The European potato germplasm originated from a few founding genotypes, and its narrow genetic base has since been broadened through introgressions from wild relatives. We combined pedigree records and genome-wide SNP data to trace the origin, spread, and contributing ancestors of modern breeding introgressions in Europe. We first used a curated pedigree database to identify the Major Contributing Ancestors (MCAs) of 1209 varieties from the European Common Catalogue, revealing influential cultivars such as Katahdin, Saskia, and Agria as the top contributors to the modern European gene pool. Building on this framework, we developed a modified MCA approach that uses SNP alleles to trace the spread of haplotypes that were introduced into the European germplasm after 1945; two of which now occur in half of European varieties. Using the pedigree database to find the origin of these modern introgressions, we traced key contributions from S. vernei, S. demissum, and S. tuberosum Group Andigena clone CPC 1673. We observed multiple distinct haplotypes of the R3a/b late blight resistance introgression on chromosome 11. Additionally, we generated a genome assembly of S. demissum to validate a single sub-genome origin of the R3a/b introgression. We also traced a putatively starch-associated introgression derived from S. vernei. Our framework links historical breeding records with genomic data, revealing the legacy of modern introgression breeding in the European germplasm.

Diploid potato breeding is frequently challenged by residual heterozygosity, which impedes the generation of pure inbred lines for F1 hybrid production. The Fixation-Restitution Breeding strategy, which employs residual heterozygosity to avoid inbreeding depression, is a promising alternative for true seed F1 hybrids, as maintaining heterozygosity throughout the fixation process is crucial to its success. In this study, we used a multiplex amplicon-sequencing assay (PotatoMASH), in conjunction with read-backed haplotyping, as an effective tool for tracing homozygosity in diploid germplasm. Utilising a collection of 271 inbred diploid clones from the Wageningen diploid breeding programme, we obtain a “snapshot” of the genetic composition shaped by over 40 years of breeding efforts. Furthermore, we examined a self-compatible individual lineage from the programme to identify key hotspots of homozygosity across chromosomes. Our results demonstrate that multiplex amplicon sequencing with read-backed haplotyping, through haplotag construction, provides a more accurate and reliable measure of homozygosity compared to traditional SNP-based methods, without the requirement for parental genomic data. In S3 progenies, we observed average homozygosity levels of 82–83.4

Common scab, caused by Streptomyces spp ., is worldwide an important skin disease of potato, capable of significant reductions in marketable value. Resistant varieties developed through phenotypic selection have been the most effective strategy thus far. Previous studies on the genetics of resistance have identified only minor-effect QTLs. In the current study, we explored the value of historical data for genetic analysis, derived from 52 sources. Based on partial replication of the 3500 + varieties, generalized (entry-mean) heritability was estimated at 0.67. For a subset of 292 varieties with genome-wide markers, the genomic (narrow-sense) heritability was only 0.10. The historical data was combined with a contemporary US dataset spanning 6 environments and 416 varieties. Genome-wide association studies identified four QTLs, which together explained 7.5% of the variation. The median reliability (r 2 ) of genomic-estimated breeding values for marker-based selection was higher for the contemporary US chip group (0.5) than for European varieties from the historical dataset (0.3). This difference can be explained by the higher genomic heritability of the contemporary US dataset (0.24), its larger population size and higher degree of relatedness. This study has illustrated the potential for leveraging historical data for genomics-assisted breeding, but genetic gain for potato common scab resistance continues to be limited by low heritability and high polygenicity.

