09Jul/20

Cryopreserved potato shoot tips showed genotype-specific response to sucrose concentration in rewarming solution (RS)

Cryopreservation protocols have been successfully developed for hundreds of species and thousands of genotypes in laboratories around the world. In many of the protocols, the rewarming process occurs in a rewarming solution (RS) with a high concentration of sucrose (0.8–1.2 M). Warming rate and associated conditions influence cell rehydration, loss of accumulated solutes (e.g. cryoprotectants) and recrystallization of small ice crystals in the nuclei. The need for, and effect of, high sucrose concentrations in the RS post-thawing regrowth rate after liquid nitrogen exposure was assessed in the range of 0.0-1.2 M sucrose with a set of 16 potato landraces cryopreserved with the PVS2-droplet vitrification method. The results showed no significant difference for the average recovery rate (81–87%) between sucrose concentrations of 0.3 M to 1.2 M. Fourteen of 16 accessions had their highest recovery rate with sucrose concentrations between 0.3 and 0.9 M. The experimental results were subsequently extended to a genetically diverse set of 85 potato accessions (nine taxa), which demonstrated significantly higher recovery rates of 55–61% with RS sucrose concentrations of 0.3–0.9 M, compared to the sucrose concentrations of 0.0 M (37%) and 1.2 M (44%). Only one of 85 accessions showed its highest recovery rate with the routinely used RS sucrose concentration of 1.2 M. Of all the concentrations tested, 0.6 M sucrose appeared to be the best bet in terms of recovery rates across the genotypes; therefore, our routine protocol has been changed from 1.2 M sucrose to 0.6 M. The specific response to low (0.0 M) and high RS sucrose concentrations (1.2 M) was highly variable within species/subspecies and appears to be genotype specific. Thus, caution should be taken in generalizing experimental cryopreservation results obtained with a limited number of accessions to larger germplasm collections.

Full content: https://link.springer.com/article/10.1007/s11240-018-1520-8

09Jul/20

A taxonomic monograph of Ipomoea integrated across phylogenetic scales

Taxonomic monographs have the potential to make a unique contribution to the understanding of global biodiversity. However, such studies, now rare, are often considered too daunting to undertake within a realistic time frame, especially as the world’s collections have doubled in size in recent times. Here, we report a global-scale monographic study of morning glories (Ipomoea) that integrated DNA barcodes and high-throughput sequencing with the morphological study of herbarium specimens. Our approach overhauled the taxonomy of this megadiverse group, described 63 new species and uncovered significant increases in net diversification rates comparable to the most iconic evolutionary radiations in the plant kingdom. Finally, we show that more than 60 species of Ipomoea, including sweet potato, independently evolved storage roots in pre-human times, indicating that the storage root is not solely a product of human domestication but a trait that predisposed the species for cultivation. This study demonstrates how the world’s natural history collections can contribute to global challenges in the Anthropocene.

Full content: https://www.nature.com/articles/s41477-019-0535-4

07Jul/20

Genome assembly of six polyploid potato genomes

Genome assembly of polyploid plant genomes is a laborious task as they contain more than two copies of the genome, are often highly heterozygous with a high level of repetitive DNA. Next Generation genome sequencing data representing one Chilean and five Peruvian polyploid potato (Solanum spp.) landrace genomes was used to construct genome assemblies comprising five taxa. Third Generation sequencing data (Linked and Long-read data) was used to improve the assembly for one of the genomes. Native landraces are valuable genetic resources for traits such as disease and pest resistance, environmental tolerance and other qualities of interest such as nutrition and fiber for breeding programs. The need for conservation and enhanced understanding of genetic diversity of cultivated potato from South America is also crucial to North American and European cultivars. Here, we report draft genomes from six polyploid potato landraces representing five taxa, illustrating how Third Generation Sequencing can aid in assembling polyploid genomes.

