Search

Your search keyword '"Gisella Orjeda"' showing total 25 results
Start Over Author "Gisella Orjeda"
25 results on '"Gisella Orjeda"'

1. Assembly, annotation and analysis of the chloroplast genome of the Algarrobo tree Neltuma pallida (subfamily: Caesalpinioideae)

Author

Esteban Caycho, Renato La Torre, and Gisella Orjeda

Subjects
Neltuma pallida, Chloroplast genome, Gene annotation, Repetitive sequences, Sequence comparison, Boundary shift, Botany, QK1-989
Abstract

Abstract Background Neltuma pallida is a tree that grows in arid soils in northwestern Peru. As a predominant species of the Equatorial Dry Forest ecoregion, it holds significant economic and ecological value for both people and environment. Despite this, the species is severely threatened and there is a lack of genetic and genomic research, hindering the proposal of evidence-based conservation strategies. Results In this work, we conducted the assembly, annotation, analysis and comparison of the chloroplast genome of a N. pallida specimen with those of related species. The assembled chloroplast genome has a length of 162,381 bp with a typical quadripartite structure (LSC-IRA-SSC-IRB). The calculated GC content was 35.97%. However, this is variable between regions, with a higher GC content observed in the IRs. A total of 132 genes were annotated, of which 19 were duplicates and 22 contained at least one intron in their sequence. A substantial number of repetitive sequences of different types were identified in the assembled genome, predominantly tandem repeats (> 300). In particular, 142 microsatellites (SSR) markers were identified. The phylogenetic reconstruction showed that N. pallida grouped with the other Neltuma species and with Prosopis cineraria. The analysis of sequence divergence between the chloroplast genome sequences of N. pallida, N. juliflora, P. farcta and Strombocarpa tamarugo revealed a high degree of similarity. Conclusions The N. pallida chloroplast genome was found to be similar to those of closely related species. With a size of 162,831 bp, it had the classical chloroplast quadripartite structure and GC content of 35.97%. Most of the 132 identified genes were protein-coding genes. Additionally, over 800 repetitive sequences were identified, including 142 SSR markers. In the phylogenetic analysis, N. pallida grouped with other Neltuma spp. and P. cineraria. Furthermore, N. pallida chloroplast was highly conserved when compared with genomes of closely related species. These findings can be of great potential for further diversity studies and genetic improvement of N. pallida.

Published
2023
Full Text
View/download PDF

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

Author

Olga Patricia Ponce, Yerisf Torres, Ankush Prashar, Robin Buell, Roberto Lozano, Gisella Orjeda, and Lindsey Compton

Subjects
drought, potato, abiotic stress, rehydration, transcriptome, Plant culture, SB1-1110
Abstract

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.

Published
2022
Full Text
View/download PDF

3. Survey of Lichenized Fungi DNA Barcodes on King George Island (Antarctica): An Aid to Species Discovery

Author

Renato Daniel La Torre, Daniel Ramos, Mayra Doris Mejía, Edgar Neyra, Edwin Loarte, and Gisella Orjeda

Subjects
Lichen-forming fungi, Admiralty Bay, DNA barcoding, diversity, Austrolecia, Buellia, Biology (General), QH301-705.5
Abstract

DNA barcoding is a powerful method for the identification of lichenized fungi groups for which the diversity is already well-represented in nucleotide databases, and an accurate, robust taxonomy has been established. However, the effectiveness of DNA barcoding for identification is expected to be limited for understudied taxa or regions. One such region is Antarctica, where, despite the importance of lichens and lichenized fungi identification, their genetic diversity is far from characterized. The aim of this exploratory study was to survey the lichenized fungi diversity of King George Island using a fungal barcode marker as an initial identification tool. Samples were collected unrestricted to specific taxa in coastal areas near Admiralty Bay. Most samples were identified using the barcode marker and verified up to the species or genus level with a high degree of similarity. A posterior morphological evaluation focused on samples with novel barcodes allowed for the identification of unknown Austrolecia, Buellia, and Lecidea s.l. species. These results contribute to better represent the lichenized fungi diversity in understudied regions such as Antarctica by increasing the richness of the nucleotide databases. Furthermore, the approach used in this study is valuable for exploratory surveys in understudied regions to guide taxonomic efforts towards species recognition and discovery.

Published
2023
Full Text
View/download PDF

4. Identification of genes related to drought in native potatoes using RNA-Seq

Author

Roberto Lozano, Carlos Merino, and Gisella Orjeda

Subjects
RNA-Seq, transcriptoma, sequía, papa, mRNA. Abstract, Science, Biology (General), QH301-705.5
Abstract

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.

