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Front. Plant Sci. | doi: 10.3389/fpls.2019.00553

Gene Duplication in the Sugarcane Genome: a Case Study of Allele Interactions and Evolutionary Patterns in Two Genic Regions

 Danilo A. Sforça1, Sonia Vautrin2,  Claudio B. Cardoso-Silva1,  Melina C. Mancini1,  Maria V. Cruz1,  Guilherme S. Pereira3, Monica Conte1,  Arnaud Bellec2, Nair Dahmer1, Joelle Fourment2,  Nathalie Rodde2,  Marie-Anne Van Sluys4,  Renato Vicentini1, Antonio A. Garcia3,  Eliana R. Forni-Martins1,  Monalisa S. Carneiro5, Hermann P. Hoffmann5,  Luciana R. Pinto6, Marcos G. Landell6, Michel Vincentz1,  HELENE BERGES2 and  Anete Pereira de Souza1*
  • 1Campinas State University, Brazil
  • 2INRA Centre National de Ressources Génomique Végétales (CNRGV), France
  • 3Luiz de Queiroz College of Agriculture, University of São Paulo, Brazil
  • 4University of São Paulo, Brazil
  • 5Federal University of São Carlos, Brazil
  • 6Centro de Cana, Instituto Agronômico de Campinas (IAC), Brazil

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. An approach using genomic, transcriptomic and genetic mapping can improve our knowledge of the behavior of genetics in sugarcane. The hypothetical HP600 and Centromere Protein C (CENP-C) genes from sugarcane were used to elucidate the allelic expression and genomic and genetic behaviors of this complex polyploid. The physically linked 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 region 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 partial duplications of HP600 and CENP-C (paralogs). This duplication resulted in a non-expressed HP600 pseudogene and a recombined fusion version of CENP-C and the orthologous gene Sobic.003G299500 with at least two chimeric gene haplotypes expressed. It was also determined that it occurred before Saccharum genus formation and after the separation of sorghum and sugarcane. A linkage map was constructed using markers from nonduplicated Region01 and for the duplication (Region01 and Region02). We compare the physical and linkage maps, demonstrating the possibility of mapping markers located in duplicated regions with markers in nonduplicated region. Our results contribute directly to the improvement of linkage mapping in complex polyploids and improve the integration of physical and genetic data for sugarcane breeding programs. Thus, we describe the complexity involved in sugarcane genetics and genomics and allelic dynamics, which can be useful for understanding complex polyploid genomes.

Keywords: chimerical gene, genetic mapping, Homologs detection, Physical mapping, polyploid, Sugarcane (Saccharum hybrid complex)

Received: 16 Jan 2019; Accepted: 11 Apr 2019.

Edited by:

Jacqueline Batley, University of Western Australia, Australia

Reviewed by:

Aureliano Bombarely, University of Milan, Italy
Robert VanBuren, Michigan State University, United States  

Copyright: © 2019 Sforça, Vautrin, Cardoso-Silva, Mancini, Cruz, Pereira, Conte, Bellec, Dahmer, Fourment, Rodde, Van Sluys, Vicentini, Garcia, Forni-Martins, Carneiro, Hoffmann, Pinto, Landell, Vincentz, BERGES and Pereira de Souza. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Prof. Anete Pereira de Souza, Campinas State University, Campinas, 13083-970, São Paulo, Brazil, anete@unicamp.br