New developments in sugarcane genetics and genomics

Abstract

Modern sugarcane cultivars (Saccharum spp.) are derived from an interspecific hybridization between Saccharum officinarum and Saccharum spontaneum and pose a significant challenge for both genotyping and data analysis. Due to their large (estimated at approximately 10 Gb) and complex genome, which can include variable ploidy levels and aneuploidy, studies involving molecular markers for genetic and quantitative trait locus (QTL) mapping are extremely laborious. Several advances in the genetics and genomics of sugarcane have recently become possible with the emergence of new sequencing technologies, the use of several types of marker systems, and the use of genotyping data analysis software. Molecular markers and comparative genomics are powerful resources that allow us to explore allelic variation and to thus understand the genome organization of sugarcane. This chapter provides an overview of what is known about the genetic structure and the genomics of sugarcane as well as the main genomics strategies developed for sugarcane. Among the strategies discussed are the use of single-nucleotide polymorphisms (SNPs) and bacterial artificial chromosome (BAC) libraries and the analysis of the syntenic relationships with related species (maize, sorghum, and rice).