Published
2014
Full Text
View/download PDF

5. Optimización de los medios de propagación y enraizamiento in vitro de las variedades 'criollas' de vid para elaborar pisco Optimization of media for in vitro propagation and rooting of creole grapevine varieties utilized for pisco making

Author

Eugenio González, Diego Pignataro, Gisella Orjeda, Wilfredo L. Gonzáles, and Daniel Clark

Subjects
Cultivo in vitro, propagación, enraizamiento, vides criollas, pisco., Science, Biology (General), QH301-705.5
Abstract

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.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.

Published
2012

6. Genome-wide identification and mapping of NBS-encoding resistance genes in Solanum tuberosum group phureja.

Author

Roberto Lozano, Olga Ponce, Manuel Ramirez, Nelly Mostajo, and Gisella Orjeda

Subjects
Medicine, Science
Abstract

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.

Published
2012
Full Text
View/download PDF

7. Simple Sequence Repeat-Based Genetic Diversity and Analysis of Molecular Variance among on-Farm Native Potato Landraces from the Influence Zone of Camisea Gas Project, Northern Ayacucho, Peru

Author

Germán De la Cruz, Gisella Orjeda, Tomás Yuret Miranda, Edgar Neyra, and Raúl Blas

Subjects
0106 biological sciences, AMOVA, Plant Science, Biology, 01 natural sciences, Analysis of molecular variance, Fixation index, Crop, Genotype, Landrace, FST, Polymorphism, Allele, Genetic diversity, food and beverages, Microsatellite, 04 agricultural and veterinary sciences, Genetic distance, DNA profiling, Evolutionary biology, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, purl.org/pe-repo/ocde/ford#4.01.06 [https], Agronomy and Crop Science, 010606 plant biology & botany
Abstract

The Andean native potato is an important food security crop and constitutes a gene pool for potato-breeding. To establish the current state of the native potatoes diversity in the influence zone of the Camisea Gas Project, North Ayacucho, Peru, landraces (n = 144) were collected. Three sampling populations (Anco, Chungui and Ticllas) were resolved using 10 simple sequence repeats (SSRs) markers that amplified 67 polymorphic alleles. Principal component, correspondence and cluster analysis revealed a minimum set of six SSRs to achieve DNA fingerprinting and cost-effective genetic diversity analysis. Analysis of molecular variance (AMOVA), average fixation index (FST = 0.279), and genetic distance index (SB) indicated that the genetic diversity of the native potatoes is high at the intra- and inter-population levels, and each of the three sampling populations constituted closed populations. The three populations were genetically distinct and contained unique genotypes and exclusive alleles. Misidentified native potatoes (10.41%) were found.

Published
2020

8. A ciencia cierta : Miradas científicas para comprender la pandemia

Author

Gisella Orjeda, MATEO PROCHAZKA, ALEJANDRA RUIZ LEÓN, Gisella Orjeda, MATEO PROCHAZKA, and ALEJANDRA RUIZ LEÓN

Subjects
Epidemics, COVID-19 (Disease)
Abstract

Un e-book que nos permite revalorar el papel de la ciencia y la investigación en tiempos de pandemia. A ciencia cierta. Miradas científicas para comprender la pandemia propone al lector una nueva valoración a la labor científica y médica para la humanidad en tiempos de crisis sanitarias. La pandemia del COVID-19 ha revelado el fundamental aporte de nuestros científicos y médicos peruanos para salvar vidas y profundizar en la investigación. Estos ensayos de Gisella Orjeda, expresidente de CONCYTEC; Mateo Prochazka, médico epidemiólogo y Alejandra Ruiz León, bioquímica y fundadora de Mitocondria Comunicación, exponen el roltrascendental que la ciencia tiene en nuestras vidas.

Published
2020

9. Genome sequence and analysis of the tuber crop potato

Author

Xun Xu, Gerard J. Bishop, Robbie Waugh, David Marshall, Sanwen Huang, Istvan Nagy, Zagorski W, Pawel Szczesny, Erwin Datema, Hu Q, Diana Martinez, Herrera Mdel R, Giovanni Giuliano, He Y, Zhang Z, Aska Goverse, De la Cruz G, Du Y, Marina Iovene, Shengkai Pan, Bo Zhang, Robert Gromadka, Alexey V. Beletsky, Frank Guzman, Gaetano Perrotta, Gisella Orjeda, Marc Ghislain, O'Brien K, Massa Ga, Chakrabarti Sk, Jiming Jiang, Jun Wang, Dan Bolser, Mads Sønderkær, van Eck H, Sanjeev Kumar Sharma, Hanhui Kuang, Jan Gawor, Ruiqiang Li, Marco Pietrella, Hekkert Bt, Li G, Kåre Lehmann Nielsen, Mu D, David M. A. Martin, Boris B. Kuznetsov, Brieanne Vaillancourt, Buell Cr, van Ham Rc, Destefanis M, Glenn J. Bryan, Brett R Whitty, Olga Ponce, de Boer J, Jeanne M. E. Jacobs, Lundback S, Susan Thomson, Theo Borm, Bjorn Kloosterman, Di Genova A, Konstantin G. Skryabin, Tatjana V. Kolganova, Andrey V. Mardanov, Shifeng Cheng, Paolo Facella, Merideth Bonierbale, Xiong X, Luis Aníbal Diambra, Yang Y, Richard G. F. Visser, Shuang Yang, Liang C, Mark Fiers, Dan Milbourne, Patil Vu, Youjun Zhang, Qu D, Nilo Mejía, Peixiang Ni, Torres M, Barreiro Le, He J, Sergio Enrique Feingold, Christian W. B. Bachem, Alicia N. Massa, Geoffroy M, Richard E. Veilleux, Boris Sagredo, Xie B, Li Y, Xu J, Dean DellaPenna, Giovana Augusta Torres, Gengyun Zhang, Roberto Lozano, Nikolai V. Ravin, and Lin H

