Recovering a Region in Sugarcane Through Sorghum Synteny

Sugarcane genome sequencing are a challenge because of their highly polyploidy and aneuploidy, exhibiting variable ploidy among different loci, genome size (around 10Gb) and high content of repetitive regions. Although the synteny between sugarcane and sorghum was explored to choose a QTL mapped for Brix in a specific position on sorghum chromosome 3 (SB-03). The sorghum genes founded in this region were used to identify the orthologous genes in sugarcane. Using the bacterial artificial chromosome (BAC) was possible access individual haplotypes for sugarcane genome. Thus, the sugarcane BAC library of the SP80-3280 variety (221,184 clones) was screened using 61 genes linked to a QTL for Brix in sorghum. Using double selection approach were selected 68 BACs, which it was positive for at least two genes. The positives BACs were pooled and sequenced using PacBio producing a deep sequencing with several millions of long reads. Each BAC was individually assembled using Celera and return 183 contigs. The contigs higher than 50 Kb were manually annotated for genes and transposable elements. The target region represenst about 700 Kb in sorghum, but in sugarcane resulted in 1.2 Mb. These results showed a high synteny between sugarcane and sorghum and can be an interesting approach for the sugarcane genome sequencing.

Keywords: Sorghum bicolor (L.) Moench, Saccharum officinarum, BAC library, polyploid, PacBio sequencing