**4. Next generation sequencing techniques in** *C. arabica*

NGS incorporate technologies which, at low cost and in short time, produce millions of short DNA sequence. The most commonly used platforms for highthroughput, useful genomic research, especially in non-model plant species include second generation sequencing techniques (SGseqTs): Illumina/Solexa, 454/Roche, ABI/SOLiD, and Helicos (read mostly in the range of 25 and 700 bp in length) [45]. Results obtained from such research point to the fact that NGS techniques (NGSTs) should not be restricted to the genomes of model organisms only as non-model plants have provided useful resources for genomic studies [45].

In contrast to classical molecular markers, SNPs are the most abundant markers, particularly in the non-coding regions of the genome [46]. NGS used jointly with different complexity reduction methods, Genotyping by sequencing (GBS) and DArTseq™ (Sequencing-based diversity array technology) methods, enable a largescale discovery of SNPs in a wide variety of non-model organisms [47–49]. These techniques provide measures of genetic divergence and diversity within the major genetic clusters that comprise crop germplasm [50].

The genotyping profiles of SNPs can be compared across laboratories and sequencing platforms. These benefits have resulted in the increasing use of SNPs as high-quality markers for genotype identification in a wide range of crops [51], as recently demonstrated in cacao (*Theobroma cacao*; [52]), pummelo (*Citrus maxima*; [53]), tea (*Camellia sinensis*; [54]), longan (*Dimocarpus longan*; [55]), and litchi (*Litchi chinensis*; [56]).

Although significant, the number of reports concerning genomic resources in *Coffea*, even for a specie of commercial importance, such as *C. arabica*, is still low. Already, genotyping profiles of SNPs were identified and tested in *C. arabica* by Moncada et al. [57], Sousa et al. [29], Sant'Ana et al. [10] and Merot-L'anthoene et al. [4]. High-throughput genotyping assays are still needed in order to rapidly characterize the coffee genetic diversity and to evaluate the introgression of different cultivars in a cost-effective way. Measures must be taken to construct high-density genetic maps in *Coffea* [57, 58]. However, the use of SNP markers to generate denser maps is still low.
