Genetic Dissection of Early Blight Resistance in Tetraploid Potato.

Early blight, caused by the fungus Alternaria solani, is one of the most economically important diseases of potatoes worldwide. We previously identified a tetraploid potato clone, B0692-4, which is resistant to early blight. To dissect the genetic basis of early blight resistance in this clone, a full-sib tetraploid potato population including 241 progenies was derived from a cross between B0692-4 and a susceptible cultivar, Harley Blackwell, in this study. The population was evaluated for foliage resistance against early blight in field trials in Pennsylvania in 2018 and 2019 and relative area under the disease progress curve (rAUDPC) was determined. The distribution of rAUDPC ranged from 0.016 to 0.679 in 2018, and from 0.017 to 0.554 in 2019. Broad sense heritability for resistance, as measured as rAUDPC, was estimated as 0.66-0.80. The population was also evaluated for foliar maturity in field trials in Maine in 2018 and 2020. A moderate negative correlation between rAUDPC and foliar maturity was detected in both years. A genetic linkage map covering a length of 1469.34 cM with 9124 SNP markers was used for mapping quantitative trait loci (QTL) for rAUDPC and foliar maturity. In 2018, three QTLs for early blight were detected; two of them on chromosome 5 overlapped with QTLs for maturity, and one of them on chromosome 7 was independent of maturity QTL. In 2019, six QTLs for early blight were detected; two QTLs on chromosome 5 overlapped with QTLs for maturity, and the other four QTLs did not overlap with QTLs for maturity. The identification of these QTLs provides new insight into the genetic basis of early blight resistance and may serve as sources for marker-assisted selection for early blight resistance breeding.

Resistance to Phytophthora infestans Clonal Lineage US-23 in Potato Cultivars and Its Relationship with Early Blight Resistance and Tuber Yield.

Resistance to late blight caused by Phytophthora infestans clonal lineage US-23 in 217 old and modern potato cultivars was evaluated in field trials in 2016 and 2017 in Pennsylvania. Significant differences in resistance were found among these cultivars (P < 0.0001). Significant interaction between cultivars and environments was found (P < 0.0001). The values of relative area under the disease progress curve ranged from 0 to 0.5841 in 2016 and from 0 to 0.5469 in 2017. Broad-sense heritability of late blight resistance was estimated to be 0.91, with a 95% confidence interval of 0.88 to 0.93. Cluster analysis classified the cultivars into five groups: resistant, moderately resistant, intermediate, moderately susceptible, and susceptible. Thirty cultivars showing resistance and 32 cultivars showing moderate resistance were identified. The 217 cultivars were also evaluated for foliar maturity, tuber yield, and resistance to early blight caused by Alternaria solani. A few cultivars with late blight resistance independent of late maturity were found. Late blight resistance and early blight resistance were positively correlated, and 17 cultivars possessed resistance to both diseases. Yield trade-off associated with late blight resistance was not observed among the cultivars in the absence of disease pressure.

Characterization of Early Blight Resistance in Potato Cultivars.

Early blight, caused by the fungus Alternaria solani, is one of the most economically important foliar diseases of potatoes worldwide. In this study, 217 tetraploid old and modern potato cultivars were evaluated for foliar resistance to early blight in field experiments in Pennsylvania in 2016 and 2017. Relative area under the disease progress curve (RAUDPC) was calculated based on visual assessment of foliar disease during the growing season each year. RAUDPC ranged from 0.0090 to 0.7372 in 2016 and from 0.0215 to 0.7889 in 2017, respectively. Significant differences in resistance to A. solani among cultivars were found (P < 0.0001). A significant interaction was found between cultivar and environment (P < 0.0001). Cluster analysis classified the cultivars into five groups: resistant, moderately resistant, intermediate, moderately susceptible, and susceptible. Broad-sense heritability for early blight resistance was estimated as 0.89 with a 95% confidence interval of 0.86 to 0.92. All cultivars were also evaluated for foliage maturity in separate field trials in 2016 and 2017, and a strong negative correlation between early blight resistance and maturity was found. Maturity-adjusted RAUDPC was calculated by regressing maturity on RAUDPC; predicted values more than two standard deviations greater or less than observed values were used to identify cultivars with greater genetic susceptibility or resistance to early blight, respectively, independent of maturity. Although most resistant and moderately resistant cultivars showed late maturity and most susceptible cultivars showed early maturity, a few exceptions were found.

Linkage analysis and QTL mapping in a tetraploid russet mapping population of potato.