Full content: https://hdl.handle.net/10568/108389

07Jul/20

Structural genome analysis in cultivated potato taxa

The common potato (Solanum tuberosum L.) is an important staple crop with a highly heterozygous and complex tetraploid genome. The other taxa of cultivated potato contain varying ploidy levels (2X–5X), and structural variations are common in the genomes of these species, likely contributing to the diversification or agronomic traits during domestication. Increased understanding of the genomes and genomic variation will aid in the exploration of novel agronomic traits. Thus, sequencing data from twelve potato landraces, representing the four ploidy levels, were used to identify structural genomic variation compared to the two currently available reference genomes, a double monoploid potato genome and a diploid inbred clone of S. chacoense. The results of a copy number variation analysis showed that in the majority of the genomes, while the number of deletions is greater than the number of duplications, the number of duplicated genes is greater than the number of deleted ones. Specific regions in the twelve potato genomes have a high density of CNV events. Further, the auxin-induced SAUR genes (involved in abiotic stress), disease resistance genes and the 2-oxoglutarate/Fe(II)-dependent oxygenase superfamily proteins, among others, had increased copy numbers in these sequenced genomes relative to the references.

 

Full content: https://cgspace.cgiar.org/handle/10568/108385

 

 

06Jul/20

Identification and Control of Latent Bacteria in in vitro Cultures of Sweetpotato [Ipomoea batatas (L.) Lam]

Bacterial microorganisms which are latent in in vitro cultures can limit the efficiency of in vitro methods for the conservation of genetic resources. In this study we screened 2,373 accessions from the in vitro sweetpotato germplasm collection of the International Potato Center in Lima, Peru for bacteria associated with plantlets in tissue culture through a combination of morphological methods and partial 16S rDNA sequencing. Bacteria were detected in 240 accessions (10% of the accessions screened) and we were able to isolate 184 different bacterial isolates from 177 different accessions. These corresponded to at least nineteen Operational Taxonomic Units (OTUs) of bacteria, belonging to the genera Sphingomonas, Bacillus, Paenibacillus, Methylobacterium, Brevibacterium, Acinetobacter, Microbacterium, Streptomyces, Staphylococcus, and Janibacter. Specific primers were developed for PCR based diagnostic tests that were able to rapidly detect these bacteria directly from tissue culture plants, without the need of microbial sub-culturing. Based on PCR screening the largest bacterial OTUs corresponded to a Paenibacillus sp. closely related to Paenibacillus taichungensis (41.67%), and Bacillus sp. closely related to Bacillus cereus (22.22%), and Bacillus pumilus (16.67%). Since in vitro plant genetic resources must be microbe-free for international distribution and use, any microbial presence is considered a contamination and therefore it is critical to clean all cultures of these latent-appearing bacteria. To accomplish this, plantlets from in vitro were transferred to soil, watered with Dimanin® (2 ml/l) weekly and then reintroduced into in vitro. Of the 191 accessions processed for bacterial elimination, 100% tested bacteria-free after treatment. It is suspected that these bacteria may be endosymbionts and some may be beneficial for the plants.

Full content: https://www.frontiersin.org/articles/10.3389

17Sep/19

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

Abstract
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. trifda. 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.
31Jul/19

CIP bestows scientist emeritus status on three outstanding researchers

The ability of the International Potato Center (CIP) to develop and deploy science-based solutions for the main challenges faced by farmers and others involved in food systems in developing countries is the result of the collective knowledge, creativity and dedication of its researchers. In recognition of the achievements of three of those researchers – Dr. David Ellis, Dr. André Devaux and Alberto Salas – CIP Director General Barbara H Wells recently named each of them a Scientist Emeritus in a ceremony attended by the CIP Board of Trustees, management and staff.

Dr. Wells dedicated a new annex of the CIP genebank that contains the herbarium and cryopreservation unit – in which plant material is frozen and conserved at -196º C – to David Ellis. She also unveiled benches with plaques commemorating the careers of André Devaux and Alberto Salas.

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