Abstract
Background and Aims Improved understanding of the secondary gene pools of crops is essential for advancing genetic gain in breeding programmes. Common bean, Phaseolus vulgaris, is a staple crop with several wild relatives in its secondary gene pool. The year-long bean, P. dumosus, an important crop in Guatemala, is considered particularly closely related to P. vulgaris and a potential source of novel variation. However, the genetic diversity and relationship to other Phaseolus species of P. dumosus remain unclear. Methods We conducted the first comprehensive investigation of P. dumosus genetic diversity using both nuclear and chloroplast genome markers. Our nuclear marker set included over 700 markers present within the Phaseolus DArT (Diversity Arrays Technology) array, which we applied to P. dumosus and other relatives of P. vulgaris (including every secondary gene pool species: P. acutifolius, P. albescens, P. coccineus and P. costaricensis). Key Results Phaseolus dumosus arose from hybridization of P. vulgaris and P. coccineus, followed by at least two later hybridizations with sympatric congener populations. Existing P. dumosus collections have low genetic diversity. Conclusions The under-utilized crop P. dumosus has a complex hybrid origin. Further sampling in the region in which it arose may uncover additional germplasm for introgressing favourable traits into crops within the P. vulgaris gene pool.
Highlights
The conservation and sustainable utilization of crop genetic resources is essential for humanity to address food security in the face of a growing global population and climate change challenges (McCouch et al, 2013)
4208 of the clones that we contributed to the Phaseolus DArT array were suitable for use as polymorphic markers in P. dumosus: we used these to build a binary matrix for each marker in each sample, performed a principal coordinates analysis (PCoA) and calculated pairwise genetic diversity
The three principal coordinates did not resolve accessions, landraces and cultivars into separate categories. This was confirmed by Analysis of molecular variance (AMOVA), which indicated that variation between categories only accounted for $15 % of total divergence (FST 1⁄4 0Á15385, P 1⁄4 0Á0127), while the majority ($85 %) of the variation corresponded to polymorphisms present within the categories (Supplementary Data Table S2)
Summary
The conservation and sustainable utilization of crop genetic resources is essential for humanity to address food security in the face of a growing global population and climate change challenges (McCouch et al, 2013). The common bean, Phaseolus vulgaris, is a staple crop throughout South America, Central America and Africa, where it is an important source of dietary protein and a target of ongoing breeding and biofortification programmes (Gepts and Debouck, 1991; Schmutz et al, 2014). Improved understanding of the secondary gene pools of crops is essential for advancing genetic gain in breeding programmes. Phaseolus vulgaris, is a staple crop with several wild relatives in its secondary gene pool. The year-long bean, P. dumosus, an important crop in Guatemala, is considered closely related to P. vulgaris and a potential source of novel variation. The genetic diversity and relationship to other Phaseolus species of P. dumosus remain unclear
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