BACKGROUND: Genome-wide single nucleotide polymorphism (SNP) markers coupled with allele dosage information has emerged as a powerful tool for studying complex traits in cultivated autotetraploid potato (Solanum tuberosum L., 2n = 4× = 48). To date, this approach has been effectively applied to the identification of quantitative trait loci (QTLs) underlying highly heritable traits such as disease resistance, but largely unexplored for traits with complex patterns of inheritance. RESULTS: In this study, an F1 tetraploid russet mapping population (162 individuals) was evaluated for multiple quantitative traits over two years and two locations to identify QTLs associated with tuber sugar concentration, processing quality, vine maturity, and other high-value agronomic traits. We report the linkage maps for the 12 potato chromosomes and the QTL location with corresponding genetic models and candidate SNPs explaining the highest phenotypic variation for tuber quality and maturity related traits. Significant QTLs for tuber glucose concentration and tuber fry color were detected on chromosomes 4, 5, 6, 10, and 11. Collectively, these QTLs explained between 24 and 46% of the total phenotypic variation for tuber glucose and fry color, respectively. The QTL on chromosome 10 was associated with apoplastic invertases, with 'Premier Russet' contributing the favorable allele for fry processing quality. On chromosome 5, minor-effect QTLs for tuber glucose concentration and fry color co-localized with various major-effect QTLs, including vine maturity, growth habit, tuber shape, early blight (Altenaria tenuis), and Verticillium wilt (Verticillium spp.). CONCLUSIONS: Linkage analysis and QTL mapping in a russet mapping population (A05141) using SNP dosage information successfully identified favorable alleles and candidate SNPs for resistance to the accumulation of tuber reducing sugars. These novel markers have a high potential for the improvement of tuber processing quality. Moreover, the discovery of different genetic models for traits with overlapping QTLs at the maturity locus clearly suggests an independent genetic control.

Genetic Variance Partitioning and Genome-Wide Prediction with Allele Dosage Information in Autotetraploid Potato.

As one of the world's most important food crops, the potato (Solanum tuberosum L.) has spurred innovation in autotetraploid genetics, including in 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. nonadditive 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 × 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 nonadditive effects improved accuracy and/or bias for all three traits when predicting total genotypic value. 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 that it will improve selection for breeding value given the substantial amount of nonadditive genetic variance in elite germplasm.

Quantitative Trait Loci for Resistance to Common Scab and Cold-Induced Sweetening in Diploid Potato.

The development of germplasm with resistance to common scab and cold-induced sweetening is a high priority for the potato ( L.) industry. A mapping population was developed from mating two individuals of a diploid family generated by crossing the susceptible cultivated potato clone US-W4 to the highly resistant wild relative ( Bitter) clone '524-8'. Progeny were evaluated in replicated field trials. Tubers were scored for percentage of surface area with scab lesions, scab lesion type, cold-induced sweetening, average tuber weight, and dry matter. Plants were evaluated for vine maturity. A genetic map was constructed, quantitative trait loci (QTLs) were identified, and the gene action of significant QTLs was characterized using 1606 single nucleotide polymorphisms (SNPs). Significant QTLs for common scab percentage of surface area covered with lesions and lesion type were identified in overlapping regions on chromosome 11 ( = 21.0 and 18.2%, respectively). Quantitative trait loci were identified on chromosomes 4 ( = 17.1%) and 6 ( = 19.4%) for cold-induced sweetening, chromosome 5 for maturity ( = 29.8%), and chromosome 1 ( = 26.3 and 22.0%) for average tuber weight. Identification of QTLs is the first step toward developing molecular markers for breeders to efficiently integrate these desirable traits into cultivars.

Field Resistance to Potato Stem Colonization by the Black Dot Pathogen Colletotrichum coccodes.

Potato (Solanum tuberosum) germplasm was tested for resistance to stem colonization by the black dot pathogen Colletotrichum coccodes. Forty-six potato selections were tested in three field trials from 2006 to 2008. Resistance was determined by comparing disease severity on aboveground stems to the mean disease severity of the industry standards Russet Burbank, Ranger Russet, and Umatilla Russet. The potato selections were also tested for genotype*environment interaction to determine their genetic stability. Heritability of resistance was calculated to be 0.13 with confidence intervals between 0.00 and 0.68. The selections A0012-5, PA95B2-4, PA98NM38-1, and PO94A009-7 had less black dot than the standards in all years, and also demonstrated genetic stability. These selections also possess resistance to the root galling stage of the powdery scab pathogen Spongospora subterranea f. sp. subterranea. PA95B2-4, PA98NM38-1, and PO94009-7 were derived from an introgression program to incorporate resistance to the Columbia root-knot nematode Meloidogyne chitwoodi from the Mexican wild species Solanum bulbocastanum, and also have the commercial cultivar Summit Russet in their ancestry. These selections are promising steps toward sustainable management of black dot and powdery scab and will be further tested and used for breeding purposes.

Assessment of linkage disequilibrium in potato genome with single nucleotide polymorphism markers.

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 (=11.5x10(-3)) and diversity (pi=14.6x10(-3)) 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 (r2=0.208 at 1 kb) but slow decay afterward (r2=0.137 at approximately 70 kb). The estimate from our data indicates that LD in potato declines below 0.10 at a distance of approximately 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.