ABSTRACT
This chapter focuses on the molecular markers that can be detected by these sequencing approaches and their application and achievement on genetic and genomic studies of coffee species; also, their importance in coffee conservation and crop improvement. Indels are less commonly used compared to SNPs, although they are relatively abundant along the genome. While SNPs are point mutations, Indels can concern a single base or a longer DNA sequence. A large proportion of eukaryotic genomes is made of transposable elements (TEs), particularly in C. canephora, where the estimated proportion is over 50%. Structural variation, referring to Indels, duplications, interchromosomal/intrachromosomal translocations, and inversions that occur in approximately 50 bp or larger, is another type of molecular marker that can only be efficiently detected using whole-genome sequencing. Some of them are mediated by TEs. Molecular markers potentially possess great information that has not been uncovered yet because of current limitations in mining and analysis tools.
