Genetic mapping and pyramiding of resistance genes in potato

Numerous pathogens can infect potato, but late blight (Phytophthora infestans (Mont.) de Bary) and potato cyst nematodes (PCN) Globodera rostochiensis and G. pallida are most damaging. Several species of root knot nematodes (RKN) are an emerging threat. Breeders have successfully deployed disease resistance genes (R-genes) to protect potato from diseases, starting from the first half of the 20th century. DNA markers facilitate the introgression of R-genes and enable the pyramiding of multiple R-genes in a potato cultivar. Pyramiding may improve the level of resistance, the resistance spectrum and the durability of the resistance. In this thesis, the experimental work is described in four chapters. Two chapters focus on the identification, mapping and characterisation of late blight and nematode resistance genes. The other two chapters focus on the pyramiding of R-genes to achieve something more in terms of resistance than was offered by the individual R-genes. In Chapter 2, a locus involved in late blight resistance, derived from Solanum microdontum, was identified and characterised. The resistance is associated with a hypersensitive response and results in a delay of infection of about 1-2 weeks. Both a quantitative as well as a qualitative genetic approach was used, based on data from a field assay. QTL analysis identified a QTL on chromosome 4. A qualitative genetic analysis resulted in the positioning of this locus on the short arm of chromosome 4. This position coincides with a conserved Phytophthora R-gene cluster which includes R2, R2-like, RPi-blb3 and RPi-abpt. This strongly suggests that RPi-mcd1 is the fifth R-gene of this NBS-LRR cluster. In Chapter 3, two resistance genes, RPi-mcd1 and RPi-ber, introgressed from the wild tuber bearing potato species S. microdontum and S. berthaultii were combined in a segregating diploid S. tuberosum population. Individual genotypes from this segregating population were classified into four groups by means of flanking molecular markers; carrying no R-gene, with only RPi-mcd1, with only RPi-ber, and a group with the pyramided RPi-mcd1 and RPi-ber. The levels of resistance between the groups were compared in a field experiment in 2007. The group with RPi-mcd1 showed a significant delay to reach 50% infection of the leaf area of three days. The group with RPi-ber showed a delay of three weeks. The resistance level in the pyramid group suggested an additive effect of RPi-mcd1 with RPi-ber. This result suggests that potato breeding can benefit from combining individual R-genes. In Chapter 4, a resistance to G. pallida Rookmaker (Pa3), originating from wild species S. tarijense was identified by QTL analysis. The resistance could largely be ascribed to one major QTL. GpaXIltar explained 81.3 % of the phenotypic variance in the disease test and mapped to the long arm of chromosome 11. Another minor QTL explained 5.3 % of the phenotypic variance and mapped to the long arm of chromosome 9. Clones containing both QTL showed no lower cyst counts than clones with only GpaXIltar. After Mendelising the phenotypic data, GpaXIltar could be more precisely mapped near markers GP163 and FEN427 thus anchoring GpaXIltar to a region with a known R-gene cluster containing virus and nematode resistance genes. In Chapter 5, a study is described that tests if pyramiding of two resistance genes against the root knot nematode Meloidogyne hapla, RMh-tar and RMh-chcA , will result in improved, or even an absolute level of resistance. RMh-tar and RMh-chcA, introgressed from the wild tuber bearing potato species Solanum tarijense and S. chacoense were combined in a segregating diploid S. tuberosum population. With the aid of markers, descendants from this segregating population were classified into four groups, carrying no R-gene, with only RMh-tar, with only RMh-chcA, and a group with the pyramided RMh-tar and RMh-chcA. Upon inoculation with M. hapla isolate Bovensmilde, the group containing only RMh-chcA showed a decline of 88 % in average developed egg masses compared to the group without RMh-chcA and RMh-tar. The group of genotypes containing only RMh-tar, but not RMh-chcA, showed a decline of 55% in developed egg masses compared to the group without RMh-chcA and RMh-tar. The effect of both loci, RMh-tar and RMh-chcA combined, did not further reduce the number of egg masses compared to the level of RMh-chcA alone. The study presented in this thesis shows that marker assisted selection is a very powerful method and sometimes the only way to screen for the presence of certain genes. It furthermore shows that pyramiding different resistance genes, even with minor effects, can result in plants with an increased level of resistance