Potato varieties with resistance to Common Scab (CS) are highly valued across different potato market segments, to avoid the economic losses up to 30-50% in severely affected fields. Phenotypic testing for CS resistance is challenging and often unreliable. Although many quantitative trait loci (QTL) mapping studies have been conducted, none have identified major-effect loci associated with scab resistance. In this study, we collected marker data with an amplicon sequencing method PotatoMASH to perform composite interval mapping in connected F1 populations to study the inheritance of scab resistance and to identify relevant-effect loci. We obtained heritability estimates between 0.47-0.74 for scab resistance across four environments. We identified multiple QTLs with additive and dominance effects, with each QTL explaining around 8.6% of the variance on average. The multi-QTL model retained 5 loci that collectively explained 31% of the variation. No QTL allele showed a statistically significant additive effect when both additive and dominance effects were fitted in the model. We observed that several QTL alleles inherited from the resistant parent Picasso had a positive effect in its resistant offspring Electra, despite exhibiting no detectable effect in Picasso. Genomic prediction (GP) showed no significant differences between the mean prediction accuracy for full-sibs compared to half-sibs, likely because the unshared parents were close relatives. Altogether, these findings demonstrate the complexity of scab resistance and suggest that marker-assisted selection alone is unlikely to be effective. However, GP has demonstrated potential to improve selection for this trait and should be considered in future breeding efforts.

Common scab in potato is caused by multiple Streptomyces species that harbour various virulence factors. Varietal resistance is commonly evaluated with multi-year – multi-location field trials with known high infection potential or using the phytotoxin thaxtomin applied to in vitro mini tubers or potato tissue culture. In this study, we aimed to develop an efficient root inoculation assay to assess the resistance levels of potato genotypes and to evaluate whether the assay could identify resistant and susceptible genotypes, thus facilitating selection of scab resistant clones. We isolated 24 potential Streptomyces strains from fields in Ireland, of which 11 were identified as S. europaescabiei . All S. europaescabiei strains tested positive for txtAB gene but lacked n ec1 and t omA genes. The root inoculation assay resulted in plants exhibiting necrotic symptoms on roots and stunted root growth. Image analysis software was used to collect quantitative data from our assay. We observed a Spearman’s rank correlation of 0.61 between field data and our assay using a panel comprising 50 clones from the bi-parental cross Electra × Désirée and five control varieties. The root inoculation assay is rapid, as symptoms are observed within 6 to 10 days post-inoculation, and requires minimal manipulation since a bacterial suspension is applied instead of purified thaxtomin. Notably, this assay identifies resistant and susceptible progeny reliably, with some disparities between the resistance pattern in the field and the assay. This tool has potential to be useful for screening large numbers of genotypes and discarding the susceptible ones in a breeding program.

Amplicon sequencing and read-backed haplotyping enable cost-effective genomic prediction in potato, with SNPs and haplotags showing similar performance across 23 traits, supporting scalable breeding applications and competitive prediction ability with GBS. Genomic prediction (GP) supports plant breeding by accelerating genetic improvement; however, the high cost associated with dense genotyping platforms restricts their use in routine breeding. This study evaluates the efficacy of PotatoMASH, a cost-effective, low-density, amplicon-sequencing platform generating SNPs and short-read multi-allelic haplotypes (haplotags), for GP in potato. First, we compared the prediction ability (PA) achieved using 2,236 SNPs and 2,000–3,390 haplotags from 339 amplicon loci of PotatoMASH with previously reported PA values obtained from a high-density 43.6 k SNP GBS dataset. PA was only moderately reduced, by 14

Potato bolters are caused by excision of a transposon from the StCDF1.3 allele, resulting in a somatic mutant with late maturity. Somatic mutations during vegetative propagation can lead to novel genotypes, known as sports. In cultivated potato (Solanum tuberosum), a recurring sport type, called ‘Bolters’, is characterized by vigorous haulms and prolonged flowering. Bolters emerge spontaneously during potato cultivation. While deviating phenotypes are typically rogued during clonal propagation, certain bolters have been selected as sub-clonal strains. Their delayed maturity results in a longer growing season and higher yield, in particular when cultivated under short daylengths. Despite their prevalence and agronomical benefits, the genetic basis of bolters has remained unresolved 160 years after their first description in the literature. We investigated whether allelic variation at the StCDF1 locus, a central regulator of potato life cycle, underlies the bolter phenotype. We describe 34 bolters from eight cultivars. Bolters are isogenic with their parent varieties and carried new StCDF1 alleles. These arose from excision events of the Class II TIR transposon disrupting the StCDF1.3 allele conferring early maturity. Among the newly formed alleles, we predominantly identified StCDF1.2 variants, characterized by a 7-nucleotide insertion and associated with a mild effect on early maturity. We also found novel variants, including StCDF1.7, with a 6-nucleotide in-frame insertion, which appears to confer an even milder shortening of the life cycle. Based on this knowledge, we propose that selecting bolters represents a promising breeding strategy to expand the cultivation range of elite varieties and to enhance allelic diversity at a key regulatory locus.

