Next generation sequencing (NGS) refers to a set of technologies based on massive parallel sequencing. NGS technologies can be included in three main groups: sequencing by synthesis, by ligation, and single-molecule sequencing. NGS technologies are improving at a fast pace and the cost of sequencing per base is decreasing, thus allowing to use NGS to approach a variety of biological questions as impossible before. In plants, tools based on genome decoding, building on NGS, contribute to increase the rate of genetic gain during selection and the precision when choosing superior genotypes. The tools used to facilitate the process leading to genomes drafts is described. The chapter also presents new methods, such as genomic selection or genome-wide association mapping, which are based on NGS to disclose an unprecedented amount of genetic variability made available to plant breeding. In addition, the use of NGS to decode the epigenome and the transcriptome is reported, as well as its power, when combined with appropriate genetic designs, to map and clone quantitative trait loci. It is out of scope of this review to provide a comprehensive repertory of sequencing efforts and techniques that are rapidly evolving and quickly becoming obsolete. The paper, moreover, does not provide a comprehensive list of all the too numerous experiments conducted in the field, but rather it describes rationales and examples of possible applications of plant genome sequencing.
Keywords: Breeding, Breeding by genotyping, Crop improvement, Genome sequencing, Genome wide association studies, Genomic selection, Next generation sequencing, Plant breeding, Pyrosequencing, QTL-seq, RNA-seq.