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 (~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.
Highlights
The Saccharum species are C4 grasses and present a high level of ploidy
Transcriptome, evolutionary patterns and genetic interactions/relationships of HP600 and CENP-C in a genomic region from the SP80-3280 sugarcane variety
A comparison of the bacterial artificial chromosomes (BACs) haplotypes from Region01 and Region02 revealed an 8-kb shared region in sugarcane
Summary
The Saccharum species are C4 grasses and present a high level of ploidy. S. officinarum L. is an octaploid (2n = 80) with x = 10 chromosomes, while S. spontaneum L. has x = 8 but presents great variations in the number of chromosomes, with main the cytotypes of 2n = 62, 80, 96, 112, or 128. The evolutionary success of polyploid species is related to their ability to present greater phenotypic novelty than is observed in their diploid counterparts or even absent in parents (Ramsey and Schemske, 2002) Among other factors, this increase in the capacity for phenotypic variation capacity may be caused by regulation of the allelic dosage (Birchler et al, 2005). The genomic similarity between sugarcane and sorghum has been frequently used to characterize the sugarcane genome (Jannoo et al, 2007; Garsmeur et al, 2011, 2018; Vilela et al, 2017; Mancini et al, 2018), demonstrating the high synteny of sugarcane × sorghum and the high gene structure retention among the different sugarcane homeologs These works contribute to understanding the genomic and evolutionary relationships among important genes in sugarcane using BAC libraries. We used molecular markers developed from these genes to genotype a segregating population and construct a linkage map and compare it with the physical map
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