Kathleen G. Haynes

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 (θ = 11.5 × 10−3) and diversity (π = 14.6 × 10−3) was high compared to the other plant species. The overall Tajimas 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 ∼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.

Mapping genes for resistance to Verticillium albo-atrum in tetraploid and diploid potato populations using haplotype association tests and genetic linkage analysis

AbstractVerticillium 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.

Segregation of total carotenoid in high level potato germplasm and its relationship to beta-carotene hydroxylase polymorphism

High carotenoid potato may have particular value for human health due to the antioxidant properties and the therapeutic value for eye health in patients at risk for macular degeneration. Carotenoid concentrations were determined among the progeny of a cross between two high carotenoid lines derived from diploidPapa Amarilla germplasm from South America. The total carotenoid content ranged from 82 to 2686 µg / 100 g fresh weight (FW). The higher values greatly exceeded the mid-parent value of the cross. An index for yellow tuber flesh color was determined for a subset of the progeny. A cleaved amplified polymorphic sequence (CAPS) assay was developed to distinguish the alleles of beta-carotene hydroxylase (bch) in the two high-carotenoid parents. Abch allele (denoted B) common to the high carotenoid parents co-segregated with yellow flesh in the progeny of a white-flesh x yellow-flesh cross, makingbch an excellent candidate for the classicalY locus, required for yellow tuber flesh. The same allele was also present in all other yellow-fleshed potato clones tested. Genotype atbch explained a portion of the variation of total carotenoid (R2=0.42). Clones homozygous for the B allele (BB) contained, on average, slightly more carotenoid than heterozygous Bb clones, which in turn had much more carotenoid than homozygous bb clones, suggesting a partially dominant gene model. Similarly, bb flesh was significantly less yellow than Bb and BB, the latter two being quite close. Total carotenoid varied considerably between progeny in the Bb and BB genotype categories, suggesting that variation at one or more additional loci have a significant effect on total carotenoid levels. Since the total carotenoid levels in manyPapa Amarilla cultivars and progeny are much higher than those in white- and yellow-fleshed tetraploid cultivars, it may be possible to breed for high carotenoid values in tetraploid germplasm by introducing one or more genes derived fromPapa Amarilla germplasm.ResumenLas papas con alto contenido de carotenoides podrían tener particular valor en la salud humana debido a las propiedades antioxidantes y al valor terapéutico para la salud ocular, en pacientes con riesgo de degeneración macular. La concentración de carotenoides fue determinada en la progenie de un cruzamiento entre dos lineas con carotenoides, derivadas de germoplasma del diploide Papa Amarilla de Sudamérica. El contenido total de carotenoides varió de 82 a 2686 microgramos por 100g de peso fresco. Los mayores valores totales excedieron al valor del progenitor medio de los cruzamientos. Para un subconjunto de la progenie, se determinó el índice del color amarillo de la pulpa. Se desarrolló una prueba de división de secuencia polimórfica amplificada (CAPS) para distinguir alelos de beta caroteno hidroxilasa (bch) en dos de los progenitores con alto contenido carotenoideo. Un alelobch (designado B), común en progenitores de alto caroteno co-segregó a pulpa amarilla en la progenie de un cruzamiento de pulpa blanca x pulpa amarilla, haciendobch un excelente candidato para el clásico locusY, requerido para pulpa amarilla del tubérculo. El mismo alelo estuvo también presente en todos los otros clones de pulpa amarilla probados. La explicación de la variación de una porción del total de carotenoide (R2=0.42) la dio el genotipobch. Clones homocigotas para el alelo B (BB) contenían en promedio, ligeramente mas carotenoide que los clones heterocigotas Bb, los cuales a su vez tienen mucho mas carotenoide que los clones homocigotas bb, sugiriendo un modelo de gen parcialmente dominante. Similarmente, la pulpa de bb fue significativamente menos amarilla que Bb y BB, siendo las dos últimas muy parecidas. El total de carotenoide varió considerablemente entre progenies en las categorías de genotipo Bb y BB, sugiriendo que la variación en uno o más loci, tienen efecto significativo sobre los niveles totales de carotenoide. Desde que el total del nivel de carotenoide en muchos cultivares y progenies de Papa Amarilla son mucho mas altos que en los cultivares tetraploides de pulpa blanca y amarilla, sería posible hacer cruzamientos para mayores valores de carotenoide en el germoplasma tetraploide, introduciendo uno o mas genes del germoplasma derivado de Papa Amarilla.