Subjects
0106 biological sciences, Gene Expression Regulation Plant, Gene Expression, eukaryotic genomes, maize, 01 natural sciences, Genome, Laboratorium voor Plantenveredeling, Gene Expression Regulation, Plant, Gene Duplication, Haplotype, Inbreeding depression, Inbreeding, 2. Zero hunger, Genetics, Tuber, 0303 health sciences, Heterozygosity, Multidisciplinary, Depression, EPS-3, Homozygote, digestive, oral, and skin physiology, food and beverages, tool, Genomics, elements, rna-seq, Multigene Family, Evolution Molecular, potato, reveals, Genome, Plant, Heterozygote, Genome evolution, Bioinformatics, Molecular Sequence Data, Biology, in-vitro, Genes, Plant, Evolution, Molecular, 03 medical and health sciences, BIOS Applied Bioinformatics, Gene mapping, Genetic variation, Bioinformatica, Gene, Laboratorium voor Nematologie, Ciencias Exactas, Plant Diseases, Solanum tuberosum, 030304 developmental biology, Whole genome sequencing, Ploidies, resistance genes, solanum, fungi, Genetic Variation, Molecular Sequence Annotation, Immunity, Innate, Immunity Innate, Plant Breeding, Haplotypes, Food Security, Genome sequence, purl.org/pe-repo/ocde/ford#3.01.00 [https], identification, Laboratory of Nematology, Genome Plant, 010606 plant biology & botany
Abstract

Potato (Solanum tuberosum L.) is the world's most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop., La lista completa de autores que integran el documento puede consultarse en el archivo., Facultad de Ciencias Exactas

Published
2011
Full Text
View/download PDF

10. Mapping multiple disease resistance genes using a barley mapping population evaluated in Peru, Mexico, and the USA

Author

I. Vales, C. Rossi, Roger P. Wise, Luz Rayda Gomez-Pando, Xianming Chen, Kazuhiro Sato, Gisella Orjeda, Kiyosumi Hori, H. Vivar, Alfonso Cuesta-Marcos, F. Capettini, and Patrick M. Hayes

Subjects
Germplasm, Population, Blumeria graminis f. sp. hordei, Plant Science, Biology, Plant disease resistance, Quantitative trait locus, Hordeum vulgare subsp. vulgare, Quantitative resistance, Genetics, education, Molecular Biology, Puccinia striiformis f. sp. hordei, Puccinia hordei, education.field_of_study, Mildew, Resistance (ecology), food and beverages, biology.organism_classification, Agronomy, Qualitative resistance, Agronomy and Crop Science, Powdery mildew, Biotechnology
Abstract

We used a well-characterized barley mapping population (BCD 47 x Baronesse) to determine if barley stripe rust (BSR) resistance quantitative trait loci (QTL) mapped in Mexico and the USA were effective against a reported new race in Peru. Essentially the same resistance QTL were detected using data from each of the three environments, indicating that these resistance alleles are effective against the spectrum of naturally occurring races at these sites. In addition to the mapping population, we evaluated a germplasm array consisting of lines with different numbers of mapped BSR resistance alleles. A higher BSR disease severity on CI10587, which has a single qualitative resistance gene, in Peru versus Mexico suggests there are differences in pathogen virulence between the two locations. Confirmation of a new race in Peru will require characterization using a standard set of differentials, an experiment that is underway. The highest levels of resistance in Peru were observed when the qualitative resistance gene was pyramided with quantitative resistance alleles. We also used the mapping population to locate QTL conferring resistance to barley leaf rust and barley powdery mildew. For mildew, we identified resistance QTL under field conditions in Peru that are distinct from the Mla resistance that we mapped using specific isolates under controlled conditions. These results demonstrate the long-term utility of a reference mapping population and a well-characterized germplasm array for locating and validating genes conferring quantitative and qualitative resistance to multiple pathogens.

