Disentangling the origins of cultivated sweet potato (Ipomoea batatas (L.) Lam.)

Sweet potato (Ipomoea batatas (L.) Lam., Convolvulaceae) counts among the most widely cultivated staple crops worldwide, yet the origins of its domestication remain unclear. This hexaploid species could have had either an autopolyploid origin, from the diploid I. trifida, or an allopolyploid origin, involving genomes of I. trifida and I. triloba. We generated molecular genetic data for a broad sample of cultivated sweet potatoes and its diploid and polyploid wild relatives, for noncoding chloroplast and nuclear ITS sequences, and nuclear SSRs. Our data did not support an allopolyploid origin for I. batatas, nor any contribution of I. triloba in the genome of domesticated sweet potato. I. trifida and I. batatas are closely related although they do not share haplotypes. Our data support an autopolyploid origin of sweet potato from the ancestor it shares with I. trifida, which might be similar to currently observed tetraploid wild Ipomoea accessions. Two I. batatas chloroplast lineages were identified. They show more divergence with each other than either does with I. trifida. We thus propose that cultivated I. batatas have multiple origins, and evolved from at least two distinct autopolyploidization events in polymorphic wild populations of a single progenitor species. Secondary contact between sweet potatoes domesticated in Central America and in South America, from differentiated wild I. batatas populations, would have led to the introgression of chloroplast haplotypes of each lineage into nuclear backgrounds of the other, and to a reduced divergence between nuclear gene pools as compared with chloroplast haplotypes. (Résumé d'auteur

Quebra da resistência em pimentão contra o Pepper yellow mosaic virus

Plants of Capsicum annuum cv. Magali R, resistant to Pepper yellow mosaic virus (PepYMV), which showed severe yellow mosaic, leaf malformation and stunting were observed during the 2003/04 growing season in Lins, São Paulo State, Brazil. Potyvirus-like particles observed in leaf sap from infected plants under the electron microscope reacted with an antiserum against PepYMV in PTA-ELISA. In addition to C. annuum cv. Magali R, this potyvirus also infected systemically the resistant C. annuum cv. Rubia R. The nucleotide sequence of part of the CP gene of this potyvirus shared 96-98% identity with that of other PepYMV isolates. The partial nucleotide sequence of the 3' NTR showed 94-96% identity with that of PepYMV. These data indicate that this potyvirus is a resistance-breaking isolate of PepYMV.Plantas de Capsicum annuum cv. Magali R, resistentes ao Pepper yellow mosaic virus (PepYMV), exibindo sintomas severos de mosaico amarelo, malformação foliar e subdesenvolvimento foram encontradas em plantios na região de Lins, SP, Brasil, em 2003/04. Partículas semelhantes àquelas do gênero Potyvirus foram observadas em extrato foliar de planta infectada examinado em microscópio eletrônico de transmissão. O extrato foliar também reagiu com anti-soro contra o PepYMV em PTA-ELISA. Além de C. annuum cv. Magali R, esse potyvirus também infectou sistemicamente C. annuum cv. Rubia R, que é resistente ao PepYMV. A seqüência de nucleotídeos de parte do gene da proteína capsidial (CP) desse potyvirus apresentou 96-98% de identidade com a de outros isolados do PepYMV. A seqüência parcial de nucleotídeos da região 3' não traduzida (3' NTR) apresentou 94-96% de identidade com a do PepYMV. Esses resultados são indicativos de que o potyvirus que quebrou a resistência em pimentão é um isolado do PepYMV

Unravelling the origins of the diversity of sweet potato (Ipomoea batatas (L.) Lam.)