Potatoes were first brought to Europe in the sixteenth century1,2. Two hundred years later, one of the species had become one of the most important food sources across the entire continent and, later, even the entire world3. However, its highly heterozygous, autotetraploid genome has complicated its improvement since then4-7. Here we present the pan-genome of European potatoes generated from phased genome assemblies of ten historical potato cultivars, which includes approximately 85% of all haplotypes segregating in Europe. Sequence diversity between the haplotypes was extremely high (for example, 20× higher than in humans), owing to numerous introgressions from wild potato species. By contrast, haplotype diversity was very low, in agreement with the population bottlenecks caused by domestication and transition to Europe. To illustrate a practical application of the pan-genome, we converted it into a haplotype graph and used it to generate phased, megabase-scale pseudo-genome assemblies of commercial potatoes (including the famous French fries potato 'Russet Burbank') using cost-efficient short reads only. In summary, we present a nearly complete pan-genome of autotetraploid European potato, we describe extraordinarily high sequence diversity in a domesticated crop, and we outline how this resource might be used to accelerate genomics-assisted breeding and research.

Background Modern cultivated potatoes have been bred for distinct market usages such as fresh eating, chip processing and starch manufacturing; however, genomic insights into this differentiation are limited. Results Here, we report a map of genomic variation encompassing ~79 million variants, constructed by genome-wide resequencing of 137 autotetraploid commercial potato varieties or accessions collected worldwide. Population genomic analysis provides evidence for divergence among modern commercial potato varieties and reveal distinct genomic composition in those bred for starch manufacturing industry, which may have been caused by continuous selection of yield-related traits and intensive exploitation of potato wild relatives. We characterize how alien introgression has reshaped the genomes of starch industry potato varieties, implicating an important role of potato wild relatives in genetic determination of yield-related traits as well as possible linkage drag. We further identify previously undiscovered genomic regions underlying agronomically important traits such as tuber bruising, maturity and tuber flesh and skin color. Conclusions These results shed light on the divergence history of modern cultivated potato and provide useful resources for genomics-guided breeding of this globally important staple crop.

We genotyped a population of 618 diploid potato clones derived from six independent potato-breeding programmes from NW-Europe. The diploids were phenotyped for 23 traits, using standardized protocols and common check varieties, enabling us to derive whole population estimators for most traits. We subsequently performed a genome-wide association study (GWAS) to identify quantitative trait loci (QTL) for all traits with SNPs and short-read haplotypes derived from read-backed phasing. In this study, we used a marker platform called PotatoMASH (Potato Multi-Allele Scanning Haplotags); a pooled multiplex amplicon sequencing based approach. Through this method, neighboring SNPs within an amplicon can be combined to generate multiallelic short-read haplotypes (haplotags) that capture recombination history between the constituent SNPs and reflect the allelic diversity of a given locus in a different way than single bi-allelic SNPs. We found a total of 37 unique QTL across both marker types. A core of 10 QTL was detected with SNPs as well as with haplotags. Haplotags allowed to detect an additional 14 QTL not found based on the SNP set. Conversely, the bi-allelic SNP set also found 13 QTL not detectable using the haplotag set. We conclude that both marker types should routinely be used in parallel to maximize the QTL detection power. We report 19 novel QTL for nine traits: Skin Smoothness, Sprout Dormancy, Total Tuber Number, Tuber Length, Yield, Chipping Color, After-cooking Blackening, Cooking Type, and Eye depth.

