An Online Potato Pedigree Database Resource

Berloo, R. van; Hutten, R.C.B.; Eck, Herman J. van; Visser, R.G.F.

doi:10.1007/s11540-007-9028-3

Cited by 93 publications

(83 citation statements)

References 14 publications

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“…Large haplotype blocks may have been preserved due to limited recombination events in the breeding history of the germplasm analysed in our study. The pedigree information for G. pallida resistant varieties that is available from the 'Potato Pedigree database ' (van Berloo et al 2007, http://www.plantbreeding.wur.nl/potatopedigree/) is partial and contains 'dead ends'. A number of S. vernei clones, which do not exist anymore, have been used several times in the pedigrees.…”

Section: Discussionmentioning

confidence: 99%

“…The historical records do not allow identifying precisely the S. vernei resistance source and the number of meiotic generations, which separate contemporary germ plasm from the original introgressions. In general, variety pedigrees that can be traced back through the last 100 years include less than 10 meiotic generations (Love 1999;Gebhardt et al 2004;van Berloo et al 2007). Reduced recombination between homeologous chromosomes caused, for example, by inversions in the introgressed S. vernei segment relative to S. tuberosum, may also have contributed to the maintenance of a large haplotype block in the breeding populations.…”

Section: Discussionmentioning

confidence: 99%

“…LD decays more rapidly in outcrossing species when compared to selWng species, where recombination has no consequence for the genotype of homozygous individuals (Nordborg 2000). In potato, the diminishing eVect of outcrossing on LD is counteracted by the vegetative propagation, which reduces the number of meiotic generations separating individual breeding clones and varieties van Berloo et al 2007). The observed phenotypic and genotypic variability not only results from recombination, but also from a larger number, when compared with diploids, of chromosomal haplotype combinations that are possible in 4x by 4x crosses with tetrasomic inheritance.…”

Section: Discussionmentioning

confidence: 99%

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Using SNP markers to dissect linkage disequilibrium at a major quantitative trait locus for resistance to the potato cyst nematode Globodera pallida on potato chromosome V

et al. 2008

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The damage caused by the parasitic root cyst nematode Globodera pallida is a major yield-limiting factor in potato cultivation . Breeding for resistance is facilitated by the PCR-based marker 'HC', which is diagnostic for an allele conferring high resistance against G. pallida pathotype Pa2/3 that has been introgressed from the wild potato species Solanum vernei into the Solanum tuberosum tetraploid breeding pool. The major quantitative trait locus (QTL) controlling this nematode resistance maps on potato chromosome V in a hot spot for resistance to various pathogens including nematodes and the oomycete Phytophthora infestans. An unstructured sample of 79 tetraploid, highly heterozygous varieties and breeding clones was selected based on presence (41 genotypes) or absence (38 genotypes) of the HC marker. Testing the clones for resistance to G. pallida conWrmed the diagnostic power of the HC marker. The 79 individuals were genotyped for 100 single nucleotide polymorphisms (SNPs) at 10 loci distributed over 38 cM on chromosome V. Forty-Wve SNPs at six loci spanning 2 cM in the interval between markers GP21-GP179 were associated with resistance to G. pallida. Based on linkage disequilibrium (LD) between SNP markers, six LD groups comprising between 2 and 18 SNPs were identiWed. The LD groups indicated the existence of multiple alleles at a single resistance locus or at several, physically linked resistance loci. LD group C comprising 18 SNPs corresponded to the 'HC' marker. LD group E included 16 SNPs and showed an association peak, which positioned one nematode resistance locus physically close to the R1 gene family.Communicated by J. E. Bradshaw. Electronic supplementary materialThe online version of this article

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Using SNP markers to dissect linkage disequilibrium at a major quantitative trait locus for resistance to the potato cyst nematode Globodera pallida on potato chromosome V

et al. 2008

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“…We restricted the scope of the potato ontology by, e.g., not including the parents of the varieties and their characteristics although such pedigree (van Berloo et al 2007) is readily available. Nor did we include the models upon which the decision support systems are based although most of them are found in the public domain.…”

Section: Delimitation Of the Present Scope Of The Potato Ontologymentioning

confidence: 99%

The Potato Ontology: Delimitation of the Domain, Modelling Concepts, and Prospects of Performance

Haverkort¹,

Top²

2011

Potato Res.