Published
2006
Full Text
View/download PDF

11. Occurrence and Cytological Mechanism of 2n Pollen Formation in a Tetraploid Accession of Ipomoea batatas (Sweet Potato)

Author

L. A. Becerra Lopez-Lavalle and Gisella Orjeda

Subjects
biology, Spindle orientation, Metaphase ii, food and beverages, medicine.disease_cause, Ipomoea, biology.organism_classification, Polyploidy, Ipomoea triloba, Gene Frequency, Pollen, Botany, otorhinolaryngologic diseases, Genetics, medicine, Anaphase, Molecular Biology, Solanaceae, Genetics (clinical), Biotechnology
Abstract

We evaluated a 4x accession of Ipomoea batatas (L.) Lam. and four 2x accessions of Ipomoea triloba for 2n pollen production. Approximately 90% of the genotypes of accession 81.2 (I. batatas, 4x) produced 2n pollen with different frequencies. In contrast, none of the genotypes of I. triloba produced 2n pollen. The diameter of the 2n pollen was approximately 30% ((3) sqrt 2) larger than that of the n pollen, making it easy to identify, measure, and quantify. The correlation (r = 0.93**) between the frequency of giant pollen and the frequency of dyads and triads was highly significant, strongly suggesting that the giant pollen grains were 2n pollen. The 2n pollen producers presented either a parallel or tripolar spindle arrangement (Y shaped) at anaphase II instead of the normal 60 degrees crossed spindle orientation. These two abnormal spindle configurations produced dyads and triads, with different frequencies (13-67%), instead of tetrads. Occasionally a metaphase II spindle variation was found with a single fused spindle, which also forms a dyad. The correlation (r = 0.89**) between the frequency of 2n pollen and the frequency of parallel, fused, and tripolar spindle arrangements was also highly significant, suggesting that these abnormal spindle configurations are involved in the production of 2n pollen in I. batatas. When we evaluated the efficiency of 2n pollen in polyploidization using 4x x 4x (2n) crosses, all progenies were 4x, suggesting the existence of barriers to crossability between 4x genotypes and their 2n pollen-producer counterparts.

Published
2002
Full Text
View/download PDF

12. Capacity building: Architects of South American science

Author

José Eduardo Krieger, Lino Barañao, Carlos A. Nobre, Gisella Orjeda, Eduardo Arzt, Juan Carlos Castilla, Sidarta Ribeiro, Pablo C Guerrero, and Claudio Bifano

Subjects
Capacity Building, Ecology (disciplines), Science, Biodiversity, Argentina, Public policy, Public Policy, Public-Private Sector Partnerships, Reward, Political science, Peru, Animals, Chile, Environmental planning, Multidisciplinary, Ecology, business.industry, Capacity building, Agriculture, Forestry, Venezuela, Research Personnel, South american, Workforce, business, Brazil
Published
2014

13. PROMUSA - A GLOBAL PROGRAMME FOR MUSA IMPROVEMENT

Author

S. Sharrock, E.A. Frison, and Gisella Orjeda

Subjects
Medical education, Geography, Research areas, Horticulture, Working group, Fusarium wilt
Abstract

Proceedings of a meeting held in Gosier, Guadeloupe, on 5-9 March 1997. the meeting brought together some 70 of the most prominent researchers involved in Musa improvement world-wide. Discussions of the proposal global programme took place in both plenary and working group meetings and the programme strategy and the medium-term plan have been defined. Five working groups were formed to address the major research areas: genetic improvement, Sigatoka disease, Fusarium wilt, nematology and virology.

Published
1998
Full Text
View/download PDF

14. G3-Genes Genomes Genetics

Author

Gisella Orjeda, Roberto Lozano, Istvan Nagy, Maria Eguiluz, Manuel Ramirez, Diana Martinez, Sanwen Huang, Germán De la Cruz, Linda Milne, Reinhard Simon, Sanjeev Kumar Sharma, David M. A. Martin, Christian W. B. Bachem, Richard E. Veilleux, Dan Milbourne, Merideth Bonierbale, Ying Li, Nilo Mejía, Karen McLean, Sergio Enrique Feingold, Martín Federico Carboni, Dan Bolser, Susan Munive, Walter Amoros, Boris Sagredo, David S. Douches, Xiao-Qiang Guo, Zhonghua Zhang, Christine A. Hackett, Richard G. F. Visser, Robbie Waugh, Glenn J. Bryan, Guangcun Li, David Marshall, Juan Martín D'Ambrosio, Alex Di Genova, Olga Ponce, Susan Thomson, John P. Hamilton, Frank Guzman, Jan M. de Boer, Alejandro Maass, Yerisf Torres, Jeanne M. E. Jacobs, Mads Sønderkær, and School of Plant and Environmental Sciences