Multiple QTLs control unreduced pollen production in potato. Two major-effect QTLs co-locate with mutant alleles of genes with homology to AtJAS, a known regulator of meiotic spindle orientation. In diploid potato the production of unreduced gametes with a diploid (2n) rather than a haploid (n) number of chromosomes has been widely reported. Besides their evolutionary important role in sexual polyploidisation, unreduced gametes also have a practical value for potato breeding as a bridge between diploid and tetraploid germplasm. Although early articles argued for a monogenic recessive inheritance, the genetic basis of unreduced pollen production in potato has remained elusive. Here, three diploid full-sib populations were genotyped with an amplicon sequencing approach and phenotyped for unreduced pollen production across two growing seasons. We identified two minor-effect and three major-effect QTLs regulating this trait. The two QTLs with the largest effect displayed a recessive inheritance and an additive interaction. Both QTLs co-localised with genes encoding for putative AtJAS homologs, a key regulator of meiosis II spindle orientation in Arabidopsis thaliana. The function of these candidate genes is consistent with the cytological phenotype of mis-oriented metaphase II plates observed in the parental clones. The alleles associated with elevated levels of unreduced pollen showed deleterious mutation events: an exonic transposon insert causing a premature stop, and an amino acid change within a highly conserved domain. Taken together, our findings shed light on the natural variation underlying unreduced pollen production in potato and will facilitate interploidy breeding by enabling marker-assisted selection for this trait.

The balanced segregation of homologous chromosomes during meiosis is essential for fertility and is mediated by crossovers (COs). A strong reduction of CO number leads to the unpairing of homologous chromosomes after the withdrawal of the synaptonemal complex. This results in the random segregation of univalents during meiosis I and ultimately to the production of unbalanced and sterile gametes. However, if CO shortage is combined with another meiotic alteration that restitutes the first meiotic division, then uniform and balanced unreduced male gametes, essentially composed of nonrecombinant homologs, are produced. This mitosis-like division is of interest to breeders because it transmits most of the parental heterozygosity to the gametes. In potato, CO shortage, a recessive trait previously referred to as desynapsis, was tentatively mapped to chromosome 8. In this article, we have fine-mapped the position of the CO shortage locus and identified StMSH4, an essential component of the class I CO pathway, as the most likely candidate gene. A 7 base-pair insertion in the second exon of StMSH4 was found to be associated with CO shortage in our mapping population. We also identified a second allele with a 3,820 base-pair insertion and confirmed that both alleles cannot complement each other. Such nonfunctional alleles appear to be common in potato cultivars. More than half of the varieties we tested are carriers of mutational load at the StMSH4 locus. With this new information, breeders can choose to remove alleles associated with CO shortage from their germplasm to improve fertility or to use them to produce highly uniform unreduced male gametes in alternative breeding schemes.

The reinvention of potato, from a tetraploid clonal crop into a diploid seed-based hybrid crop, requires insight in the mutational load, recombination landscape, and the genetic basis of fertility. Genomics-based breeding and QTL discovery rely on efficient genotyping strategies such as skim sequencing, to gather genotypic information. The application of skim sequencing to full-sib population of non-inbred parents remains challenging. Here, we report on an R implementation of the OutcrossSeq pipeline for diploids. We applied this pipeline to a large diploid skim sequenced potato population. We used the resulting bin-markers for the construction of high-density parent specific linkage maps, highlighting variation in parental recombination rate and structural variations. We subsequently explored transmission ratio distortion and non-independent assortment of alleles, indicative of large-effect deleterious mutations. Finally, we identified QTLs for seedling tuber yield in pots and pollen shed. This study showcases the range of genetic analyses, from marker inference, identification of transmission ratio distortion, and linkage map construction to QTL mapping, resulting in new insights that contribute to breeding diploid potato.

