Population genomics integrates advances in sequencing technologies, bioinformatics tools, statistical methods and software into research on evolutionary and population genetics. Its application has provided novel approaches that have significantly advanced our understanding of new and long-standing questions in evolutionary processes. This has allowed the disentangling of locus-specific effects from genome-wide effects and has shed light on the genomic basis of fitness, local adaptation and phenotypes. “-Omics” tools have provided a comprehensive genome-wide view of the action of evolution. The specific features of the Phaseolus genus have made it a unique example for the study of crop evolution. The well-documented history of multiple domestications in Phaseolus vulgaris L. (common bean) and its further adaptation to different environments have provided the opportunity to investigate evolutionary issues, such as convergent evolution in the same species across different domestication events. Moreover, the availability of the P. vulgaris reference genome now allows adaptive variations to be easily mapped across the entire genome. Here, we provide an overview of the most significant outcomes obtained in common bean through the use of different computational tools for analysis of population genomics data.

Domesticated crops have been disseminated by humans over vast geographic areas. Common bean (Phaseolus vulgaris L.) was introduced in Europe after 1492. Here, by combining whole-genome profiling, metabolic fingerprinting and phenotypic characterisation, we show that the first common bean cultigens successfully introduced into Europe were of Andean origin, after Francisco Pizarro’s expedition to northern Peru in 1529. We reveal that hybridisation, selection and recombination have shaped the genomic diversity of the European common bean in parallel with political constraints. There is clear evidence of adaptive introgression into the Mesoamerican-derived European genotypes, with 44 Andean introgressed genomic segments shared by more than 90% of European accessions and distributed across all chromosomes except PvChr11. Genomic scans for signatures of selection highlight the role of genes relevant to flowering and environmental adaptation, suggesting that introgression has been crucial for the dissemination of this tropical crop to the temperate regions of Europe.

Food legumes are at the crossroads of many societal challenges that involve agriculture, such as climate change and food sustainability and security. In this context, pulses have a crucial role in the development of plant-based diets, as they represent a very good source of nutritional components and improve soil fertility, such as by nitrogen fixation through symbiosis with rhizobia. The main contribution to promotion of food legumes in agroecosystems will come from plant breeding, which is guaranteed by the availability of well-characterized genetic resources. Here, we analyze seeds of 25 American and European common bean purified accessions (i.e., lines of single seed descent) for different morphological and compositional quality traits. Significant differences among the accessions and superior genotypes for important nutritional traits are identified, with some lines showing extreme values for more than one trait. Heritability estimates indicate the importance of considering the effects of environmental growth conditions on seed compositional traits. They suggest the need for more phenotypic characterization in different environments over different years to better characterize combined effects of environment and genotype on nutritional trait variations. Finally, adaptation following the introduction and spread of common bean in Europe seems to have affected its nutritional profile. This finding further suggests the relevance of evolutionary studies to guide breeders in the choice of plant genetic resources.

Association panels represent a useful tool for quantitative trait loci (QTL) mapping and pre-breeding. In this study, we report on the development of a European and Mediterranean chickpea association panel as a useful tool for gene discovery and breeding. Chickpea (Cicer arietinum L.) is one of the most important food legumes worldwide and a key crop in the Mediterranean environments. The selection of genotypes followed criteria aimed to build a set of materials representative of the genetic diversity of chickpea germplasm focusing on the European and Mediterranean environments, which have largely been ignored to date. This tool can help breeders to develop novel varieties adapted to European and Mediterranean agro-ecosystems. Initially, 1931 chickpea accessions were phenotypically evaluated in a field trial in central Italy. From these, an association panel composed by 480 genotypes derived from single-seed descent was identified and phenotypically evaluated. Current and future phenotypic data combined with the genotypic characterization of the association panel will allow to dissect the genetic architecture of important adaptive and quality traits and accelerate breeding. This information can be used to predict phenotypes of unexploited chickpea genetic resources available in genebanks for breeding.

The remarkable evolutionary history of the common bean (Phaseolus vulgaris L.) has led to the emergence of three wild main genepools corresponding to three different ecogeographic areas: Mesoamerica, the Andes and northern Peru/Ecuador. Recent works proposed novel scenarios and the northern Peru/Ecuador population has been described as a new species called P. debouckii, rekindling the debate about the origin of P. vulgaris. Here we shed light on the origin of P. vulgaris by analysing the chloroplast and nuclear genomes of a large varietal collection representing the entire geographical distribution of wild forms. We assembled 37 chloroplast genomes de novo and used them to construct a time frame for the divergence of the genotypes under investigation, revealing that the separation of the Mesoamerican and northern Peru/Ecuador genepools occurred ~0.15 Mya. Our results clearly support a Mesoamerican origin of the common bean and reject the recent P. deboukii hypothesis. These results also imply two independent migratory events from Mesoamerica to the North and South Andes, probably facilitated by birds. Our work represents a paradigmatic example of the importance of taking into account recombination events when investigating phylogeny and of the analysis of wild forms when studying the evolutionary history of a crop species.