Current approaches and methods in plant domestication studies

Background: The domestication process has left signatures in the genomes of domesticated species. Before the existence of molecular markers, only phenotypic traits could be used in domestication studies and breeding programs, but these approaches required long time and effort. In the last decades, the use of molecular markers dramatically increased, and the development of massive sequencing tools have enable to obtain thousands or even millions of molecular markers. Questions: The main goal of this review us to bring a general and an integrative perpective of the data, approaches and questions that can be answered using new sequencing tools. Species study and data description: This work focuses on domesticated plants, comparing genetic and genomic data. Results: The use of molecular markers in the last decades has increased the efficiency and accuracy of plant breeding, allowing to access information about domestication history and to identify genes affected by domestication. Some patterns have been identified in domesticated species: (1) genetic diversity reductions due to demographic bottlenecks and artificial selection; (2) frequently, mutations related with domestication syndrome preexisted at low frequency in natural populations; (3) accumulation of deleterious mutation; (4) gene flow between wild and cultivated populations; (5) phenotypic convergence usually do not result from molecular convergence. There are several approaches that can be used in massive sequencing tools: de novo genome sequencing, whole genome resequencing, reduction of genome complexity using restriction enzymes, transcriptome analysis and epigenetic studies. Conclusions: Despite the progress made, enormous challenges remain: storage of large databases; development of fast and accurate methods to evaluate phenotypes; identification of paralogous genes in polyploid species; and the analysis of large and highly diverse genomes.