Au travers d'une approche de génétique des populations et de phylogéographie, basée sur la comparaison des patrons de diversité chloroplastiques et nucléaires, cette étude s'attache à retracer les processus qui ont façonné la diversité de la patate douce depuis sa domestication en Amérique tropicale jusqu'à son introduction et sa diffusion en Océanie. Dans un premier temps, cette étude s'intéresse à l'histoire de la domestication et à l'identification de l'origine botanique et géographique de la patate douce dans son aire d'origine - l'Amérique tropicale. La patate douce est un taxon hexaploïde pour lequel les différents contributeurs sauvages n'ont pas encore été clairement identifiés. Deux hypothèses sont classiquement invoquées: 1) une origine autopolyploide à partir d'un taxon sauvage diploide I. tridida et 2) une origine allopolyploide ayant impliqué l'hybridation de deux espèces distinctes I. trifida et I. triloba. Nos résultats génétiques viennent corroborer le scénario auto-polyploïde. Néanmoins, contrairement à ce qui était avancé auparavant, I. trifida ne peut être considérée comme l'ancêtre sauvage de la patate douce. Des formes sauvages de I. batatas existent, populations à partir desquelles les formes cultivées ont été domestiquées. Par ailleurs, nous révélons l'existence de deux lignées chloroplastiques distinctes au sein des cultivars de patate douce, ce qui laisse penser que plusieurs parents sauvages, différenciés génétiquement mais probablement conspécifiques, sont impliqués dans la formation du génome de I. batatas. Deux scénarios (non exclusifs) peuvent alors être envisagés: i) I. batatas résulte de l'hybridation de plusieurs lignées distinctes (conspécifiques ou proches); ii) I. batatas est un complexe autopolyploïde avec une origine multiple. La caractérisation génétique des cultivars de patate douce met en lumière l'existence de deux groupes génétiques différenciés et géographiquement structurés: l'un correspond aux variétés d'Amérique centrale et caribéenne et l'autre aux variétés de la région du Pérou et de l'Equateur. Ce patron de diversité suggère fortement une domestication multi-locale - en Amérique centrale et en Amérique du Sud - et renforce l'hypothèse d'une origine autopolyploïde multiple dans ces deux régions. Dans un deuxième temps, notre étude nous conduit en Océanie, une aire d'introduction de la patate douce. La distribution de la patate douce dans le Pacifique s'explique par une (des) introduction(s) pré-historique(s) en Polynésie en provenance d'Amérique du Sud (par les polynésiens eux-mêmes) et des introductions historiques dans le Pacifique Ouest, en provenance du Mexique et des Caraïbes. Il s'agit là d'une hypothèse élaborée par des linguistes, ethnobotanistes et archéologues, mais qui à ce jour manquait de preuves génétiques. En combinant un échantillonnage de variétés traditionnelles contemporaines et des spécimens d'herbiers datant du 18ième au début du 20ième siècle, nous avons pu retracer l'évolution temporelle et spatiale de la diversité dans le Pacifique. Nous montrons que les variétés de patate douce présentes jusqu'au début du 20ième siècle en Polynésie ont clairement une signature génétique sud-américaine, c'est-à-dire qu'elles dérivent directement des variétés de la région Pérou-Equateur. Ainsi nos données génétiques apportent une preuve supplémentaire à l'existence d'au moins une connexion préhistorique entre la Polynésie et l'Amérique du Sud. A l'Ouest du Pacifique, les cultivars de patate douce ont une origine principalement centraméricaine. Nous montrons également qu'il y a eu un remaniement de la base génétique au fil des nouvelles introductions, effaçant progressivement la signature des introductions d'origine. En revanche, les phénotypes reconnus par les cultivateurs et les noms associés - c'est-à-dire les déterminants « culturels » des variétés - ont probablement été maintenus. La patate douce est essentiellement propagée par voie clonale par les cultivateurs.Following a population genetics and phylogeography approach, based on the comparison of chloroplastic and nuclear diversity patterns, this study aims at describing the processes which built sweet potato diversity from its domestication in tropical America to its introduction and diffusion into Oceania. We first studied the history of sweet potato domestication and identified its botanic and geographic origin in the area from which it originates - tropical America. Sweet potato is a hexaploid taxa of which the wild parents still remain to be identified. Two hypothesis are classically refered to: 1) an autopolyploid origin deriving from a wild diploid I. tridida and 2) an allopolyploid origin implying the hybridization between I. trifida et I. triloba. Our genetic results corroborate the autopolyploid scenario. However, in contrast to what was previously anticipated, I. trifida cannot be considered the wild ancestor of sweet potato. Wild forms of I. batatas do exist, these are populations from which cultivated forms were domesticated. In addition, we highlighted the existence of two distinct chloroplastic lineages within sweet potato cultivars, suggesting that several wild parents, genetically differenciated but probably conspecifics are involved in the formation of the I. batatas genome.Two scenari (non exclusive) are to be envisaged: i) I. batatas would result from the hybridization of several independent lines (conspecific or near); ii) I. batatas is an autoploid complex with multiple origin. The genetic characterization of sweet potato cultivars highlight the existence of two genetically differentiated and geographically structured groups: one includes central american and caribbean varieties while the other is made of varieties from Peru and Equador region. This diversity pattern is strongly suggestive of multilocal domestication events - in Central America and in South America - and strengthens the hypothesis of a multiple autopolyloid origin in these two regions.Next, we investigated Oceania as area of introduction of sweet potato. The sweet potato distribution in the Pacific can be explained by pre-historic introductions in Polynesia originating from South America (brought by Polynesians), and historical introductions in West-Pacific originating from Mexico and the Caribbean islands.This is a hypothesis originally proposed by linguists, ethnobotanists and archeologists, but which was lacking until now of genetic proves. Combining the sampling of contemporary traditional varieties and herbarium specimens dating from the 18th to the early 20st century, we were able to refine the temporal and spatial evolution of sweet potato diversity in the Pacific. We demonstrate that sweet potato varieties present until the early 20th century in Polynesia clearly harbor a south-american genetic signature, indicating that they directly derive from varieties found in the Peru-Ecuador area. Thus our genetic data provide an additional prove to the existence of at least one prehistoric connection between Polynesia and South America. On the west side of Pacific, sweet potato cultivars mainly display a central-american origin. We also demonstrate that a reshuffling of the genetic base happened in line with the occurrence of new introductions, progressively erasing the signature of original introductions. In contrast, phenotypes and associated names known by farmers, i.e. cultural determinants of these varieties - were probably maintained over time. Sweet potato is essentially propagated clonally by farmers. However, it also maintained active sexual reproduction. Our genetic data demonstrate that the impressive numbers of cultivars found nowadays in Oceania mainly derive from independent recombination events and from the local selection of true-seed plants. In some regions, this diversification process even lead to the emergence of secondary diversity centers, as exemplified by New Guinea highlands

