The horizontal gene transfer of Agrobacterium T-DNAs into the series Batatas (genus Ipomoea) genome is not confined to hexaploid sweetpotato

The discovery of the insertion of IbT-DNA1 and IbT-DNA2 into the cultivated (hexaploid) sweetpotato [Ipomoea batatas (L.) Lam.] genome constitutes a clear example of an ancient event of Horizontal Gene Transfer (HGT). However, it remains unknown whether the acquisition of both IbT-DNAs by the cultivated sweetpotato occurred before or after its speciation. Therefore, this study aims to evaluate the presence of IbT-DNAs in the genomes of sweetpotato's wild relatives belonging to the taxonomic group series Batatas. Both IbT-DNA1 and IbT-DNA2 were found in tetraploid I. batatas (L.) Lam. and had highly similar sequences and at the same locus to those found in the cultivated sweetpotato. Moreover, IbT-DNA1 was also found in I. cordatotriloba and I. tenuissima while IbT-DNA2 was detected in I. trifida. This demonstrates that genome integrated IbT-DNAs are not restricted to the cultivated sweetpotato but are also present in tetraploid I. batatas and other related species

CARACTERIZACIÓN MORFOLÓGICA Y MOLECULAR DE GENOTIPOS MEJORADOS DE CAMOTE (Ipomoea batatas L.) PARA ECOSISTEMAS ÁRIDO-SALINO-BÓRICOS

El camote (Ipomoea batatas L) es un cultivo de importancia agronómica y social por sus múltiples aplicaciones para la alimentación humana, agroindustria y como forraje para el ganado, por lo que resulta de gran interés generar nuevos genotipos superiores, que contribuyan a combatir el hambre o la desnutrición en las zonas de mayor necesidad del Tercer Mundo. En el presente trabajo de investigación se han caracterizado a clones élites y variedades mejoradas, adaptadas a las condiciones árido—salino—bóricas de la costa del Pacífico Sur de Sudamérica. El proceso se inició con una caracterización morfológica del follaje y de las raíces reservantes de los genotipos en estudio; luego, una evaluación de sus principales atributos agronómicos, su reacción frente al Virus del Moteado Plumoso del Camote (SPFMY) bajo condiciones de campo, así como su rendimiento, tolerancia al frío y resistencia a otras condiciones de estrés abiótico, cultivados en suelos árido-salino-bóricos. Finalmente, se realizó una caracterización molecular mediante la técnica del AFLP. Estos datos fueron analizados con el software NTSYS, obteniendo dendogramas en los que se demostró que todos los genotipos tienen un coeficiente de similaridad menor a 1 (uno), lo que significa que los genotipos en estudio son diferentes y distintivos, lográndose diferenciar claramente entre ellos, mostrando una gran diversidad genética interclonal. Asimismo, estos resultados brindan información que puede ser usada para los registros internacionales de patentes de clones y variedades mejoradas

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

A sweetpotato gene index established by de novo assembly of pyrosequencing and Sanger sequences and mining for gene-based microsatellite markers

<p>Abstract</p> <p>Background</p> <p>Sweetpotato (<it>Ipomoea batatas </it>(L.) Lam.), a hexaploid outcrossing crop, is an important staple and food security crop in developing countries in Africa and Asia. The availability of genomic resources for sweetpotato is in striking contrast to its importance for human nutrition. Previously existing sequence data were restricted to around 22,000 expressed sequence tag (EST) sequences and ~ 1,500 GenBank sequences. We have used 454 pyrosequencing to augment the available gene sequence information to enhance functional genomics and marker design for this plant species.</p> <p>Results</p> <p>Two quarter 454 pyrosequencing runs used two normalized cDNA collections from stems and leaves from drought-stressed sweetpotato clone <it>Tanzania </it>and yielded 524,209 reads, which were assembled together with 22,094 publically available expressed sequence tags into 31,685 sets of overlapping DNA segments and 34,733 unassembled sequences. Blastx comparisons with the UniRef100 database allowed annotation of 23,957 contigs and 15,342 singletons resulting in 24,657 putatively unique genes. Further, 27,119 sequences had no match to protein sequences of UniRef100database. On the basis of this gene index, we have identified 1,661 gene-based microsatellite sequences, of which 223 were selected for testing and 195 were successfully amplified in a test panel of 6 hexaploid (<it>I. batatas</it>) and 2 diploid (<it>I. trifida</it>) accessions.</p> <p>Conclusions</p> <p>The sweetpotato gene index is a useful source for functionally annotated sweetpotato gene sequences that contains three times more gene sequence information for sweetpotato than previous EST assemblies. A searchable version of the gene index, including a blastn function, is available at <url>http://www.cipotato.org/sweetpotato_gene_index</url>.</p

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

We analyzed 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 super-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 kind 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 Meso-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 germplasm collections

cpSSRs data

Choloroplast microsatellites data. Each accession number is presented with its allelic composition for the seven loci used in our study (ccmp2, ntcp18, ntcp28, ntcp26, ibcp5, ibcp8 and ibcp10)

DRYAD Sample Location

Passeport data of the 334 accessions used in the present manuscript. Accession CIP number, accession name, Collection number, Accession country of origin, Elevation of collecting site, Latitude and Longitude of collecting site, are provided. All accessions are issued from CIP genebank (International potato center). Complete passeport data are also available on the CIP web site (http://germplasmdb.cip.cgiar.org/biomart/martview/acc7fbd28f3343fa2c81be86a979e5a3)

nuclear SSRs data

Nuclear microsatellites data of the 130 New World sweet potato landraces. 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 provided for each accession, for the 13 microsatellites used in our study