Phenotypic stability of resistance to late blight in potato clones evaluated at eight sites in the United States

Changes in the fungal pathogenPhytophthora infestans in the United States pose a significant threat to potato production. Sources of resistance to these new genotypes of P.infestans need to be identified for potato breeders to have parental materials for crossing, and the phenotypic stability of late blight resistance in these potato clones needs to be determined. Sixteen potato clones which reportedly have some resistance to late blight were evaluated at eight locations: Florida (FL), Maine (ME), Michigan (MI), Minnesota (MN), North Dakota (ND), New York (NY), Pennsylvania (PA) and Wisconsin (WI) in 1996. Percent infected foliage was recorded at approximately weekly intervals following the onset of the disease at each location. Area under the disease progress curve (AUDPC) was calculated. Clones were ranked for mean AUDPC within location and the nonparametric stability statistics, mean absolute rank differences and variance of the ranks, were analyzed for phenotypic stability. Neither of these statistics was significant, indicating a lack of genotype x environment interaction on the rankings of these clones across locations in 1996. The four clones with lowest AUDPC scores were U.S. clones AWN86514-2, B0692-4, B0718-3 and B0767-2. These clones should be useful parental materials for breeders seeking to incorporate genes for late blight resistance into potatoes.

Relative resistance of the potato cultivar krantz to common scab caused byStreptomyces scabies as determined by cluster analysis

Twenty potato breeding selections and five potato cultivars (25 clones) were evaluated in replicated field plots for their resistance to common scab caused byStreptomyces scabies, at Presque Isle, ME and Cranesville, WV in 1993. At harvest, all tubers in each plot were individually scored for the surface area covered (0=0% to 5>75%) and for lesion type (0=no lesions to 5=pitted lesions). The individual tuber scores for either surface area covered or lesion type for each plot were totaled and divided by five times the number of tubers to create an index of surface area covered (SAI) or lesion type (LI), respectively. Clonal mean SAI ranged from 0.05 to 0.96 in Maine and 0.21 to 0.89 in West Virginia. Clonal mean LI ranged from 0.06 to 1.0 in Maine and 0.48 to 1.0 in West Virginia. There were significant differences among clones for SAI and LI. Clones were clustered on mean SAI and LI in ME and WV. The clones clustered into four groups. The resistance of Krantz and two breeding selections, B0348-2 and B0339-1, was similar to Ontario.CompendioVeinte selecciones de mejoramiento de papa y cinco cultivares (25 clones) fueron evaluados, en 1993, en parcelas de campo con repeticiones, para su resistencia a la sarna común causada por Streptomyces scabies, en Presque Isle, ME y Cranesville, WV. Al momento de la cosecha, todos los tubérculos en cada parcela fueron calificados individualmente por el área de superficie cubierta (0=0 % a 5>75 %) y por el tipo de lesión (0=sin lesiones a 5=lesiones profundas). Las calificaciones individuates por tubérculo, tanto por área de superficie cubierta como por el tipo de lesiones, para cada parcela, fue totalizada y dividida por cinco veces el número de tubérculos, para crear un indice de área de superficie cubierta (SAI) o de tipo de lesión (LI), respectivamente. El promedio clonal del SAI varió de 0.05 a 0.96 en Maine, y de 0.21 a 0.89 en West Virginia. El promedio clonal del LI varió de 0.06 a 1.0 en Maine, y de 0.48 a 1.0 en West Virginia. Hubo diferencias significativas entre los clones, para SAI y LI. Los clones fueron agrupados de acuerdo al promedio de SAI y LI en ME y WV. Los clones se agruparon en cuatro grupos. La resistencia de Krantz y dos selecciones de mejoramiento, B0348-2 y B0339-1, fue similar a la de Ontario.

