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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 (~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.

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