Genome-wide association studies (GWAS) are a useful tool to unravel the genetic architecture of complex traits, but the results can be difficult to interpret. Population structure, genetic heterogeneity, and rare alleles easily result in false positive or false negative associations. This paper describes the analysis of a GWAS panel combined with three bi-parental mapping populations to validate GWAS results, using phenotypic data for steroidal glycoalkaloid (SGA) accumulation and the ratio (SGR) between the two major glycoalkaloids α-solanine and α-chaconine in potato tubers. SGAs are secondary metabolites in the Solanaceae family, functional as a defence against various pests and pathogens and in high quantities toxic for humans. With GWAS, we identified five quantitative trait loci (QTL) of which Sga1.1, Sgr8.1, and Sga11.1 were validated, but not Sga3.1 and Sgr7.1. In the bi-parental populations, Sga5.1 and Sga7.1 were mapped, but these were not identified with GWAS. The QTLs Sga1.1, Sga7.1, Sgr7.1, and Sgr8.1 co-localize with genes GAME9, GAME 6/GAME 11, SGT1, and SGT2, respectively. For other genes involved in SGA synthesis, no QTLs were identified. The results of this study illustrate a number of pitfalls in GWAS of which population structure seems the most important. We also show that introgression breeding for disease resistance has introduced new haplotypes to the gene pool involved in higher SGA levels in certain pedigrees. Finally, we show that high SGA levels remain unpredictable in potato but that α-solanine/α-chaconine ratio has a predictable outcome with specific SGT1 and SGT2 haplotypes.

Cultivated potato is a clonally propagated autotetraploid species with a highly heterogeneous genome. Phased assemblies of six cultivars including two chromosome-scale phased genome assemblies revealed extensive allelic diversity, including altered coding and transcript sequences, preferential allele expression, and structural variation that collectively result in a highly complex transcriptome and predicted proteome, which are distributed across the homologous chromosomes. Wild species contribute to the extensive allelic diversity in tetraploid cultivars, demonstrating ancestral introgressions predating modern breeding efforts. As a clonally propagated autotetraploid that undergoes limited meiosis, dysfunctional and deleterious alleles are not purged in tetraploid potato. Nearly a quarter of the loci bore mutations are predicted to have a high negative impact on protein function, complicating breeder’s efforts to reduce genetic load. The StCDF1 locus controls maturity, and analysis of six tetraploid genomes revealed that 12 allelic variants of StCDF1 are correlated with maturity in a dosage-dependent manner. Knowledge of the complexity of the tetraploid potato genome with its rampant structural variation and embedded deleterious and dysfunctional alleles will be key not only to implementing precision breeding of tetraploid cultivars but also to the construction of homozygous, diploid potato germplasm containing favorable alleles to capitalize on heterosis in F1 hybrids.

Abstract Potato OFP20 is associated with the regulation of tuber shape. To further characterise the role of this gene in tuber shape, a panel of 136 potato varieties was re-sequenced to identify variants in the coding region of StOFP20. These SNPs were assembled into haplotypes and their allelic dosage was determined. Haplotype StOFP20.1 is the most common allele (65%) which in quadruplex condition results in long tubers. StOFP20.3 represents the second most common haplotype (22%) and is recognized as a dominant allele that is associated with round tubers in a dosage dependent manner. StOFP20.4 represents the third common haplotype (5%) and encodes a non-functional gene. The remaining haplotypes represent rare alleles and their phenotypic effect is unclear. We developed reliable DNA markers that distinguish between the long and round alleles for marker-assisted selection of tuber shape in a diverse collection of varieties. We also demonstrate that we can genetically engineer the tuber shape of two commercial tetraploid varieties and the diploid clone DM. Knock down of StOFP20 in the variety Atlantic using the RNAi strategy changed the tubers from round to oval and long-oval shapes. Conversely, overexpression of StOFP20 in Spunta changed tuber shape from long to round. The most dramatic change from very long into round tubers was achieved by overexpression of StOFP20 in DM. Our results demonstrate that engineering potato tuber shape is readily achieved by modulating StOFP20 gene expression in a dose dependent manner, either by traditional breeding or by using genetic engineering methods.

