Validation of single nucleotide polymorphisms (SNPs) in sugarcane ESTs as useful genetic markers : SRDC final report ICB010

Abstract

Sugarcane is one of the most important field crops grown in the tropics and subtropics. It possesses a highly complex genome, with multiple copies of a single gene present. Breeding of improved cultivars of sugarcane is difficult because most traits are derived from multiple genes and are quantitatively inherited. The complexity of the sugarcane genome makes sugarcane breeding and genetic analysis a challenge. Commercial sugarcane plants are the result of a limited series of crosses and backcrosses derived from the domesticated species Saccharum officinarum L. (2n = 80) and the wild species S. spontaneum (2n = 40 – 120). As a result of this process, commercial sugarcane plants are interspecific poly-aneuploid hybrids with chromosome numbers usually in excess of 100. Single nucleotide polymorphisms (SNPs) are an alteration of one nucleotide in a DNA sequence. These single changes can be detected and used as markers, and because their occurrence is frequent, they provide a large source of genetic markers. SNP markers represent the smallest possible genetic difference and the largest source of genetic markers. This project takes advantage of these nucleotide differences as a new strategy for analysis of traits in sugarcane, and also takes advantage of new technologies to measure these sequence variations. The marker system makes use of the Pyrosequencer, a sophisticated instrument that uses, through a series of biochemical reactions, light emissions to detect these differences in the genetic sequence and ultimately determines the different proportions of alleles present for a particular gene. The application of this technology although not new to organisms carrying only a diploid genome such as humans, has never been applied to a genetic system with such a high level of complexity as sugarcane. Through a collaborative effort with the International Consortium for Sugarcane Biotechnology (ICSB), an initial set of 33 markers have been developed. We have now shown that with the aid of these markers, it is possible to utilise these minor differences in gene sequence to deduce the allele content in different sugarcane genotypes. The technology is able to identify the origins of an allele in commercial canes, indicating its history from either a Saccharum officinarum or S. spontaneum parent. It also provides a ‘fingerprint’ of different sugarcane genotypes that allows the breeder to determine the genetic relatedness of any two varieties. However, the most powerful application of the SNP marker system will be in the identification of combinations of SNPs in a gene sequence which act to identify individual gene haplotypes that may be considered as the allele equivalents in the sugarcane genome. This would provide sugarcane breeders with the means to select parents with the greatest number of desirable gene haplotypes to maximise the number of offspring carrying the desired trait. Hence, it is now possible to identify candidate gene sequences that may underpin important traits in sugarcane and to characterise single nucleotide polymorphisms (SNPs) in these genes.