Population Genomics of Phaseolus spp.: A Domestication Hotspot

Abstract

The genus Phaseolus includes five domesticated species. Collectively, Phaseolus beans are produced across all inhabited continents under a variety of environments, mainly for dry beans but also green pods. Building on the development of genetic tools, the last two decades have seen an active development of genomic resources, comprising several whole-genome reference sequences (in common, lima, and tepary beans), gene expressions databases, and genotyped diversity and MAGIC populations. The genus is a domestication hotspot with seven independent domestication events, including two species (common and lima beans) that were each domesticated twice. The five domesticated species represent diverse ecological niches and form a gradient in the intensity of domestication, perenniality, and rate of outcrossing. In common bean, genomic regions and candidate genes have been correlated with different climatic variables to which these wild populations are adapted. The different domestications have induced – to varying extents – a reduction in molecular diversity. Bottom-up (or reverse genetic) approaches have identified regions with reduced genetic diversity (potential selective sweeps) and high differentiation in ~15% of the genome. Although such a large proportion is probably an overestimate due to linkage disequilibrium and background selection, some genome regions coincide with domestication quantitative loci identified through top-down (or direct genetic) approaches, and contain candidate genes. Genes have been identified that control several domestication syndrome traits. These often are loss-of-function mutations, underscoring the importance of this mutation type in adaptation. Traits such as photoperiod insensitivity, determinacy and pigmentation changes reflect convergent evolution intra-specifically and possibly inter-specifically. Further developments in Phaseolus population genomics should involve a more detailed analysis of the domestication process across the five domesticated species, a better understanding of differential gene expression networks, application to marker-assisted and genomic selections, and transfer of traits from unadapted germplasm into advanced cultivars.