Generation of a 345K sugarcane SNP chip

DNA markers can enhance rates of genetic gain in breeding programs and are currently being applied in many animal and crop species. The very large sugarcane genome means that many current 'best bet' markers associated with agronomic traits of interest are probably not in very close linkage with underlying causal genes. This will limit gains from future applications of markers in sugarcane breeding. The development of single nucleotide polymorphism markers (SNPs) in sugarcane can overcome the current limitations as large numbers throughout the genome can be easily screened across many genotypes. To generate a SNP chip for sugarcane with large enough numbers of polymorphic single dose markers 16 lines were selected based on their contribution to the Australian breeding program. A reduced representation method (RRS) was used to generate sequencing libraries and two samples per lane were run on an Illumina Hi-seq to generate an expected coverage of at least 50x of a given genomic region. Sequences were aligned to a de novo reference contig assembly generated previously. SNPs were selected using categories designed to maximise low dose (single/double) and polymorphic SNPs across all the 16 lines. To determine genome-wide distribution, the selected SNPs were aligned to the sorghum genome. Affymetrix® Axiom® technology was identified as the most appropriate technology to use for sugarcane SNP screening. A 345K SNP chip was developed and used to screen a large association mapping population. We present preliminary data of this analysis and implications for application of this technology in sugarcane breeding.