Estimation of the coefficient of double reduction in the cultivated tetraploid potato.

SummaryTheoretical models to estimate the coefficient of double reduction in tetraploid organisms and the standard error of this estimate are derived. Using these models, we were able to estimate the coefficient of double reduction for several loci in tetraploid potatoes, Solanum tuberosum L., through examination of segregating isozyme loci in a series of 4x-2x crosses and in haploid progeny derived from six cultivated tetraploid potatoes. Tetraploid x diploid crosses are useful for estimating the frequency of double reduction because of the availability of homozygous diploid tester lines and the large number of tetraploid progeny generated via the functioning of 2n pollen. The strength of haploid analysis is the examination of diploid progeny. However, it is frequently difficult to obtain large numbers of progeny for testing. Based on our results, we conclude that double reduction occurs sporadically in tetraploid potatoes.

The use of area under the disease progress curve to assess resistance to late blight in potato germplasm

The multiple evaluation of potato cultivais and breeding selections (clones) for disease during the season can be costly and may not be necessary for accurate assessments of disease resistance or susceptiblity. For diseases whose progression can be described by sigmoid curves, an estimate of the area under the disease progress curve from two data points may provide as much information as from repeated assessments. Twentythree clones were planted in a randomized complete block design in Hastings, FL, in 1997 and evaluated for percent diseased foliage 14 times during a 31-day period after late blight was first noticed in the plots. The area under the disease progress curve (AUDPC) was calculated for all 14 assessments. The AUDPC was also calculated for nine sub-sets of the original data set. There was a high correlation between all the methods in the calculation of the AUDPC. The AUDPC calculated based on two dates (representing the beginning of the epidemic and the time until two of the clones were dead from late blight) was as informative as the AUDPC calculated on the entire data set. The AUDPC could be calculated based on any two dates from this time frame as long as one date was shortly after the epidemic started and the other date was as the epidemic was reaching its peak. Much information was lost if AUDPC was calculated based on dates involved only in the early part of the epidemic. A considerable savings in time and effort can be realized by only a few assessments.ResumenLa evaluación multiple de cultivares de papa y selecciones en proceso de mejoramiento (clones) durante la Època de cultivo puede ser muy costosa y tal vez no necesaria para evaluar resistencia o susceptibilidad a las enfermedades. Para enfermedades cuyo progreso puede ser representado por medio de curvas sigmoidales, el estimado del área debajo de la curva de progreso de la enfermedad en base a dos evaluaciones puede proporcionar tanta información como la que se obtiene de evaluaciones múltiples. Se sembraron 23 clones en un diseno de bloque completamente al azar en Hastings, Florida en 1997 y se evaluó el porcentaje de follaje infectado por 14 veces durante un periodo de 31 dias después de que el tizón tardío fuera observado por primera vez en las parcelas. Para las 14 evaluaciones se calculó el área debajo de la curva de progreso de la enfermedad (AUPDC). El AUDPC también fue calculado para nueve sub-conjuntos del conjunto de datos original. Como resultado, se observó que había una correlación muy estrecha entre todos los métodos empleados para el cálculo del AUDPC. El AUDPC calculado en base a dos fechas (representando el inicio de la epidemia y el tiempo en el que murieron dos de los clones por causa del tizón tardío), fue tan informativo como el AUDPC calculado con todo el conjunto de datos. El AUDPC puede ser calculado en base a cualquiera de dos fechas dentro del periodo evaluado siempre y cuando una de las fechas sea tan pronto se inicie la epidemia y la otra cuando la epidemia esté alcanzando el máximo. Mucha de la información se perdió cuando el AUDPC fue calculado en base a las fechas proximas al inicio de la epidemia. Se puede ahorrar considerable tiempo y esfuerzo cuando se hacen pocas evaluaciones.

