Single nucleotide polymorphism (SNP) genotyping as basis for developing a PCR-based marker highly diagnostic for potato varieties with high resistance to Globodera pallida pathotype Pa2/3
- 404 Downloads
Globodera pallida is a parasitic root cyst nematode of potato, which causes reduction of crop yield and quality in infested fields. Field populations of G. pallida containing mixtures of pathotypes Pa2 and Pa3 (Pa2/3) are currently most relevant for potato cultivation in middle Europe. Genes for resistance to G. pallida have been introgressed into the cultivated potato gene pool from the wild, tuber bearing Solanum species S. spegazzinii and S. vernei. Selection of resistant genotypes in breeding programs is hampered by the fact that the phenotypic evaluation of resistance to G. pallida is time consuming, costly and often ambiguous. DNA-based markers diagnostic for resistance to G. pallida would facilitate the development of resistant varieties. A tetraploid F1 hybrid family SR-Gpa segregating for quantitative resistance to G.␣pallida was developed and evaluated for resistance to G. pallida population ‘Chavornay’. Two subpopulations of 30 highly resistant and 30 susceptible individuals were selected and genotyped for 96 single nucleotide polymorphism (SNP) markers tagging 12 genomic regions on 10 potato chromosomes. Seven SNPs were found significantly linked to the nematode resistance, which were all located within a resistance ‘hotspot’ on potato chromosome V. A haplotype model for these seven SNPs was deduced from the SNP patterns observed in the SR-Gpa family. A PCR assay ‘HC’ was developed, which specifically detected the SNP haplotype c that was linked with high levels of nematode resistance. The HC marker was only found in accessions of S.␣vernei. Screening with the HC marker 34 potato varieties resistant to G. pallida pathotypes Pa2 and/or Pa3 and 22 susceptible varieties demonstrated that the HC marker was highly diagnostic for presence of high levels of resistance to G. pallida pathotype Pa2/Pa3.
KeywordsPotato Globodera pallida Root cyst nematodes Single nucleotide polymorphism (SNP) Diagnostic marker Haplotype
Unable to display preview. Download preview PDF.
The authors gratefully acknowledge the funding of this work under the GABI program (Genome analysis in the biological system of plants) by BMBF (Bundesministerium für Bildung und Forschung), Project No 0312290 CONQUEST (Genes CONtrolling QUantitativE traits of Solanum Tuberosum). Part of this work was carried out in the department of plant breeding research and yield physiology, headed by Francesco Salamini, and in the department of plant breeding research and genetics, headed by Maarten Koornneef.
- Behringer P (1969) Feststellung zystenbildender Nematoden mit dem Biotest im Vierkammergefäß Mitt. Biol Bundesanst 136:5Google Scholar
- Bormann CA, Rickert AM, Castillo Ruiz RA, Paal J, Lübeck J, Strahwald J, Buhr K, Gebhardt C (2004) Tagging quantitative trait loci for maturity-corrected late blight resistance in tetraploid potato with PCR-based candidate gene markers. Mol Plant–Microbe Interac 17:1126–1138Google Scholar
- Bradshaw JE, Hackett CA, Meyer RC, Milbourne D, McNicol JW, Phillips MS, Waugh R (1998) Identification of AFLP and SSR markers associated with quantitative resistance to Globodera pallida (Stone) in tetraploid potato (Solanum tuberosum ssp. tuberosum) with a view to marker-assisted selection. Theor Appl Genet 97:202–210CrossRefGoogle Scholar
- Caromel B, Mugniéry D, Lefebvre V, Andrzejewski S, Ellissèche D, Kerlan MC, Rousselle P, Rousselle-Bourgeois F (2003) Mapping QTLs for resistance against Globodera pallida (Stone) Pa2/3 in a diploid potato progeny originating from Solanum spegazzinii. Theor Appl Genet 106:1517–1523PubMedGoogle Scholar
- Caromel B, Mugniéry D, Kerlan MC, Andrzejewski S, Palloix A, Ellissèche D, Rousselle-Bourgeois F, Lefebvre V (2005) Resistance quantitative trait loci originating from Solanum sparsipilum act independently on the sex ratio of Globodera pallida and together for developing a necrotic reaction. Mol Plant– Microbe Interact 18:1186–1194PubMedGoogle Scholar
- Evans K, Trudgill DL (1992) Pest aspects of potato production. Part 1. The nematode pests of potato. In: Harris P (ed), The Potato Crop 2nd edn. Chapman and Hall, London, pp 438–475Google Scholar
- Gebhardt C, Ballvora A, Walkemeier B, Oberhagemann P, Schüler K (2004) Assessing genetic potential in germ plasm collections of crop plants by marker-trait association: a case study for potatoes with quantitative variation of resistance to late blight and maturity type. Mol Breed 13:93--102Google Scholar
- Kuang H, Wei F, Marano MR, Wirtz U, Wang X, Liu J, Shum WP, Zaborsky J, Tallon LJ, Rensink W, Lobst S, Zhang P, Tornqvist C-E, Tek A, Bamberg J, Helgeson J, Fry W, You F, Luo M-C, Jiang J, Buell CR, Baker B (2005) The R1 resistance gene cluster contains three groups of independently evolving, type I R1 homologues and shows substantial structural variation among haplotypes of Solanum demissum. Plant J 44:37–51PubMedCrossRefGoogle Scholar
- Okimoto R, Dodgston JB (1996) Improved PCR amplification of multiple specific alleles (PAMSA) using internally mismatched primers. Biotechiques 21:20– 26Google Scholar
- Phillips MS (1994) Inheritance of resistance to nematodes. In: Bradshaw JE, Mackay GR (eds), Potato Genetics. CAB International, Wallingford, pp 319–337Google Scholar
- Ross H (1986) Potato breeding – problems and perspectives. Advances in Plant Breeding, Supplement 13 to Journal of Plant Breeding, Paul Parey, Berlin, Hamburg, pp 75–82Google Scholar
- Rouppe van der Voort J, van der Vossen E, Bakker E, Overmars H, van Zandvoort P, Hutten R, Klein-Lankhorst R, Bakker J (2000) Two additive QTLs conferring broad-spectrum resistance in potato to Globodera pallida are localized on resistance gene clusters. Theor Appl Genet 101:1222–1230CrossRefGoogle Scholar
- Van der Vossen EAG, Rouppe van der Voort JNAM, Kanyuka K, Bendahmane A, Sandbrink H, Baulcombe DC, Bakker J, Stiekema WJ, Klein-Lankhorst RM (2000) Homologues of a single resistance-gene cluster in potato confer resistance to distinct pathogens: a virus and a nematode. Plant J 23:567–576CrossRefGoogle Scholar