Identificación de genes relacionados a sequía en papas nativas empleando RNA-Seq

The recent advent RNA sequencing technology (RNA-Seq), a massively parallel sequencing method for transcriptome analysis, provides an opportunity to understand the expression profile of plants in response to biotic and abiotic stress. In this study, the mRNA was sequencing from leaves and roots of two native potato varieties at different levels of drought. Fifty-base-pair reads from whole mRNAs were mapped to the potato genomic sequence: 75 – 82% mapped uniquely to the genome, 6 – 14% mapped to several locations in the genome and 9 – 12% had no match in the genome. Comparing expression profiles, 887 to 1925 genes were found to be induced/repressed by drought in the sensible variety and 998 to 1995 in the tolerant. This research provides valuable information for future studies and deeper understanding of the molecular mechanism of drought resistance in potato and related species.El reciente desarrollo del RNA-Seq, un método de secuenciamiento masivo en paralelo para el análisis de transcriptomas permite conocer el perfil de expresión de las plantas en respuesta a estrés de tipo abiótico y biótico. En este estudio, se secuenció el mRNA proveniente de hojas y raíces de dos variedades de papas nativas expuestas a diferentes niveles de sequía. Lecturas o readsde 50 pares de bases provenientes de mRNA se mapearon al genoma de papa: 75 – 82% mapearon a posiciones únicas, 6 – 14% mapearon a múltiples posiciones y 9 – 12% no mapearon a posición alguna del genoma. Comparando los perfiles de expresión, se encontraron entre 887 – 1925 genes inducidos/reprimidos por sequía en la variedad sensible y 998 – 1995 en la tolerante. Este estudio generó información de gran valor que podrá ser utilizada en futuros estudios para comprender mejor los mecanismos moleculares de resistencia a sequía en papa y especies cercanas

A physical map covering the nsv locus that confers resistance to Melon necrotic spot virus in melon (Cucumis melo L.)

Melon necrotic spot virus (MNSV) is a member of the genus Carmovirus, which produces severe yield losses in melon and cucumber crops. The nsv gene is the only known natural source of resistance against MNSV in melon, and confers protection against all widespread strains of this virus. nsv has been previously mapped in melon linkage group 11, in a region spanning 5.9 cM, saturated with RAPD and AFLP markers. To identify the nsv gene by positional cloning, we started construction of a high-resolution map for this locus. On the basis of the two mapping populations, F2 and BC1, which share the same resistant parent PI 161375 (nsv/nsv), and using more than 3,000 offspring, a high-resolution genetic map has been constructed in the region around the nsv locus, spanning 3.2 cM between CAPS markers M29 and M132. The availability of two melon BAC libraries allowed for screening and the identification of new markers closer to the resistance gene, by means of BAC-end sequencing and mapping. We constructed a BAC contig in this region and identified the marker 52K20sp6, which co-segregates with nsv in 408 F2 and 2.727 BC1 individuals in both mapping populations. We also identified a single 100 kb BAC that physically contains the resistance gene and covers a genetic distance of 0.73 cM between both BAC ends. These are the basis for the isolation of the nsv recessive-resistance gene.This work was partly funded by grants GEN2003-20237-C06-02 and AGL2003-02739 from the Spanish ‘Ministerio de Ciencia y Tecnología’.Peer reviewe

Sequencing the Potato Genome: Outline and First Results to Come from the Elucidation of the Sequence of the World’s Third Most Important Food Crop

Potato is a member of the Solanaceae, a plant family that includes several other economically important species, such as tomato, eggplant, petunia, tobacco and pepper. The Potato Genome Sequencing Consortium (PGSC) aims to elucidate the complete genome sequence of potato, the third most important food crop in the world. The PGSC is a collaboration between 13 research groups from China, India, Poland, Russia, the Netherlands, Ireland, Argentina, Brazil, Chile, Peru, USA, New Zealand and the UK. The potato genome consists of 12 chromosomes and has a (haploid) length of approximately 840 million base pairs, making it a medium-sized plant genome. The sequencing project builds on a diploid potato genomic bacterial artificial chromosome (BAC) clone library of 78000 clones, which has been fingerprinted and aligned into ~7000 physical map contigs. In addition, the BAC-ends have been sequenced and are publicly available. Approximately 30000 BACs are anchored to the Ultra High Density genetic map of potato, composed of 10000 unique AFLPTM markers. From this integrated genetic-physical map, between 50 to 150 seed BACs have currently been identified for every chromosome. Fluorescent in situ hybridization experiments on selected BAC clones confirm these anchor points. The seed clones provide the starting point for a BAC-by-BAC sequencing strategy. This strategy is being complemented by whole genome shotgun sequencing approaches using both 454 GS FLX and Illumina GA2 instruments. Assembly and annotation of the sequence data will be performed using publicly available and tailor-made tools. The availability of the annotated data will help to characterize germplasm collections based on allelic variance and to assist potato breeders to more fully exploit the genetic potential of potat

Genome-Wide Identification and Mapping of NBS-Encoding Resistance Genes in Solanum tuberosum Group Phureja

The majority of disease resistance (R) genes identified to date in plants encode a nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domain containing protein. Additional domains such as coiled-coil (CC) and TOLL/interleukin-1 receptor (TIR) domains can also be present. In the recently sequenced Solanum tuberosum group phureja genome we used HMM models and manual curation to annotate 435 NBS-encoding R gene homologs and 142 NBS-derived genes that lack the NBS domain. Highly similar homologs for most previously documented Solanaceae R genes were identified. A surprising ∼41% (179) of the 435 NBS-encoding genes are pseudogenes primarily caused by premature stop codons or frameshift mutations. Alignment of 81.80% of the 577 homologs to S. tuberosum group phureja pseudomolecules revealed non-random distribution of the R-genes; 362 of 470 genes were found in high density clusters on 11 chromosomes

