Comparison of Homologous Haplotypes Around the Bru1 Locus Between Saccharum Species and Hybrid

Comparison of Homologous Haplotypes around the Bru1 Locus between Saccharum Species and Hybrid

Jisen Zhang, Qingyi Yu, Lin Zhu, Leiting Li, Ray Ming

Abstract:

Modern sugarcane cultivars are derived from interspecific hybridization between S. officinarum and S. spontaneum with 70-80% of the genome from S. officinarum, 10-20% of the genome from S. spontaneum, and 10% recombinants.  In order to investigate the pattern and degree of DNA sequence divergence between modern sugarcane and its ancestor genomes, we identified and characterized two haplotypes from S. spontaneum and four haplotypes from S. officinarum around the Bru1 locus, and compared them withthe seven homologous haplotypes from sugarcane hybrid R570. Our comparison analysis demonstrated that among the seven haplotypes from R570, four evolved from S. officinarum , two from S. spontaneum, and one recombinant. Gene exon splitting was observed only in the hybrid genome, not in its ancestor genomes, indicating genome rearrangements occurred after hybridization. Ka/Ks analysis of 12 unique genes revealed most homologous alleles were under purifying selection. Gene 6 haplotypes are highly conserved with a Ka of 0 between and within S. officinarum haplotypes and S.officinarum-origin haplotypes in hybrid, which indicated gene 6 might play an essential role. Significantly higher selective constraints were found in Saccharum-Sorghum than in Saccharum-Saccharum, suggesting a relaxed selection pressure in polyploidy genomes.

Keywords: Saccharum, polyploidy, Bru1 Locus, homologous genes, haplotypes