Abstract
Key messageTwo novel major effect loci (Sen4 and Sen5) and several minor effect QTLs for potato wart disease resistance have been mapped. The importance of minor effect loci to bring full resistance to wart disease was investigated. Using the newly identified and known wart disease resistances, a panel of potato breeding germplasm and Solanum wild species was screened. This provided a state-of-the-art “hitch-hikers-guide” of complementary wart disease resistance sources.Potato wart disease, caused by the obligate biotrophic soil-born fungus Synchytrium endobioticum, is the most important quarantine disease of potato. Because of its huge impact on yield, the lack of chemical control and the formation of resting spores with long viability, breeding for resistant varieties combined with strict quarantine measures are the only way to efficiently and durably manage the disease. In this study, we set out to make an inventory of the different resistance sources. Using a Genome-Wide Association Study (GWAS) in the potato breeding genepool, we identified Sen4, associated with pathotypes 2, 6 and 18 resistance. Associated SNPs mapped to the south arm of chromosome 12 and were validated to be linked to resistance in one full-sib population. Also, a bulked segregant analysis combined with a Comparative Subsequence Sets Analysis (CoSSA) resulted in the identification of Sen5, associated with pathotypes 2, 6 and 18 resistance, on the south arm of chromosome 5. In addition to these two major effect loci, the GWAS and CoSSA allowed the identification of several quantitative trait loci necessary to bring full resistance to certain pathotypes. Panels of varieties and Solanum accessions were screened for the presence of Sen1, Sen2, Sen3, Sen4 and Sen5. Combined with pedigree analysis, we could trace back some of these genes to the ancestral resistance donors. This analysis revealed complementary resistance sources and allows elimination of redundancy in wart resistance breeding programs.
Highlights
Every year, food crop production suffers huge yield losses due to pests and pathogen attacks
In order to identify SNPs and loci involved in potato wart disease resistance, we performed a Genome-Wide Association Study (GWAS) study in a panel of varieties that was previously described and genotyped (Vos et al 2015)
Seven SNPs were associated with both P6 and P18 resistance, six of which were located on the south arm of chromosome 12 between 43.3 and 50.4 Mb
Summary
Food crop production suffers huge yield losses due to pests and pathogen attacks. For potato (Solanum tuberosum), the yield losses have been estimated between 8 and 21% depending on the region of production (Savary et al 2019). The potato wart disease, caused by Synchytrium endobioticum, can cause yield losses up to 100%. After the sexual phase of its life cycle, S. endobioticum produces winter spores (Curtis 1921) which can remain viable in the soil for decades (Przetakiewicz 2015). Because of this longevity and the lack of efficient chemical control (Hampson 1988), S. endobioticum has a quarantine status worldwide. The fungus originates from the Andean region of South America where it co-evolved with potato species and was introduced in North America and
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