As one of the world's most important food crops, potato (Solanum tuberosum L.) has spurred innovation in autotetraploid genetics, including the use of SNP arrays to determine allele dosage at thousands of markers. By combining genotype and pedigree information with phenotype data for economically important traits, the objectives of this study were to (1) partition the genetic variance into additive vs. non-additive components, and (2) determine the accuracy of genome-wide prediction. Between 2012 and 2017, a training population of 571 clones was evaluated for total yield, specific gravity, and chip fry color.Genomic covariance matrices for additive (G), digenic dominant (D), and additive x additive epistatic (G#G) effects were calculated using 3895 markers, and the numerator relationship matrix (A) was calculated from a 13-generation pedigree. Based on model fit and prediction accuracy, mixed model analysis with G was superior to A for yield and fry color but not specific gravity. The amount of additive genetic variance captured by markers was 20% of the total genetic variance for specific gravity, compared to 45% for yield and fry color. Within the training population, including non-additive effects improved accuracy and/or bias when predicting total genotypic value, for all three traits. When six F1 populations were used for validation, prediction accuracy ranged from 0.06 to 0.63 and was consistently lower (0.13 on average) without allele dosage information. We conclude that genome-wide prediction is feasible in potato and will improve selection for breeding value given the substantial amount of non-additive genetic variance in elite germplasm.4

The third most important food crop worldwide, potato (Solanum tuberosum L.) is a tetraploid outcrossing species propagated from tubers. Breeders have long been challenged by polyploidy, heterozygosity, and asexual reproduction. It has been assumed that tetraploidy is essential for high yield, that the creation of inbred potato is not feasible, and that propagation by seed tubers is ideal. In this paper, we question those assumptions and propose to convert potato into a diploid inbred line-based crop propagated by true seed. Although a conversion of this magnitude is unprecedented, the possible genetic gains from a breeding system based on inbred lines and the seed production benefits from a sexual propagation system are too large to ignore. We call on leaders of public and private organizations to come together to explore the feasibility of this radical and exciting new strategy in potato breeding.

The extent of linkage disequilibrium (LD) is an important factor in designing association mapping experiments. Unlike other plant species that have been analyzed so far for the extent of LD, cultivated potato (Solanum tuberosum L.), an outcrossing species, is a highly heterozygous autotetraploid. The favored genotypes of modern cultivars are maintained by vegetative propagation through tubers. As a first step in the LD analysis, we surveyed both coding and noncoding regions of 66 DNA fragments from 47 accessions for single nucleotide polymorphism (SNP). In the process, we combined information from the potato SNP database with experimental SNP detection. The total length of all analyzed fragments was .25 kb, and the number of screened sequence bases reached almost 1.4 million. Average nucleotide polymorphism (u ¼ 11.5 3 10 À3) and diversity (p ¼ 14.6 3 10 À3) was high compared to the other plant species. The overall Tajima's D value (0.5) was not significant, but indicates a deficit of low-frequency alleles relative to expectation. To eliminate the possibility that an elevated D value occurs due to population subdivision, we assessed the population structure with probabilistic statistics. The analysis did not reveal any significant subdivision, indicating a relatively homogenous population structure. However, the analysis of individual fragments revealed the presence of subgroups in the fragment closely linked to the R1 resistance gene. Data pooled from all fragments show relatively fast decay of LD in the short range (r 2 ¼ 0.208 at 1 kb) but slow decay afterward (r 2 ¼ 0.137 at $70 kb). The estimate from our data indicates that LD in potato declines below 0.10 at a distance of $10 cM. We speculate that two conflicting factors play a vital role in shaping LD in potato: the outcrossing mating type and the very limited number of meiotic generations.

