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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

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

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Sforca, Danilo Augusto [1] ; Vautrin, Sonia [2] ; Cardoso-Silva, Claudio Benicio [1] ; Mancini, Melina Cristina [1] ; Romero-da Cruz, Maria Victoria [1] ; Pereira, Guilherme da Silva [3] ; Conte, Monica [1] ; Bellec, Arnaud [2] ; Dahmer, Nair [1] ; Fourment, Joelle [2] ; Rodde, Nathalie [2] ; Van Sluys, Marie-Anne [4] ; Vicentini, Renato [1] ; Franco Garcia, Antonio Augusto [3] ; Forni-Martins, Eliana Regina [1] ; Carneiro, Monalisa Sampaio [5] ; Hoffmann, Hermann Paulo [5] ; Pinto, Luciana Rossini [6] ; de Andrade Landell, Marcos Guimaraes [6] ; Vincentz, Michel [1] ; Berges, Helene [2] ; de Souza, Anete Pereira [1]
Total Authors: 22
Affiliation:
[1] Univ Estadual Campinas UNICAMP, Campinas, SP - Brazil
[2] INRA, CNRGV, Castanet Tolosan - France
[3] Univ Sao Paulo, Escola Super Agr Luiz de Queiroz ESALQ, Piracicaba - Brazil
[4] Univ Sao Paulo, Inst Biociencias, Sao Paulo - Brazil
[5] Univ Fed Sao Carlos UFSCAR, Ctr Ciencias Agr, Araras - Brazil
[6] IAC, Ctr Cana, Ribeirao Preto - Brazil
Total Affiliations: 6
Document type: Journal article
Source: FRONTIERS IN PLANT SCIENCE; v. 10, MAY 7 2019.
Web of Science Citations: 0
Abstract

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. (AU)

FAPESP's process: 15/16399-5 - Balance between dosage and allelic expression to map the global gene expression profile in sugarcane
Grantee:Cláudio Benício Cardoso da Silva
Support type: Scholarships in Brazil - Post-Doctorate
FAPESP's process: 08/52197-4 - Genomic-assisted breeding of sugarcane: using molecular markers for understanding the genetic architecture of quantitative traits and to implement marker assisted selection
Grantee:Anete Pereira de Souza
Support type: Program for Research on Bioenergy (BIOEN) - Thematic Grants
FAPESP's process: 14/11482-9 - Evaluation of genomic synteny between sorghum (Sorghum bicolor) and sugarcane (Saccharum officinarum): comparision of genes involved in a QTL for Brix in sorghum to syntenic region in sugarcane
Grantee:Melina Cristina Mancini
Support type: Scholarships in Brazil - Post-Doctorate