Development of a high-throughput, low-cost SNP genotyping panel for sugarcane breeding

SUGARCANE (SACCHARUM SPP.) IS one of the world's most important economic crops, grown for its sugar and biofuel production. Investigating genomic sequence variation is critical for identifying alleles contributing to important agronomic traits. The development and delivery of varieties that are higher yielding and disease resistant is one of the main research goals in sugarcane breeding. To achieve this, sugarcane breeding is focusing on genetic improvement programs assisted by single nucleotide polymorphisms (SNP) molecular markers. SNPs are now the molecular marker of choice in animal and crop breeding programs around the world because very large numbers of SNPs per genotype can be accurately screened for, and are amenable to high-throughput screening. However, a particular difficulty when working at the DNA level with sugarcane is its highly complex and polyploid genome. The development of SNP markers in sugarcane can overcome the current limitations as large numbers throughout the genome can be easily screened across many genotypes. Recently, an Affymetrix® Axiom® 45K SNP chip was developed for sugarcane and has dramatically improved the construction of high-density linkage maps and identification of target QTLs for agronomic traits in sugarcane. Marker-assisted selection (MAS) in plant breeding requires markers that are tightly linked to genes of interest and are cost-effective. The use of high-density SNP chips, such as the Axiom® sugarcane SNP chip, for MAS is still price-prohibitive in sugarcane breeding. The objective of this study was to develop a low-density, low-cost SNP panel that could be used for selection of disease resistant clones in the breeding program. Initially, we used the 45K sugarcane SNP chip to identify new markers, which were found to be linked to resistance to smut across different genetic backgrounds. A comparison was then made of these SNP markers converted to two different SNP marker technologies, the LGC® KASPTM assay and the Fluidigm® SNPTypeTM assay, for the development of a high-throughput, low-cost SNP marker panel for disease resistance in sugarcane. We discuss aspects that should be considered during the design of these SNP genotyping arrays, including the importance of validation of SNP markers in diverse genetic backgrounds, costs of marker implementation and decisions on where to use markers in the breeding program. These results offer promise for making selection during the breeding process more rapid, accurate and less expensive and could result in the faster delivery of new disease resistant varieties to the sugarcane industry.