Advances in the Utilization of Next Generation Sequencing Data in the Colombian Sugarcane Breeding Program

Sugarcane is a polyploid/aneuploid crop with a chromosome number ranging between 2n = 80-130. This genomic complexity has made difficult the implementation of breeding strategies based on molecular markers. Importantly, the recent advances in next generation sequencing technologies (NGS) has increased the number of markers that can be used in genotyping studies and thus offer new possibilities in breeding programs.

At CENICAÑA, a diversity panel of 220 sugarcane genotypes, 130 representing the phenotypic diversity of CENICAÑA’s germplasm collection and 90 of breeding and economic importance for the center, was sequenced by means of GBS and RAD. Independently, each dataset was analyzed to identify high quality SNPs, determine the ratio of homozygous:heterozygous SNPs within a genotype, calculate genetic distances among individuals, define populations structure and explore phenotype-genotype, GWAS, associations.

Among our most relevant results we found that phylogenetic trees derived from GBS and RAD were not identical (groups coincided in 60%-70% of the cases), despite the high number of SNP markers used (>5,000). The ratio of homozygous:heterozygous SNPs always favored homozygosity, which was higher in RAD compared to GBS. These data combined with genetic distances indexes revealed parental genotypes with potential for crossings aiming to increase overall genetic diversity. Population structure analyses detected four subpopulations, which is in agreement with previous studies based on microsatellites. RAD sequencing performed better than GBS in detecting these subpopulations. This information was used in a GWAS approach were preliminary, significant, SNP-alleles were found for traits such as brix, reducing sugars and sucrose production.