Subjects
0106 biological sciences, genomic DNA, plant genome, Sequencetagged sites, genotype, physical map, tomato, dna, 01 natural sciences, Genome, microsatellites, purl.org/becyt/ford/1 [https], Genética y Herencia, User-Computer Interface, Laboratorium voor Plantenveredeling, genetic linkage, plant chromosome, genetic map, Genetics (clinical), 2. Zero hunger, Genetics, 0303 health sciences, education.field_of_study, Pseudomolecules potato, Chromosome Mapping, food and beverages, genome anchoring, Solanaceae genome, centromere, sequence-tagged sites, Microsatellite, potato, Biological Markers, genetic marker, CIENCIAS NATURALES Y EXACTAS, Genome, Plant, chromosome inversion, Anchoring scaffold, Population, solanaceae, Investigations, Biology, pseudomolecules, Chromosomes, Plant, Ciencias Biológicas, Sequence-tagged site, 03 medical and health sciences, Genetic linkage, Orientation, evolution, chromosome 4, education, purl.org/becyt/ford/1.6 [https], Molecular Biology, plant DNA, Solanum tuberosum, 030304 developmental biology, diploidy, Internet, molecule, nonhuman, species difference, fungi, Chromosome, gene mapping, plant genetics, centromeres, sequence, tomato genome, Plant Breeding, sequence tagged site, Genetic marker, identification, computer model, segregation distortion, EPS, Biomarkers, scaffold orientation, purl.org/pe-repo/ocde/ford#1.06.07 [https], 010606 plant biology & botany, Reference genome
Abstract

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 marker-based 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 similar to 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 (similar to 93%) of the 723 Mb genome assembly and 37,482 (similar to 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. Potato Genome Sequencing grant, UK; Scottish Government Rural and Environmental Science and Analytical Services Division (RESAS); Department for Environment, Food and Rural Affairs (DEFRA)Department for Environment, Food & Rural Affairs (DEFRA); Agriculture and Horticulture Development Board (AHDB)-Potato Council; Biotechnology and Biological Sciences Research Council (BBSRC)Biotechnology and Biological Sciences Research Council (BBSRC) [BB/F012640]; New Zealand Institute for Crop & Food Research Ltd Strategic Science Initiative; New Zealand Institute for Plant & Food Research Ltd Capability Fund, New Zealand; NMEA (Netherlands Ministry of Economic Affairs); CBSG (Centre for BioSystems Genomics); STW (Netherlands Technology Foundation), The Netherlands [07796]; Teagasc Core Funding; DAFF-Research Stimulus Fund, Ireland; International Potato Center (CIP-CGIAR)/CRP RTB, Peru; CONICYTComision Nacional de Investigacion Cientifica y Tecnologica (CONICYT) [Fondap 1509007, PBCT-PSD-03]; CONICYT (Basal CMM); CIRIC INRIA; INIA-Ministry of Agriculture of Chile, Chile; FEMCIDI OEA [PE/09/02 MINCyT-CONCyTEC]; Instituto Nacional de Tecnologia Agropecuaria (INTA-Core Funds); Ministerio de Ciencia y Tecnologia (MINCyT), Argentina; Proyecto FEMCIDI-OEA [SEDI/AE-305 /09]; Proyecto Bilateral Argentina, Per; FINCyT [099-FINCyT-EQUIP-2009) / (076-FINCyT-PIN-2008)]; Prestamo BID [1663/OC-PE]; Instituto Nacional de Innovacion Agraria, Ministry of Agriculture of Peru; Peruvian Ministry of Agriculture, Technical Secretariat of coordination; CGIAR; Consejo Nacional de Ciencia, Tecnologia e Innovacion Tecnologica, Peru (CONCYTEC); Special Multilateral Fund of the Inter-American Council for Integral Development (FEMCIDI-Peru); Biotechnology and Biological Sciences Research CouncilBiotechnology and Biological Sciences Research Council (BBSRC) [BB/F012640/1] We thank Andrzej Kilian (Diversity Arrays Technology, Australia) for DArT genotyping of the DMDD mapping population. We acknowledge Peter E. Hedley and Clare Booth (The James Hutton Institute, UK) for help with SNP genotyping. We thank S. B. Divito (Instituto Nacional de Tecnologia Agropecuaria, Balcarce, Argentina) for technical assistance. We are also grateful to Luke Ramsay and Peter E. Hedley (The James Hutton Institute, UK) for comments on the manuscript. AFLP and WGP are (registered) trademarks owned by KeyGene N.V. We acknowledge the funding made available by the Potato Genome Sequencing grant, UK [Scottish Government Rural and Environmental Science and Analytical Services Division (RESAS), Department for Environment, Food and Rural Affairs (DEFRA), Agriculture and Horticulture Development Board (AHDB)-Potato Council, Biotechnology and Biological Sciences Research Council (BBSRC, Grant BB/F012640)]; New Zealand Institute for Crop & Food Research Ltd Strategic Science Initiative and the New Zealand Institute for Plant & Food Research Ltd Capability Fund, New Zealand; NMEA (Netherlands Ministry of Economic Affairs), CBSG (Centre for BioSystems Genomics), STW (Netherlands Technology Foundation grant 07796), The Netherlands; Teagasc Core Funding, DAFF-Research Stimulus Fund, Ireland; International Potato Center (CIP-CGIAR)/CRP RTB, Peru; CONICYT (Fondap 1509007, Basal CMM, PBCT-PSD-03), CIRIC INRIA, INIA-Ministry of Agriculture of Chile, Chile; FEMCIDI OEA, PE/09/02 MINCyT-CONCyTEC, 2010-2011, Instituto Nacional de Tecnologia Agropecuaria (INTA-Core Funds) and Ministerio de Ciencia y Tecnologia (MINCyT), Argentina; Proyecto FEMCIDI-OEA SEDI/AE-305 /09 (2008-2012), Proyecto Bilateral Argentina, Per; FINCyT (099-FINCyT-EQUIP-2009) / (076-FINCyT-PIN-2008), Prestamo BID no. 1663/OC-PE, Instituto Nacional de Innovacion Agraria, Ministry of Agriculture of Peru, Peruvian Ministry of Agriculture, Technical Secretariat of coordination with the CGIAR, Consejo Nacional de Ciencia, Tecnologia e Innovacion Tecnologica, Peru (CONCYTEC), Special Multilateral Fund of the Inter-American Council for Integral Development (FEMCIDI-Peru).

