Recent and Historical Gene Flow in Cultivars, Landraces, and a Wild Taxon of Cucurbita pepo in Mexico

Abstract

Gene flow among crops and their wild relatives is an active study area in evolutionary biology and horticulture, because genetic exchange between them may impact their evolutionary trajectories and increase the genetic variation of the cultivated lineages. Mexico is a center of diversity for the genus Cucurbita that includes pumpkins, squash and gourds. Gene flow between domesticated and wild species has been reported as common in Cucurbita; but gene flow among populations of C. pepo ssp. pepo from Mexico and its wild relative has not been studied. We used 2,061 SNPs, derived from tunable genotyping by sequencing (tGBS) to estimate gene flow among 14 Mexican traditional landraces of C. pepo ssp. pepo, also including individuals from five improved cultivars of C. pepo ssp. pepo and C. pepo ssp. ovifera var. ovifera, and individuals of their wild relative C. pepo ssp. fraterna. We found moderate to high levels of genetic diversity, and low to moderate genetic differentiation. In the test of introgression between lineages, we found that all possible arrangements for ancestral and derived sites between the lineages showed similar frequencies; thus, incomplete lineage sorting, but also gene flow, might be taking place in C. pepo. Overall, our results suggest that gene flow between these subspecies and cultigens, incomplete lineage sorting and the retention of ancestral characters shaped the evolutionary trajectory of C. pepo in its area of origin and diversification. In addition, we found evidence of the use of Mexican landraces as genetic material for the improvement of commercial cultivars. The landraces of Mexico are an important source of genetic diversity for C. pepo, which has been preserved both by management practices of small farmers and by the natural gene flow that exists between the different crop fields of the region.

Conservation genomics of Agave tequilana Weber var. azul: low genetic differentiation and heterozygote excess in the tequila agave from Jalisco, Mexico

“…For instance, in the common pumpkin (zucchini, Cucurbita pepo ssp. pepo ) Martínez-González et al (2021) found a H E = 0.185 in populations distributed along Mexico using tunable genotyping by sequencing (tGBS), or for the cultivated runner-red bean ( Phaseolus coccineus ), Guerra-García et al (2017) , reported a range in H E = 0.167 to 0.221 using genotyping by sequencing (GBS), values similar to what we found in A. tequilana .…”

Influence of plant domestication on plant‐pollinator interactions: Floral attributes and floral visitor communities in wild and cultivated squash plants

“…There have been six separate domestication events in the genus Cucurbita , resulting in multiple groupings of domesticated and wild species and subspecies (Kates et al, 2017; Castellanos‐Morales et al, 2018). Introgression and gene flow have been reported between domesticated and wild progenitor Cucurbita species (Barrera‐Redondo et al, 2021; Martínez‐González et al, 2021) as well as between domesticated species (Barrera‐Redondo et al, 2021). Although the Argyrosperma clade is composed of two species and three separate taxa, Barrera‐Redondo et al, 2021 report gene flow among all three.…”

Genomic analysis unveils reduced genetic variability but increased proportion of heterozygotic genotypes of the intensively managed mezcal agave, Agave angustifolia

“…Genetic differentiation ( F ST ) between crops and their wild relatives varies widely among species, from as low as 0.006 for the squash Cucurbita pepo , to moderate differentiation for maize and grapes ( F ST = 0.11 and 0.12, respectively) and high ( F ST = 0.35) for soybean (Hufford et al, 2012; Zhou et al, 2015; Marrano et al, 2018; Martínez‐González et al, 2021). For agave species, the divergence between wild and cultivated conspecifics seems to be related to time under management and management intensity (Cabrera‐Toledo et al, 2022; Klimova et al, 2022).…”