Foliar resistance to late blight in potato clones evaluated in national trials in 1997

Changes in the oomycetePhytophthora infestans in the United States and other parts of the world pose a significant threat to potato production. A continual evaluation of potato clones for resistance to late blight is necessary to identify clones with resistance and to monitor the stability of resistance in light of the emergence of new and more aggressive strains of this pathogen. Twentytwo potato clones (10 cultivars and 12 selections) were evaluated in 1997 for late blight resistance at seven U.S. locations. Seven late blight differentials (R1R2R3R4, R1R2R4, R1R3R4 R3, R8 R10, and Rmulti) were also included in the test at five of these locations. The US-8 strain of P.infestans was present at all locations. Percent infected foliage was recorded at approximately weekly intervals following the onset of disease. Area under the disease progress curve (AUDPC) was calculated. The nonparametric stability statistics mean absolute rank differences (Si(1)) and variances of the ranks (Si(2)) were used to analyze phenotypic stability. Although neither of these statistics was significant for individual clones, both of these statistics were significant when summed over clones, indicating the importance of genotype × environment interactions on the rankings of these clones across locations. The most late blight-resistant and susceptible clones were the most stable; clones in the intermediate ranges were most subject to rank changes due to genotype × environment interactions. The most late blight-resistant clones were AWN86514-2, B0692-4, B0718-3, and B0767-2. The most susceptible clones were B0811-13, B1004-8, Nor-Donna, and Krantz. AUDPC was very low for the late blight differentials R8 and Rmulti, moderately low for R10 and very high for the remaining differentials. This study is important in characterizing the reaction of potato clones to new strains of P.infestans.

Evaluation and characterization of advanced potato breeding clones for resistance to scab by cluster analysis

A total of 17 potato breeding lines and 4 cultivars were evaluated in replicated field trials in Presque Isle, Maine, USA, during 1988-91 for their reaction to scab (Streptomyces scabies). All tubers were individually scored for type of lesion (0 = none to 5 = pitted scab) and surface area covered (0 = 0% to 12 = 100%). Computations were made for lesion index (LI), surface area index (SAI) and overall scab index (OSI). Analyses of variance of LI, SAI and OSI revealed significant differences among potato lines during 1989-91. Cluster analyses on the combination of LI and SAI were superior to clustering on OSI alone. Five clusters were defined in 1989-91. It is suggested that cluster analysis provides a means to quantitatively compare the scab reactions of new germ plasm with that of cultivars used as disease standards.

Mining data from potato pedigrees: tracking the origin of susceptibility and resistance to Verticillium dahliae in North American cultivars through molecular marker analysis

Potato (Solanum tuberosum L.) cultivated in North America is an autotetraploid species with a narrow genetic base. Most of the popular commercial cultivars are susceptible to Verticillium dahliae, a fungal pathogen causing Verticillium wilt disease, though some cultivars with relatively high resistance also exist. We have used the available pedigree information to track the origin of susceptibility and resistance to Verticillium wilt present in cultivated potatoes. One hundred thirty-nine potato cultivars and breeding selections were analyzed for resistance to the pathogen and for the presence of the microsatellite marker allele STM1051–193 that is closely linked to the resistance quantitative trait locus located on the short arm of chromosome 9. We detected an unusually high frequency of susceptible genotypes in the progeny descending from the breeding selection USDA X96–56. Molecular analysis revealed that USDA X96–56 does not have the STM1051–193 allele. Most of the first-generation progeny of this breeding selection also lack the allele. On the other hand, pedigree analysis indicated that breeding selection USDA 41956 often transfers V. dahliae resistance to its progeny. Molecular analysis detected presence of (at least) three STM1051–193 alleles in this breeding selection. These two genotypes (USDA X96–56 and USDA 41956) appear to have contributed greatly to the susceptibility or resistance, respectively, found in present commercial cultivars. Our results also indicate that the maturity class substantially affects the plant resistance response. In the intermediate to very late maturing class, the presence of the STM1051–193 allele significantly increases the resistance. Early to very early potatoes are usually more susceptible to the disease regardless of the allelic status, though the pattern of the allele effect is always the same. The results indicate that the STM1051–193 allele can be used for marker-assisted selection, but the potato maturity class also needs to be considered when making the final decision about the plant resistance level.