Data from: Historical collections reveal patterns of diffusion of sweet potato in Oceania obscured by modern plant movements and recombination

The history of sweet potato in the Pacific has long been an enigma. Archaeological, linguistic and ethnobotanical data suggest that prehistoric human-mediated dispersal events contributed to the distribution in Oceania of this American domesticate. According to the “tripartite hypothesis”, sweet potato was introduced into Oceania from South America in pre-Columbian times, and was then later newly introduced, and diffused widely across the Pacific, by Europeans via two historically documented routes from Mexico and the Caribbean. Although sweet potato is the most convincing example of putative pre-Columbian connections between human occupants of Polynesia and South America, the search for genetic evidence of pre-Columbian dispersal of sweet potato into Oceania has been inconclusive. Our study attempts to fill this gap. Using complementary sets of markers (chloroplast and nuclear microsatellites), and both modern and herbarium samples, we test the tripartite hypothesis. Our results provide strong support for prehistoric transfer(s) of sweet potato from South America (Peru-Ecuador region) into Polynesia. Our results also document a temporal shift in the pattern of distribution of genetic variation in sweet potato in Oceania. Later re-introductions, accompanied by recombination between distinct sweet potato genepools, have reshuffled the crop’s initial genetic base, obscuring primary patterns of diffusion and at the same time giving rise to an impressive number of local variants. Moreover, our study shows that phenotypes, names and neutral genes do not necessarily share completely parallel evolutionary histories. Multidisciplinary approaches thus appear necessary for accurate reconstruction of the intertwined histories of plants and humans

nuclear SSR data

Nuclear genetic data of the samples used in the present study and obtained for the eleven nuclear microsatellite loci (J263, J315E, J522A, J116a, Ib297, J260A, J1809E, IbR16, IbC5, J544b, IbS11). Sheet 1 provides nuclear data of the samples collected in ex situ collections (in total 890 samples) and sheet 2, the genetic data obtained for the herbarium specimens (41 specimens in total). For hexaploids, we can obtain from 1 to 6 peaks or bands (6 alleles) per locus. Allelic composition (from allele 1 to allele 6) is then provided for each accession. The sheet 3 provides passeport data of all the accessions, referenced in the previous sheets 1 and 2 by their "Dryad number": - for ex situ samples (from line 1 to 891), it includes names of ex situ collections, full geographical origin data and local landrace names. - for herbarium specimens (from line 892 to line 933), it includes herbarium codes, geographical origin, dates of collection and collector names

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

New Guinea is considered the most important secondary centre of diversity for sweet potato (Ipomoea batatas). We analysed nuclear and chloroplast genetic diversity of 417 New Guinea sweet potato landraces, representing agro-morphological diversity collected throughout the island, and compared this diversity with that in tropical America. The molecular data reveal moderate diversity across all accessions analysed, lower than that found in tropical America. Nuclear data confirm previous results, suggesting that New Guinea landraces are principally derived from the Northern neotropical genepool (Camote and Batata lines, from the Caribbean and Central America). However, chloroplast data suggest that South American clones (early Kumara line clones or, more probably, later reintroductions) were also introduced into New Guinea and then recombined with existing genotypes. The frequency distribution of pairwise distances between New Guinea landraces suggests that sexual reproduction, rather than somaclonal variation, has played a predominant role in the diversification of sweet potato. The frequent incorporation of plants issued from true seed by farmers, and the geographical and cultural barriers constraining crop diffusion in this topographically and linguistically heterogeneous island, has led to the accumulation of an impressive number of variants. As the diversification of sweet potato in New Guinea is primarily the result of farmers’ management of the reproductive biology of their crop, we argue that on-farm conservation programmes that implement distribution of core samples (clones representing the useful diversity of the species) and promote on-farm selection of locally adapted variants may allow local communities to fashion relatively autonomous strategies for coping with ongoing global change