Association analysis resulted in the identification of specific StGWD alleles causing either an increase or decrease in starch phosphate content which was verified in diploid and tetraploid potato mapping populations. Potatoes are grown for various purposes like French fries, table potatoes, crisps and for their starch. One of the most important aspects of potato starch is that it contains a high amount of phosphate ester groups which are considered to be important for providing improved functionalization after derivatization processes. Little is known about the variation in phosphate content as such in different potato varieties and thus we studied the genetic diversity for this trait. From other studies it was clear that the phosphate content is controlled by a quantitative trait locus (QTL) underlying the candidate gene α-Glucan Water Dikinase (StGWD) on chromosome 5. We performed direct amplicon sequencing of this gene by Sanger sequencing. Sequences of two StGWD amplicons from a global collection of 398 commercial cultivars and progenitor lines were used to identify 16 different haplotypes. By assigning tag SNPs to these haplotypes, each of the four alleles present in a cultivar could be deduced and linked to a phosphate content. A high value for intra-individual heterozygosity was observed (Ho = 0.765). The average number of different haplotypes per individual (Ai) was 3.1. Pedigree analysis confirmed that the haplotypes are identical-by-descent (IBD) and offered insight in the breeding history of elite potato germplasm. Haplotypes originating from introgression of wild potato accessions carrying resistance genes could be traced. Furthermore, association analysis resulted in the identification of specific StGWD alleles causing either an increase or decrease in starch phosphate content varying from 12 nmol PO4/mg starch to 38 nmol PO4/mg starch. These allele effects were verified in diploid and tetraploid mapping populations and offer possibilities to breed and select for this trait.

Self-compatible (SC) diploid potatoes allow innovative potato breeding. Therefore, the Sli gene, originally described in S. chacoense , has received much attention. In elite S. tuberosum diploids, spontaneous berry set is occasionally observed. We aimed to map SC from S. tuberosum origin. Two full-sib mapping populations from non-inbred diploids were used. Bulks were composed based on both pollen tube growth and berry set upon selfing. After DNA sequencing of the parents and bulks, we generated k -mer tables. Set algebra and depth filtering were used to identify bulk-specific k -mers. Coupling and repulsion phase k -mers, transmitted from the SC parent, mapped in both populations to the distal end of chromosome 12 . Intersection between the k -mers from both populations, in coupling phase with SC, exposed a shared haplotype of approximately 1.5 Mb. Subsequently, we screened read archives of potatoes and wild relatives for k -mers specific to this haplotype. The well-known SC clones US-W4 and RH89-039-16, but surprisingly, also S. chacoense clone M6 were positives. Hence, the S. tuberosum source of SC seems identical to Sli . Furthermore, the candidate region drastically reduced to 333 kb. Haplotype-specific KASP markers were designed and validated on a panel of diploid clones including another renown SC dihaploid G254. Interestingly, k -mers specific to the SC haplotype were common in tetraploid varieties. Pedigree information suggests that the SC haplotype was introduced into tetraploid varieties via the founder “Rough Purple Chili”. We show that Sli is surprisingly widespread and indigenous to the cultivated gene pool of potato.

KEY MESSAGE:A Genome-Wide Association Study using 330 commercial potato varieties identified haplotype specific SNP markers associated with pathotype 1(D1) wart disease resistance. Synchytrium endobioticum is a soilborne obligate biotrophic fungus responsible for wart disease. Growing resistant varieties is the most effective way to manage the disease. This paper addresses the challenge to apply molecular markers in potato breeding. Although markers linked to Sen1 were published before, the identification of haplotype-specific single-nucleotide polymorphisms may result in marker assays with high diagnostic value. To identify hs-SNP markers, we performed a genome-wide association study (GWAS) in a panel of 330 potato varieties representative of the commercial potato gene pool. SNP markers significantly associated with pathotype 1 resistance were identified on chromosome 11, at the position of the previously identified Sen1 locus. Haplotype specificity of the SNP markers was examined through the analysis of false positives and false negatives and validated in two independent full-sib populations. This paper illustrates why it is not always feasible to design markers without false positives and false negatives for marker-assisted selection. In the case of Sen1, founders could not be traced because of a lack of identity by descent and because of the decay of linkage disequilibrium between Sen1 and flanking SNP markers. Sen1 appeared to be the main source of pathotype 1 resistance in potato varieties, but it does not explain all the resistance observed. Recombination and introgression breeding may have introduced new, albeit rare haplotypes involved in pathotype 1 resistance. The GWAS approach, in such case, is instrumental to identify SNPs with the best possible diagnostic value for marker-assisted breeding.

Two 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.