Mapping of the cyst nematode resistance locus Gpa2 in potato using a strategy based on comigrating AFLP markers

Voort, J.N.A.M. Rouppe van der; Wolters, Petra; Folkertsma, R.T.; Hutten, R.C.B.; Zandvoort, Peter van; Vinke, Henk; Kanyuka, K.; Bendahmane, A.; Jacobsen, E.; Jansen, Ritsert C.; Bakker, J.

doi:10.1007/s001220050638

Cited by 104 publications

(55 citation statements)

References 31 publications

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“…no need for prior sequence information, a large number of polymorphisms and a small amount of genomic DNA required) have made AFLP a very attractive method to study DNA polymorphism in general. AFLP analysis has been applied to genetic mapping (Becker et al 1995;Waugh et al 1997; Van der Voort et al 1997;Alonso-Blanco et al 1998), phylogenetic relationships and genetic diversity (Donini et al 1997;Pakniyat et al 1997;Russell et al 1997;Schut et al 1997;Miyashita et al 1999) studies. The ability of the AFLP method to differentiate individuals in a population has also made it useful for paternity analyses (Krauss 1999), gene-flow experiments and for Plant Variety registration (Law et al 1998).…”

Section: Introductionmentioning

confidence: 98%

AFLP genetic polymorphism in wild barley (Hordeum spontaneum) populations in Israel

et al. 2003

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The genetic diversity produced by the amplified fragment length polymorphism (AFLP) method was studied in 94 genotypes of wild barley, Hordeum spontaneum (C. Koch) Thell., originating from ten ecologically and geographically different locations in Israel. Eight primer pairs produced 204 discernible loci of which 189 (93%) were polymorphic. Each genotype had a unique banding profile and the genetic similarity coefficient varied between 0.74 and 0.98. The phenogram generated from these similarities by the UPGMA method did not group genotypes strictly according to their geographical origin, which pattern was also seen in the principal coordinate (PCO) plot. Genetic diversity was larger within (69%) than among (31%) populations. Associations between ecogeographical variables and the mean gene diversity were found at one primer pair. The results are discussed and compared with data obtained by the simple sequence repeat (SSR) method.

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Section: Introductionmentioning

confidence: 98%

AFLP genetic polymorphism in wild barley (Hordeum spontaneum) populations in Israel

et al. 2003

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“…For selective mapping purposes a subset of 29 informative genotypes (RHSH#11, ¡#13, ¡#34, ¡#101, ¡#130, ¡#138, ¡#164, ¡#178, ¡#179, ¡#185, ¡8, ¡11, ¡24, ¡29, ¡33, ¡46, ¡48, ¡51, ¡54, ¡55, ¡58, ¡60, ¡71, ¡77, ¡79, ¡83, ¡84, ¡86, ¡89) were selected with MapPop (Vision et al 1999) from a diploid mapping population consisting of 120 F1 progeny derived from a cross between the diploid parent genotypes SH83-92-488 (SH) and RH89-039-16 (RH) (Rouppe van der Voort et al 1997). This population was previously used to construct an ultra dense genetic map of potato comprising »10,000 AFLP-markers divided over approximately 900 bins (Isidore et al 2003;van Oss et al 2006; http://www.dpw.wageningen-ur.nl/ uhd/).…”

Section: Plant Materials and Dna Isolationunclassified

Genetic mapping and transcription analyses of resistance gene loci in potato using NBS profiling