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The ever increasing amount of data gathered by more growers in more years offers possibilities to add value. Therefore-for interested parties and stakeholders-a common and controlled vocabulary of the potato domain that describes concepts, attributes, and the relations between them in a formal way using a standardised knowledge representation language is being developed: a potato ontology. The advantage is that all possible stakeholders will be able to understand the data expressed by this ontology and that software applications can process them automatically. It will also allow the application of advanced numerical techniques that may help to uncover previously unknown correlations. This version of the potato ontology aims at the domain of processing potatoes in a setting of mechanised potato production where growers have access to automated decision support systems and exchange data electronically. This paper describes the procedures to establish such an ontology where competency questions formulated by stakeholders and potential users take a central position. The potato ontology formally describes "Concepts" or "Classes". The three main classes are those used in crop ecology: Crop, Environment and Management. Classes, e.g., biocides are a subclass of agrochemicals, and in turn have a subclass Fungicides. The ontology also describes the "Properties" of classes, e.g., agrochemicals are produced synthetically in a factory; biocides are used to protect crops and fungicides to control fungi. The ontology also describes the "Attributes" (properties) of the concepts, e.g., all agrochemicals have attributes such as dose and time of application and mode of application. "Restrictions" may be that a particular chemical can only be applied with a certain type of equipment, or its application is restricted to a certain period or dose. The ontology also features "Instances" which are the individual data such as a particular herbicide treatment with values for field, time, dose, active ingredient, trademark,

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“…This organic breeding programme does not have to start from scratch as two new late blight resistant varieties were registered in 2007 and are available for the Dutch organic market: Toluca and Bionica, see http://www.pedigree.com (Van Berloo et al 2007). The P. infestans resistance of these varieties is based on resistance from the wild potato species Solanum bulbocastanum.…”

Section: Genetic Resourcesmentioning

confidence: 99%

Cisgenesis Does Not Solve the Late Blight Problem of Organic Potato Production: Alternative Breeding Strategies

2008

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Average potato yields in Dutch organic farming systems vary from 15 to 29 Mg/ha and are limited by low input of nitrogen and severe late blight attacks caused by the oomycete Phytophthora infestans. Under Dutch late blight regulations it is mandatory to kill the haulm at 7% infestation. The late blight attacks have been so early in the organic potato production of the past few years that its acreage is now gradually decreasing whereas consumer demand is increasing. Agronomic control strategies have limited success. First priority lies in breeding for highly resistant varieties to safeguard organic potato production in the Netherlands. Cisgenesis, however, is not an option for the organic sector. Although the product of cisgenesis does not contain genes from non-crossable species it is a result of a genetic engineering process which is excluded from use in organic agriculture. As the principles and standards of organic agriculture are process-based, cisgenesis does not comply with the norms and standards of organic agriculture. The arguments of the organic sector go well beyond the alleged risks of the gene technology and relate to the technology itself. Breeding at DNA-level, instead of at whole-plant level, violates the integrity of life as described in the concept of naturalness. The Dutch organic sector is now aiming at increasing the traditional breeding activities including the participation of farmer-breeders in close cooperation with the formal breeding companies. Additional selection methods need to be developed to include required traits other than late blight resistance, such as nutrient efficiency. Recently

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An Online Potato Pedigree Database Resource

Cited by 93 publications

References 14 publications

Using SNP markers to dissect linkage disequilibrium at a major quantitative trait locus for resistance to the potato cyst nematode Globodera pallida on potato chromosome V

Using SNP markers to dissect linkage disequilibrium at a major quantitative trait locus for resistance to the potato cyst nematode Globodera pallida on potato chromosome V

The Potato Ontology: Delimitation of the Domain, Modelling Concepts, and Prospects of Performance

Cisgenesis Does Not Solve the Late Blight Problem of Organic Potato Production: Alternative Breeding Strategies

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