Published
2013
Full Text
View/download PDF

15. Optimización de los medios de propagación y enraizamiento in vitro de las variedades 'criollas' de vid para elaborar pisco

Author

Gisella Orjeda, Wilfredo L. Gonzáles, Diego Pignataro, Eugenio González, and Daniel Clark

Subjects
Physics, Tissue culture, pisco, rooting, propagation, Cultivo in vitro, enraizamiento, vides criollas, General Agricultural and Biological Sciences, creole grapevines, Humanities, propagación
Abstract

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., 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.

Published
2011

16. Use of Ipomoea trifida (HBK.) G. Don germ plasm for sweet-potato improvement. 2. Fertility of synthetic hexaploids and triploids with 2n gametes of I. trifida, and their interspecific crossability with sweet potato

Author

Rosanna Freyre, Masaru Iwanaga, and Gisella Orjeda

Subjects
biology, media_common.quotation_subject, Fertility, General Medicine, Interspecific competition, biology.organism_classification, medicine.disease_cause, Interspecific hybridization, Ipomoea trifida, Pollen, Botany, Genetics, medicine, Convolvulaceae, Molecular Biology, Biotechnology, Germ plasm, media_common
Abstract

Twenty-two synthetic hexaploids and 33 triploids with 2n pollen production of Ipomoea trifida were used in crosses to estimate their male and female fertility and their crossability with sweet potato, Ipomoea batatas (L.) Lam. Several important conclusions were drawn. (i) The fertility of pollen of the triploid plants was confirmed, which suggested they are truly functional 2n pollen. (ii) The average male fertility of hexaploid plants was higher than that of triploid with 2n pollen production plants. (iii) 2n egg production was observed in several triploid genotypes, (iv) From a polycross, 3079 seeds with normal shapes were produced. These represent a population of hexaploid I. trifida with a wide genetic base, and they may be important material for sweet-potato improvement, (v) A total of 3275 seeds were obtained from crosses with six sweet-potato female parents, of which only 60 germinated, indicating the existence of an interspecific barrier. The implications of 2n gametes for breeding and evolution of sweet potato are also discussed.Key words: Ipomoea batatas, Ipomoea trifida, 2n gametes, sexual polyploidization, triploid.

Published
1991
Full Text
View/download PDF

18. An eIF4E allele confers resistance to an uncapped and non-polyadenylated RNA virus in melon

Author

Miguel A. Aranda, Jordi Garcia-Mas, Christian Clepet, Michel Caboche, Michel Pitrat, Catherine Dogimont, Pere Puigdomènech, Abdelhafid Bendahmane, Cristina Nieto, Amparo Monfort, Mónica Morales, Gisella Orjeda, Bénédicte Sturbois, Ministerio de Educación y Ciencia (España), Ministerio de Ciencia e Innovación (España), Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Institut de Recerca i Tecnologia Agroalimentàries = Institute of Agrifood Research and Technology (IRTA), Génétique et Amélioration des Fruits et Légumes (GAFL), Institut National de la Recherche Agronomique (INRA), and Institute of Agrifood Research and Technology (IRTA)