Optimización de los medios de propagación y enraizamiento in vitro de las variedades “criollas” de vid para elaborar pisco

The protocols and culture media available for in vitro propagation and rooting of grapevine have not yet been adjusted to the creole varieties used for pisco making. In this paper we explored the use of culture media for the propagation of varieties Quebranta, Negra Criolla, Albilla, Italia and Torontel and for rooting varieties of Quebranta, Albilla and Torontel based on known standard culture media.To address this issue, 11 media derived from the standard propagation medium for grapevine (1X Murashige & Skoog medium, 3% sucrose, 1 mg/L benzilaminopurine, and 0,8% agar) with diminished medium strength and/or hormone concentration were tested. In addition, 5 concentrations of naphtalen acetic acid or indol acetic acid were tested for rooting. We found that Quebranta, Albilla, and Italia varieties show a better growth in the standard propagation medium; by contrast, Negra Criolla and Torontel grew better in media with diminished benzilaminopurine concentrations (0,25 and 0,5 mg/L, respectively). Quebranta rooted better with 80 μg/L naphtalen acetic acid or 2 mg/L indol acetic acid, while Albilla and Torontel showed better rooting results with 2 and 1 mg/L indol acetic acid, respectively.Los protocolos y medios disponibles para la propagación y enraizamiento in vitro de la vid no han sido ajustados todavía a las variedades “criollas” con las que se elabora el pisco. En este trabajo se exploró el uso de medios para la propagación de las variedades Quebranta, Negra Criolla, Albilla, Italia y Torontel, así como para el enraizamiento de las variedades Quebranta, Albilla y Torontel, a partir de los medios estándares reportados en la literatura científica. Para ello, se pusieron a prueba 11 variantes del medio estándar de propagación de vid (medio Murashige y Skoog 1X, 3% de sucrosa, 1 mg/L de benzilaminopurina y 0,8% de agar) en las que se combinaron reducciones en la fuerza del medio con reducciones en la concentración de hormona. Para el enraizamiento posterior, se probaron el ácido naftalen acético y el ácido indol acético a 5 concentraciones distintas por cada hormona. Los resultados mostraron que el mejor medio para la propagación de las variedades Quebranta, Albilla e Italia es el estándar; las variedades Negra Criolla y Torontel tuvieron mejor desempeño con una reducción de la concentración de benzilaminopurina a 0,25 y 0,5 mg/L, respectivamente. El mejor enraizamiento en la variedad Quebranta ocurrió con 80 μg/L de ácido naftalen acético y 2 mg/L de ácido indol acético; las variedades Albilla y Torontel tuvieron una mejor respuesta al ácido indol acético a concentraciones de 2 y 1 mg/L, respectivamente

Distribution of <i>Solanum tuberosum</i> group <i>phureja</i> sequences that are predicted to encode NBS resistance proteins.

<p>Gray bars represent all 12 linkage groups in potato. Boxes across each bar designate the location of each gene. Color code: CNL (green), TNL (red) or a partial NBS gene (yellow). Distance in Megabases is shown at the top of each column.</p

Transcriptome profiling shows a rapid variety-specific response in two Andigenum potato varieties under drought stress

Potato is a drought-sensitive crop whose global sustainable production is threatened by alterations in water availability. Whilst ancestral Solanum tuberosum Andigenum landraces retain wild drought tolerance mechanisms, their molecular bases remain poorly understood. In this study, an aeroponic growth system was established to investigate stress responses in leaf and root of two Andigenum varieties with contrasting drought tolerance. Comparative transcriptome analysis revealed widespread differences in the response of the two varieties at early and late time points of exposure to drought stress and in the recovery after rewatering. Major differences in the response of the two varieties occurred at the early time point, suggesting the speed of response is crucial. In the leaves and roots of the tolerant variety, we observed rapid upregulation of ABA-related genes, which did not occur until later in the susceptible variety and indicated not only more effective ABA synthesis and mobilization, but more effective feedback regulation to limit detrimental effects of too much ABA. Roots of both varieties showed differential expression of genes involved in cell wall reinforcement and remodeling to maintain cell wall strength, hydration and growth under drought stress, including genes involved in lignification and wall expansion, though the response was stronger in the tolerant variety. Such changes in leaf and root may help to limit water losses in the tolerant variety, while limiting the reduction in photosynthetic rate. These findings provide insights into molecular bases of drought tolerance mechanisms and pave the way for their reintroduction into modern cultivars with improved resistance to drought stress and yield stability under drought conditions

Number of Solanum tuberosum group phureja genes that encode NBS-domains with homology to plant resistance proteins.

<p>Number of Solanum tuberosum group phureja genes that encode NBS-domains with homology to plant resistance proteins.</p

MEME analysis of NBS and LRR regions between CC(I) and CC(II) proteins.

<p>(<b>a</b>) NBS domain analysis. Different color boxes represent different subdomains. CC(I) and CC(II) were analyzed separately. Even though CC(II) has two different configurations, (subdomains 7-4 and 8-2) they are clustered together due to strong similarities on principal subdomains (P-loop, kinases and GLPL. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034775#pone.0034775.s005" target="_blank">Figure S5</a>). (<b>b</b>) Predominant LRR motifs are also different between these two groups; CC(I) proteins have smaller and more abundant LRR. Different color letters represent amino acid belonging to different families.</p