The genomic signature of wild-to-crop introgression during the domestication of scarlet runner bean (Phaseolus coccineusL.)

Abstract

The scarlet runner bean is an open-pollinated legume from the highlands of Mesoamerica that is cultivated in small-scale agriculture for its dry seeds and immature pods. Demographic bottlenecks associated with domestication might reduce genetic diversity and facilitate the accumulation of deleterious mutations. Conversely, introgression from wild relatives could be a source of variation. Using Genotyping by Sequencing data (79,286 SNVs) from 237 cultivated and wild samples, we evaluated the demographic history of traditional varieties from different regions of Mexico and looked for evidence of introgression between sympatric wild and cultivated populations. Traditional varieties have high levels of diversity, even though there is evidence of a severe initial genetic bottleneck, followed by a population expansion. Introgression from wild to domesticated populations was detected, but not in the opposite direction. This asymmetric introgression might contribute to the recovery of genetic variation and it has occurred at different times: constantly in the center of Mexico; recently in the North West; and anciently in the South. Several factors are acting together to increase and maintain genetic diversity in P. coccineus cultivars, such as demographic expansion and introgression. Wild relatives represent a valuable genetic resource and have played a key role in scarlet runner bean evolution via introgression into traditional varieties.

Morphological and Molecular Characterization of Selected Chilean Runner Bean (Phaseolus coccineus L.) Genotypes Shows Moderate Agronomic and Genetic Variability

“…Some studies have confirmed that P. coccineus presents a wide variability in morpho-agronomic traits, and low to moderate levels of genetic diversity in wild and cultivated populations, being little affected by the domestication process [ 1 , 2 , 16 , 17 , 18 , 19 ]. In this sense, demographic expansion and the introgression of alleles from wild relatives are some of the factors that have increased and/or maintained the genetic diversity in cultivated populations of P. coccineus [ 20 ]. However, few studies have focused on the improvements of P. coccineus itself, and therefore there are few breeding programs focused on this species in the world, mainly in Europe [ 11 ].…”