Subjects
0106 biological sciences, RNA Caps, Positional cloning, Molecular Sequence Data, MAP-BASED CLONING, Arabidopsis, Plant Science, 01 natural sciences, Chromosomes, Plant, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Eukaryotic translation, EIF4E, Genetics, RNA Viruses, MICROSYNTENY, Amino Acid Sequence, RNA, Messenger, Cloning, Molecular, Gene, Alleles, 030304 developmental biology, DNA Primers, AVIRULENCE DETERMINANT, 0303 health sciences, biology, Base Sequence, Sequence Homology, Amino Acid, Melon necrotic spot virus, Potyviridae, Carmovirus, CAP-BINDING, food and beverages, ARABIDOPSIS THALIANA, RNA virus, Cell Biology, biology.organism_classification, 3. Good health, ARN, Tombusviridae, CARMOVIRUS, Cucurbitaceae, Eukaryotic Initiation Factor-4E, VIRUS, RESISTANCE, 010606 plant biology & botany
Abstract

The characterization of natural recessive resistance genes and virus-resistant mutants of Arabidopsis have implicated translation initiation factors of the 4E family [eIF4E and eIF(iso)4E] as susceptibility factors required for virus multiplication and resistance expression. To date, viruses controlled by these genes mainly belong to the family Potyviridae. Melon necrotic spot virus (MNSV) belongs to the family Tombusviridae (genus Carmovirus) and is an uncapped and non-polyadenylated RNA virus. In melon, nsv-mediated resistance is a natural source of recessive resistance against all strains of MNSV except MNSV-264. Analyses of chimeras between non-resistance-breaking and resistance-breaking strains have shown that the avirulence determinant maps to the 3′-untranslated region (3′-UTR) of the viral genome. Using a combination of positional cloning and microsynteny analysis between Arabidopsis thaliana and melon, we genetically and physically delimited the nsv locus to a single bacterial artificial chromosome clone and identified the melon eukaryotic translation initiation factor 4E (Cm-eIF4E) as a candidate gene. Complementation analysis using a biolistic transient expression assay, confirmed Cm-eIF4E as the product of nsv. A single amino acid change at position 228 of the protein led to the resistance to MNSV. Protein expression and cap-binding analysis showed that Cm-eIF4E encoded by a resistant plant was not affected in it's cap-binding activity. The Agrobacterium-mediated transient expression of the susceptibility allele of Cm-eIF4E in Nicotiana benthamiana enhanced MNSV-264 accumulation. Based on these results, a model to explain melon resistance to MNSV is proposed. These data, and data from other authors, suggest that translation initiation factors of the eIF4E family are universal determinants of plant susceptibility to RNA viruses., G. Orjeda was supported by Le Conseil Régional-IDF, C. Nieto and M. Morales were supported by short-stay Marie Curie fellowships. C. Nieto was also the recipient of a ‘‘Formación de Personal Investigador’’ fellowship of the Ministerio de Educación y Ciencia (Spain). This work was supported by grants AGL2003-02739, 2FD97-0286 and HF2003-176.

Published
2006
Full Text
View/download PDF

19. Analysis of the interaction melon-melon necrotic spot virus controlled by the recessive resistance gene Nsv

Author

Christine Nieto, Monica Morales, Gisella Orjeda, Veronica Truniger, Caboche, Michel M., Catherine Dogimont, Jordi Garcia-Mas, Miguel Aranda, Abdelhafid Bendahmane, Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut de Recerca i Tecnologia Agroalimentàries = Institute of Agrifood Research and Technology (IRTA), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Génétique et Amélioration des Fruits et Légumes (GAFL), Institut National de la Recherche Agronomique (INRA), Institute of Agrifood Research and Technology (IRTA), and ProdInra, Migration

Subjects
[SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], MELON NECROTIC SPOT VIRUS, MNSV, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2006

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

Author

Abdelhafid Bendahmane, Cristina Nieto, Hans C. van Leeuwen, Pere Puigdomènech, Mónica Morales, Michel Caboche, Amparo Monfort, Gisella Orjeda, Pere Arús, Jordi Garcia-Mas, Miguel A. Aranda, Myriam Charpentier, Catherine Dogimont, and Ministerio de Ciencia y Tecnología (España)

Subjects
Chromosomes, Artificial, Bacterial, Positional cloning, DNA, Plant, Melon, Locus (genetics), Biology, Polymerase Chain Reaction, Cucumis melo, Genetics, DNA Primers, Plant Diseases, Contig, Base Sequence, Melon necrotic spot virus, food and beverages, Chromosome Mapping, General Medicine, biology.organism_classification, Immunity, Innate, Genetic distance, Amplified fragment length polymorphism, Carmovirus, Agronomy and Crop Science, Cucumis, Biotechnology
Abstract

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’.

