)
    • Evolutionary Biology (13594)
    • Genetics (9532)
    • Genomics (12834)
    • Immunology (7917)
    • Microbiology (19525)
    • Molecular Biology (7651)
    • Neuroscience (42027)
    • Paleontology (307)
    • Pathology (1254)
    • Pharmacology and Toxicology (2196)
    • Physiology (3263)
    • Plant Biology (7029)
    • Scientific Communication and Education (1294)
    • Synthetic Biology (1949)
    • Systems Biology (5422)
    • Zoology (1114)