Combining chloroplast and nuclear microsatellites to investigate origin and dispersal of New World sweet potato landraces

Abstract

We analysed a representative collection of New World sweet potato landraces (329 accessions from Mexico to Peru) with both chloroplast and nuclear microsatellite markers. Both kinds of markers supported the existence of two geographically restricted genepools, corresponding to accessions from the north-western part of South America and accessions from the Caribbean and Central America region. Our conservative cpSSRs markers revealed that the divergence between the two haplotype groups is associated with numerous mutation events concerning various markers, supporting the idea that this divergence may be ancient, predating domestication. For both kinds of markers, we found no significant difference in diversity between the two genepools and detected region-specific alleles in both groups. Previous studies have favoured the hypothesis of a single domestication of this crop. Our analysis suggests at least two independent domestications, in Central/Caribbean America and in the north-western part of South America. Sweet potato was then dispersed from these centres throughout tropical America. Comparison of nuclear and chloroplast data suggests that exchanges of clones and sexual reproduction were both important processes in landrace diversification in this clonally propagated crop. Our analysis provides useful tools for rationalizing the conservation and use of sweet potato germplasm collections.

On the origin of sweet potato (Ipomoea batatas (L.) Lam.) genetic diversity in New Guinea, a secondary centre of diversity

“…First, they may already have been present in clones introduced from the Northern genepool. Recombination between migrant clones of Northern and Southern genepools has occurred since ancient times in tropical America (Roullier et al, 2011), blurring the phylogeographic pattern in chloroplast DNA diversity and complicating assignation of clones introduced into New Guinea to areas of origin in the Neotropics. In fact, the most common haplotypes of cp group 1 are also found, albeit at lower frequency (14.7%), in the Northern genepool.…”

“…For purposes of comparison, we added to the New Guinea data set nuclear and chloroplast data sets already published in a previous study (Roullier et al, 2011). The tropical America data set comprises 130 individuals (76 accessions from the Northern genepool and 54 from the Southern genepool) for nuclear data, and 329 individuals (192 from the Northern genepool and 137 from the Southern genepool) for chloroplast data.…”

“…Out of 21 haplotypes found in tropical America, 6 were found in New Guinea (H1_2, H5, H6_9, H12, H13 and H14). New Guinea haplotypes included representatives of both cp groups 1 and 2, defined in a previous study (Roullier et al, 2011): H14 and H13 were the most frequent haplotypes of cp group1. Widespread throughout the Southern region in the neotropics, they are also present in the Northern region, although H13 is rare there.…”

“…All individuals were genotyped with six chloroplast microsatellites (ccmp2, NTCP 26, NTCP 28, Ibcp 5, Icbp 8 and Ibcp 10) and 11 nuclear microsatellites (J263, J315E, J522A, J116a, Ib297, J206A, J1809E, IbR16, IbC5, J544b and IbS11) described in a previous study (Roullier et al, 2011). All loci were amplified independently using Multiplex PCR Taq (Qiagen) in a final volume of 10 ml, using 30 ng of DNA per reaction.…”

“…A recent molecular study (Roullier et al, 2011) analysed 329 landraces collected from Mexico to Peru by nuclear and chloroplast microsatellite markers. Both kinds of markers supported the existence of two geographically restricted genepools, corresponding to accessions from the Peru-Ecuador region of South America (hereafter called the Southern genepool) and accessions from the Caribbean and Central America region (hereafter called the Northern genepool).…”