Genetic map in sugarcane using SNPs

Abstract

Sugarcane (Saccharum spp.) is one of the most important source of income, employment and energy in Brazil. As a result of their genetic complexity, sugarcane breeding programs require approximately 12 years to obtain a new cultivar. Thus molecular markers can be used as a valuable tool, since it enables the early selection of superior genotypes by mapping QTLs (Quantitative Trait Loci), that is by identifying genomic regions associated with quantitative traits of great agronomic and economic importance. SNPs (Single Nucleotide Polymorphism) have been widely used since they are the most abundant source of variation in the genome and are useful to construct high resolution genetic maps facilitating the location of QTLs. For autopolyploid species, SNPs still have the great advantage of behaving as co-dominant since they allow the number of copies of each allele to be identified. Using sequences generated by the SUCEST program, 943 SNPs loci were developed and of these 245 were analyzed in a F1 biparental mapping population from the cross between varieties IACSP 95-3018 and IACSP 93-3046. Within this context, this project has various scientifically relevant main objectives: 1) the analysis of the remaining SNPs loci for the saturation of the genetic map in the mapping population under study; 2) use the same set of SNPs loci for the analysis and construction of genetic map in two other mapping populations (SP 80-3280x RB 83-5486 and SP 81-3250 x RB 92-5345); 3) develop new SNPs loci based on second generation sequecing (Illumina). This will enable a breakthrough in the genetic studies of this species. Besides this, additional experiments for the study of some SNPs loci that have been analyzed and shown interesting results will be done. The SNPs will be analyzed and classified using a new approach suitable for polyploids with SuperMASSA software, developed by the research team of the supervisor of this project and new maps will be all built using multipoint approach for the estimation of distances and orders of the markers by using a new software that is in the final phase of development. Combining these two new approaches of classification and mapping in polyploids it will be possible to include marks of all dosage, which is new in sugarcane and will allow us to obtain more saturated maps than those currently available. The results generated in this project will therefore be useful for genetic studies and the breeding program of this species, providing important information for the understanding of the genetic architecture of sugarcane.