Brugmans

Wouters²,

Os³

et al. 2008

Theor Appl Genet

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NBS proWling is a method for the identiWcation of resistance gene analog (RGA) derived fragments. Here we report the use of NBS proWling for the genome wide mapping of RGA loci in potato. NBS proWling analyses on a minimal set of F1 genotypes of the diploid mapping population previously used to generate the ultra dense (UHD) genetic map of potato, allowed us to eYciently map polymorphic RGA fragments relative to 10,000 existing AFLP markers. In total, 34 RGA loci were mapped, of which only 13 contained RGA sequences homologous to RGAs genetically positioned at approximately similar positions in potato or tomato. The remaining RGA loci mapped either at approximate chromosomal regions previously shown to contain RGAs in potato or tomato without sharing homology to these RGAs, or mapped at positions not yet identiWed as RGA-containing regions. In addition to markers representing RGAs with unknown functions, segregating markers were detected that were closely linked to four functional R genes that segregate in the UHD mapping population. To explore the potential of NBS proWling in RGA transcription analyses, RNA isolated from diVerent tissues was used as template for NBS proWling. Of all the fragments ampliWed approximately 15% showed putative intensity or absent/present diVerences between diVerent tissues suggesting putative tissue speciWc RGA or R gene transcription. Putative absent/present diVerences between individuals were also found. In addition to being a powerful tool for generating candidate gene markers linked to R gene loci, NBS proWling, when applied to cDNA, can be instrumental in identifying those members of an R gene cluster that are transcribed, and thus putatively functional.

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“…The F1 mapping population descended from a cross between the diploid parents SH83-92-488 and RH89-039-16 (Rouppe van der Voort et al 1997b;Isidore et al 2003). The 120 genotypes of this mapping population are maintained in a screen house by annual propagation of seed tubers.…”

Section: Plant Materialsmentioning

confidence: 99%

“…It was assumed that a single linkage map with >10,000 AFLP marker loci should offer such a level of saturation of the 850 Mb potato genome that BAC landing becomes feasible with markers within a BAC length distance of the target gene. Therefore, in potato a diploid mapping population was established (Rouppe van der Voort et al 1997b) in which several interesting traits and genes are segregating, including a locus involved in the resistance against Synchytrium endobioticum. This population with >10,000 marker loci should be an ideal starting point for map-based cloning of this resistance gene, and comparable to earlier work on this material Huang et al 2004).…”

Section: Introductionmentioning

confidence: 99%

Exploitation of a marker dense linkage map of potato for positional cloning of a wart disease resistance gene

Brugmans¹,

Hutten²,

Rookmaker³

et al. 2005

Theor Appl Genet

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A marker-saturated linkage map of potato was used to genetically map a locus involved in the resistance against wart disease Synchytrium endobioticum race 1. The locus mapped on the long arm of chromosome 4 and is named Sen1-4 in contrast to a Sen1 locus on chromosome 11. The AFLP markers from the Sen1-4 interval enabled the isolation of BAC clones from an 11 genome equivalent BAC library. This was achieved via fingerprinting of BAC pools with the AFLP primer pairs that resemble the genetic marker loci. With non-selective AFLP primers, fingerprints of individual BAC clones were generated to analyse the overlap between BAC clones using FPC. This resulted in a complete contig and a minimal tiling path of 14 BAC clones enclosing the Sen1-4 locus. The BAC contig has a genetic length of $6 cM and a physical length of $1 Mb. Our results demonstrate that map-based cloning of Sen1-4 can be pursued on the basis of a strategy of marker saturation alone. Genetic resolution achieved by screening large numbers of offspring for recombination events may not be required. Together with the construction of the BAC contig, a physical map with the position of the markers is accomplished in one step. This provides proof of concept for the utility of the marker saturation that is offered by the ultra dense AFLP map of potato for gene cloning.

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Mapping of the cyst nematode resistance locus Gpa2 in potato using a strategy based on comigrating AFLP markers

Cited by 104 publications

References 31 publications

AFLP genetic polymorphism in wild barley (Hordeum spontaneum) populations in Israel

AFLP genetic polymorphism in wild barley (Hordeum spontaneum) populations in Israel

Genetic mapping and transcription analyses of resistance gene loci in potato using NBS profiling

Exploitation of a marker dense linkage map of potato for positional cloning of a wart disease resistance gene

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