Genomic Variation in Sugarcane Home(o)logous Haplotypes

Modern sugarcane cultivars (Saccharum spp.) are derived from hybridization between S. officinarum (domesticated) and S. spontaneum (non-domesticate). The genome is highly polyploid, aneuploid and its size is estimated to be around 10Gb; in addition, it can exhibit variable ploidy among different loci. Due the sugarcane genome is highly polymorphic we investigate the variation in homo(e)logous haplotypes. For this purpose, the sugarcane bacterial artificial chromosome (BAC) library for the SP80-3280 variety (221,184 clones) was screened using one hypothetical gene to study the genome architecture. Twenty-two positive BAC clones were individually sequenced, assembled and manually annotated for genes and repeat regions. Twenty-three genes found in BACs have their orthologues compared with Sorghum (Sorghum bicolor), maize (Zea mays) and rice (Oryza sativa). The BACs revealed two different genomics regions with high conservative gene structure: a region composed by eight haplotypes having high colinearity with sorghum, rice and maize; and a second region, composed by nine haplotypes presenting low collinearity with sorghum, maize and rice. Two haplotypes groups revealed the gene used in BAC selection are duplicated in genome. The conservation in gene structure in both regions was used to analysis the molecular clock revealing a divergence time around 2.96 million years ago (Mya; +-0.12 Mya). Since the divergence between S. officinarum x S. Spontaneum happened around 1.5-2.7 Mya, this duplication probably exists in all Saccharum genus. In addition, exclusive repeat regions were found among the haplotypes. These results shown a high variation between haplotypes from same loci in sugarcane.