1. Gene Duplication in the Sugarcane Genome: A Case Study of Allele Interactions and Evolutionary Patterns in Two Genic Regions
- Author
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Nathalie Rodde, Marie-Anne Van Sluys, Luciana Rossini Pinto, Melina Cristina Mancini, Marcos Guimarães de Andrade Landell, Hermann Paulo Hoffmann, Antonio Augusto Franco Garcia, Guilherme da Silva Pereira, Maria Victoria Romero-da Cruz, Michel Vincentz, Claudio Benicio Cardoso-Silva, Sonia Vautrin, Arnaud Bellec, Monalisa Sampaio Carneiro, Ana Paula de Souza, Renato Vicentini, Nair Dahmer, Joelle Fourment, M. Conte, Hélène Bergès, Eliana Regina Forni-Martins, Danilo Augusto Sforça, Universidade Estadual de Campinas (UNICAMP), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo (USP), Centro de Ciências Agrárias, Universidade Federal de Santa Catarina = Federal University of Santa Catarina [Florianópolis] (UFSC), Instituto Agronômico de Campinas, Sao Paulo Research Foundation (FAPESP) [2008/52197-4], Coordination for the Improvement of Higher Education Personnel (CAPES, Computational Biology Program), FAPESP [2010/50119-6, 2014/11482-9, 2015/16399-5], and National Council for Scientific and Technological Development (CNPq)
- Subjects
0106 biological sciences ,0301 basic medicine ,cartographie génomique ,physical mapping ,Pseudogene ,chimerical gene ,genetic mapping ,homologs ,polyploid ,sugarcane ,Genomics ,Plant Science ,lcsh:Plant culture ,Biology ,01 natural sciences ,Genome ,03 medical and health sciences ,Gene mapping ,Gene duplication ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,lcsh:SB1-1110 ,Gene ,Genome size ,Original Research ,2. Zero hunger ,Genetics ,Vegetal Biology ,food and beverages ,ALELOS ,030104 developmental biology ,Biologie végétale ,canne à sucre ,Orthologous Gene ,010606 plant biology & botany - Abstract
International audience; 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 (similar to 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.
- Published
- 2019