Published
2005

21. Abortion and determination of stages for embryo rescue in crosses between sweet-potato, Ipomoea batatas Lam. (2n=6x=90) and its wild relative, I. trifida (H. B. K.) G. Don. (2n=2x=30)

Author

Masaru Iwanaga, Kazuo Watanabe, José Mont, and Gisella Orjeda

Subjects
animal structures, biology, Embryogenesis, Embryo, Cell Biology, Plant Science, Interspecific competition, Abortion, Ipomoea, biology.organism_classification, Intraspecific competition, Embryo rescue, Horticulture, embryonic structures, Paraffin section, Botany
Abstract

The frequency of aborted fruits and the changes and abnormalities that occur during the embryo development in intraspecific crosses of sweet-potato Ipomoea batatas (2n=6x=90) and interspecific crosses between I. batatas and I. trifida (2n=2x=30) were investigated in order to study the causes of the low seed production. Three genotypes of I. batatas and 18 genotypes of I. trifida were intermated. The frequency of aborted fruits was below 25% in the intraspecific crosses and over 90% in the interspecific crosses. Paraffin sections were used to examine the developmental stages of fruits and seeds. Embryos in different developmental stages were observed to determine the stage of abortion. These observations permitted the identification of developmental stages of embryo rescue in interspecific crosses. There were no significant differences in the frequency of embryo abortion before the early globular stage among female sweet-potato progenitors for the intraspecific and interspecific crosses. The frequency of the late occurrence of embryo abortion (when embryo abortion occurs after the pre-globular stage) was higher in interspecific crosses (19.1%) than in intraspecific crosses (5.5%). The frequency of the late occurrence of embryo abortion in interspecific crosses was higher at the globular stage (9.6%) than at the heart stage (4.3%). Providing that embryo rescue is conducted in interspecific crosses, the estimated number of potentially viable embryos could be increased: 30 times with embryos at the globular stage; 20 times with embryos at the heart stage; and 11 times if embryos at the torpedo stage were used for the rescue with respect to the seed set. The results suggested that the appropriate time for embryo rescue in interspecific crosses is at the globular stage. If embryos could be rescued at the globular stage, it would be possible to increase the number of surviving embryos up to 30 times in interspecific crosses and 0.02 times in intraspecific crosses with respect to natural conditions without embryo rescue.

Published
1993
Full Text
View/download PDF

22. Use of Ipomoea trifida germ plasm for sweet potato improvement. 3. Development of 4x interspecific hybrids between Ipomoea batatas (L.) Lam. (2n=6x=90) and I. trifida (H.B.K) G. Don. (2n=2x=30) as storage-root initiators for wild species

Author

Rosanna Freyre, Masaru Iwanaga, and Gisella Orjeda

Subjects
biology, fungi, food and beverages, General Medicine, Ipomoea, biology.organism_classification, Interspecific hybrids, Gene flow, Ipomoea trifida, Genus, Botany, Genetics, Ploidy, Agronomy and Crop Science, Biotechnology, Germ plasm, Hybrid
Abstract

More than 28,000 pollinations were carried out between 5 Ipomoea batatas and 41 diploid I. trifida accessions of diverse origins to obtain 4x interspecific hybrids. From the resultant 730 seeds, 248 plants were finally obtained. Ploidy level determination of the progeny showed unexpected results: 52 individuals were hexaploid, 5 were pentaploid, 190 were tetraploid, as expected, and one was not determined. The existence of 5x and 6x progenies from 6x x 2x crosses not only confirmed the presence of 2n gametes but also their successful function in gene flow between ploidy levels and polyploidization within this genus. The progeny and their cultivated parents were planted in an observation field. The cultivated parents produced 0.49 kg/plant or less. Most 4x progenies did not produce storage roots or had very poor yields; nonetheless, and despite their cultivated parents' poor yields, 8 genotypes yielded between 0.81 and 1.50 kg/plant.A new scheme, using the 4x interspecific hybrids, is proposed for evaluating 2x and 4x wild accessions of the section Batatas to which the sweet potato belongs. Other possible uses of the 4x hybrids in breeding and genetics of the sweet potato are also discussed.

Published
1991

24. 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

Author

Sergio Enrique Feingold, Jeanne M. E. Jacobs, Xiaomin Tang, Christian W. B. Bachem, Robert Gromadka, Glenn J. Bryan, Paulo Melo, Richard G. F. Visser, Swarup K. Chakrabati, Roeland C. H. J. van Ham, Boris Kuznetsov, Boris Sagredo, Sanwen Huang, Jan M. de Boer, Dan Milbourne, and Gisella Orjeda

Subjects
disease resistance, Bioinformatics, phytophthora-infestans, late blight resistance, Plant Science, broad-spectrum resistance, macromolecular substances, system, tomato, Genome, DNA sequencing, bacterial wilt, Laboratorium voor Plantenveredeling, solanum-bulbocastanum, Bioinformatica, Solanum bulbocastanum, Genetics, Whole genome sequencing, Bacterial artificial chromosome, biology, Contig, Shotgun sequencing, EPS-3, musculoskeletal, neural, and ocular physiology, fungi, food and beverages, Genome project, biology.organism_classification, gene-cluster, PRI Bioscience, Plant Breeding, nervous system, quantitative trait loci, Agronomy and Crop Science
Abstract

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 potato.

Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results