The yellow pigment in potato (Solanum L. sp.) tuber flesh is caused by various carotenoids that may protect against cancer, cardiovascular disease, and macular eye degeneration. The objectives of this research were to 1) identify and quantify the carotenoids present in 11 diploid clones from a hybrid population of Solanum phureja ssp. phureja Juz. & Bukasov-S. stenotomum ssp. stenotomum Juz. & Bukasov and two tetraploid potato cultivars (the yellow-fleshed `Yukon Gold' and the white-fleshed `Superior'), and 2) determine the relationship between tuber yellow intensity and carotenoid content. Yellow intensity was measured by a colorimeter programmed to calculate a yellowness index, YI E-313. Carotenoid analyses were performed on an automated high-performance liquid chromatography system with software for integration and quantitation with detection at 450 nm using a diode array detector. Six major carotenoids were detected: neoxanthin, violaxanthin, lutein-5,6-epoxide, lutein, zeaxanthin, and an unknown carotenoid. Total carotenoid content in the yellow-fleshed diploid clones was 3 to 13 times higher than `Yukon Gold' and 4 to 22 times higher than `Superior'. Both total and individual carotenoid contents were positively correlated with tuber yellow intensity. There was an exponential relationship between total carotenoid content and tuber yellow intensity. This suggests that selecting for more intense yellow flesh will result in higher levels of carotenoids. These specific diploid clones were selected for this study because they produced at least five percent 2n pollen; they have the potential to make significant contributions to improving the nutritional status of tetraploid potatoes through 4x-2x hybridizations.

We have used the linkage disequilibrium mapping method to test for an association between a candidate gene marker and resistance to Verticillium dahliae in tetraploid potato. A probe derived from the tomato Verticillium resistance gene ( Ve1) identified homologous sequences ( StVe1) in potato, which in a diploid population map to chromosome 9, in a position analogous to that of the tomato resistance gene. When a molecular marker closely linked (1.5 cM) to the homologues was used as a candidate gene marker on 137 tetraploid potato genotypes (mostly North American cultivars), the association between the marker and resistance was confirmed ( P<0.001). The amount of phenotypic variation in resistance explained by the allele of the STM1051 marker was greater than 10% and 25% in two subpopulations that were inferred from coancestry data matrix. Cloning of homologues from the highly resistant potato cv. Reddale indicates that the resistance quantitative trait locus (QTL) comprises at least an eleven-member family, encoding plant-specific leucine-rich repeat proteins highly similar to the tomato Ve genes. The sequence analysis shows that all homologues are uninterrupted open reading frames and thus represent putative functional resistance genes. This is the first time that the linkage disequilibrium method has been used to find an association between a resistance gene and a candidate gene marker in tetraploid potato. We have shown that it is possible to map QTL directly on already available potato cultivars, without developing a new mapping population.

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Verticillium wilt disease of potato is caused predominantly by Verticillium albo-atrum and V. dahliae. StVe1 -a putative QTL for resistance against V. dahliae -was previously mapped to potato chromosome 9. To develop allele-specific, SNP-based markers within the locus, the StVe1 fragment from a set of 30 North American potato cultivars was analyzed. Three distinct and highly diverse haplotypes can be distinguished at the StVe1 locus. These were detected in 97%, 33%, and 10% of the cultivars analyzed. We tested for haplotype association and for genetic linkage between the StVe1 haplotypes and resistance of tetraploid potato to V. albo-atrum. Moreover, field resistance was assessed in diploid populations with known molecular linkage maps in order to identify novel QTLs. Resistance QTLs against V. albo-atrum were detected on four chromosomes (2, 6, 9, and 12) at the diploid level, with one QTL on chromosome 2 contributing over 40% to the total phenotypic variation of the trait. At the tetraploid level, a significant association between the StVe1-839-C haplotype and susceptibility to the disease was detected, suggesting that resistance-related genes directed against V. albo-atrum and V. dahliae are located in the same genomic region of chromosome 9. However, on the basis of the present analysis, we cannot determine whether these genes are closely linked or if a single gene provides resistance against both Verticillium species. To assess the usefulness of the StVe1-839-C haplotype for marker-assisted selection, we subjected the resistance data to Bayesian analysis, and calculated positive (0.65) and negative (0.75) predictive values, and overall predictive accuracy (0.72). Our results indicate that tagging of additional genes for resistance to Verticillium with molecular markers will be required for efficient marker-assisted selection.

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