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Sharma S.K.,James Hutton Institute | Bolser D.,University of Dundee | Bolser D.,European Bioinformatics Institute | de Boer J.,Laboratory of Plant Breeding | And 45 more authors.
G3: Genes, Genomes, Genetics | Year: 2013

The genome of potato, a major global food crop, was recently sequenced. The work presented here details the integration of the potato reference genome (DM) with a new sequence-tagged site marker2based linkage map and other physical and genetic maps of potato and the closely related species tomato. Primary anchoring of the DM genome assembly was accomplished by the use of a diploid segregating population, which was genotyped with several types of molecular genetic markers to construct a new ~936 cM linkage map comprising 2469 marker loci. In silico anchoring approaches used genetic and physical maps from the diploid potato genotype RH89-039-16 (RH) and tomato. This combined approach has allowed 951 superscaffolds to be ordered into pseudomolecules corresponding to the 12 potato chromosomes. These pseudomolecules represent 674 Mb (~93%) of the 723 Mb genome assembly and 37,482 (~96%) of the 39,031 predicted genes. The superscaffold order and orientation within the pseudomolecules are closely collinear with independently constructed high density linkage maps. Comparisons between marker distribution and physical location reveal regions of greater and lesser recombination, as well as regions exhibiting significant segregation distortion. The work presented here has led to a greatly improved ordering of the potato reference genome superscaffolds into chromosomal "pseudomolecules". © 2013 Sharma et al. doi: 10.1534/g3.113.007153. Source


Bonomelli C.,University of Santiago de Chile | Pereira J.,University of Santiago de Chile | Ruiz R.,INIA La Platina
Acta Horticulturae | Year: 2010

Plants have developed physiological mechanisms to adapt to high soil salinity, such as stomatal closure and osmoregulation. The latter allows maintenance of water flux because of an increased internal osmotic pressure. We carried out an experiment in a commercial 'Thompson Seedless' table grape vineyard in central Chile (34°20' S, 71°17' W) where concentrated solutions of CaCI2 and KCl were applied to the soil regularly during December and January of the 2005/06 and 2006/07 growing seasons. Soil analyses showed that, where the salt solutions were applied, chloride (Cl) levels and electrical conductivity (EC) were higher, but K and Ca levels were similar to the control. Foliar and fruit analyses showed that Cl concentrations were higher in both seasons in leaves and fruits from vines exposed to the applied salts. Shoot, bunch and berry weight did not differ between treatments. Berry firmness at harvest and 30 days postharvest was higher in the salt treatment while berry dry matter percentage was lower. Cell area was measured in histological sections of berries from both treatments, and larger cells were found in fruit from the salt treatment. These results suggest that grapes have osmoregulation mechanisms that respond to high amounts of Cl in soil. Source


Munoz C.,Andres Bello University | Di Genova A.,University of Chile | Maass A.,University of Chile | Orellana A.,Andres Bello University | And 2 more authors.
Acta Horticulturae | Year: 2014

Grapevine (Vitis spp.) is the most widely cultivated and economically important fruit crop. Even though the genus exhibits a huge diversity present in more than 50 species, the main products are derived from Vitis vinifera whose origin is from the Southern Caucasus to central Europe. Besides, grapevine constitutes per se a model for the study of woody species. In the Southern hemisphere, Chile has become a large wine producer and the main exporter of table grapes. Our present aim is to develop a bioinformatic platform able to identify SNPs, detect splicing variants and annotate new genes, all tools that could finally give support to select traits of interest. We analyzed data from 18 Vitis species, including cultivars of V. vinifera and wild species of the Vitis genus. The data was obtained by Illumina sequencing from two RNA-seq experiments performed by Zenoni et al. (2010) and Myles et al. (2010), both available at NCBI. The first one reported data from cv. 'Corvina' while the latter from 'Pinot Noir', 'Inbred Pinot Noir' and 15 other cultivated cultivars and wild species. The sequence reads were aligned onto the 12X draft sequence of the 'Pinot Noir'-derived 40024 genome whereas the reported data was aligned onto 8X genome. The alignments were analyzed to detect alternative splicing events and expressed single nucleotide polymorphisms (SNPs). We aligned 116,665,608 reads selecting hits with at most two mismatches. Over 55% of the reads showed only one alignment to the reference genome, 19% had multiple matches and 26% of them were unmatched. Preliminary results detected 387,278 putative SNPs using a Q-score of 20, coverage over 8x and a variability of over 25%. This study will help to improve the current Vitis genome annotation as well as to increase our knowledge about Vitis phylogenetic relationships. Our next step will be to search for new genes as well as spliced variants within Vitis genus. Future perspectives involve the integration of transcriptomic and proteomic data. Source


Barra M.,University of the Frontier | Correa J.,INIA La Platina | Salazar E.,INIA La Platina | Sagredo B.,University of the Frontier
American Journal of Potato Research | Year: 2013

Chile is center of origin and diversity of potato (Solanum tuberosum L.). Potato yield is affected under water stress conditions, so development of varieties with better tolerance to this stress is desirable. In this study we determined the differential response of INIA-Chile potato germplasm to water stress under in vitro assays with polyethylene glycol. One-hundred-and-fourty- nine genotypes were evaluated. Polyethylene glycol 4.8 % w/v was able to distinguish genotype response by considering the morphological variables (plantlet height, leaf and root number) and fresh and dry weight. Through multivariate statistical analysis, and in comparison with their respective controls without treatment, genotypes were clustered with high (74 - 79 %), intermediate (29 - 94 %), low (29 - 57 %), and very low (4- 28 %) water stress tolerance. The high-tolerance-response cluster was mainly made up of Chilean potato landraces. These results highlight the importance of this germplasm in food security, which could be directly cultivated and/or be used as progenitors to produce new varieties with increased tolerance to water-deficit stress. © 2013 Potato Association of America. Source

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