Target Enrichment Sequencing of 300 Representative Accessions in the Sugarcane World Germplasm Collection

Sugarcane (Saccharum spp.) is an important sugar and bioenergy crop. High level of polyploid have been challenges to unlock the genetic machinery controlling complex traits of sugarcane. Target enrichment sequencing of 300 representative accessions, a condensed assembly of the World Collection of Sugarcane and Related Grasses (WCSRG), will not only shed light on characterization of sequence divergence of this complex crop, but also on identification of the alleles controlling agronomic traits. Genomics regions spanning a total of 6 Mb of 307 accessions, including 300 accessions from WCSRG and seven modern cultivars were deep sequenced. In total, 3,4 million SNPs across 307 clones were identified, which included 2.5 million bi-allelic and 0.9 million multi-allelic SNP loci. Out of 3.4 million SNPs, 1,192,505 (35.3 %) and 1,365,196 (40.4 %) were located in exons and introns of the gene models, respectively, according to sorghum genome. The SNPs located on the exon regions included 697,275 nonsynonymous and 457,712 synonymous SNPs. The rest SNPs, 358,213 (13%) and 465,803 (10%) located on intergenic regions and UTRs. A total of 32,467 SNPs with significant effects on gene functions were predicted. Linkage disequilibrium (LD) was measured within sub-populations defined by using the discriminant analysis of principal components (DAPC) method. The compressed MLM approach was used to identify association signals and positive association for five traits: stalk number, glucan content, internode length, leaf width and xylan content were identified. The findings provided deep insight of the sugarcane complex genome variations and substantial genetic information for sugarcane and energy cane improvement.