Genomic-assisted breeding of sugarcane: using molecular markers for understanding the genetic architecture of quantitative traits and to implement marker assisted selection

Abstract

Breeding programs have been successfully over the years in the generation of new improved sugarcane varieties (Saccharum spp.), which are more productive and resistant to pests, diseases and abiotic stresses. These varieties are of central importance for sugar and ethanol production. However, breeding process takes about 10 to 15 years to release new varieties, mainly because of the difficulty to correctly identify good genotypes on the fields, since there is strong influence of environmental conditions. This process could be speed up with the development and the use of genetic markers, which are genomic regions that could be observed (evaluated) on each individual. By studying the segregation of those markers, it is possible to estimate the genetic distances between them, resulting in the so called genetic maps. After, linkage studies are performed in order to associate genotype (based on molecular traits) and phenotypes (traits that are evaluated on field conditions, such as sugar and fiber content). If the genomic regions are strongly linked with genes that control agronomic traits, they could be used for help the breeding process. Since most of the traits of agronomic and economic importance are quantitative (controlled by many loci), the major goal is to identify genomic regions associated with such traits, named quantitative trait loci (QTL). The use of markers in genetic studies, including QTL mapping, has allowed important progress in the knowledge of the genomic structure, genetics and evolution of sugarcane. In this project, new markers will be developed and used for QTL mapping. A new class of very useful markers called genic molecular markers (GMMs) will be developed and used. This kind of marker (EST-SSRs and SNPs), also named Functional Markers, will be obtained from expressed sequences from the SUCEST data bank, and sequencing genes from BAC clones. BAC libraries will be constructed using DNA from parental sugarcane varieties employed in the biparental crosses used for genetic mapping. The GMMs developed will be used for: 1) QTL mapping in biparental crosses; 2) association studies using sugarcane genotypes important in breeding programs, using a panel of about 150 genotypes important for Brazilian breeding programs. Once the genomic regions are found, strategies for marker assisted selection will be developed. (AU)