Kimberly J. Felcher

Integration of Two Diploid Potato Linkage Maps with the Potato Genome Sequence

To facilitate genome-guided breeding in potato, we developed an 8303 Single Nucleotide Polymorphism (SNP) marker array using potato genome and transcriptome resources. To validate the Infinium 8303 Potato Array, we developed linkage maps from two diploid populations (DRH and D84) and compared these maps with the assembled potato genome sequence. Both populations used the doubled monoploid reference genotype DM1-3 516 R44 as the female parent but had different heterozygous diploid male parents (RH89-039-16 and 84SD22). Over 4,400 markers were mapped (1,960 in DRH and 2,454 in D84, 787 in common) resulting in map sizes of 965 (DRH) and 792 (D84) cM, covering 87% (DRH) and 88% (D84) of genome sequence length. Of the mapped markers, 33.5% were in candidate genes selected for the array, 4.5% were markers from existing genetic maps, and 61% were selected based on distribution across the genome. Markers with distorted segregation ratios occurred in blocks in both linkage maps, accounting for 4% (DRH) and 9% (D84) of mapped markers. Markers with distorted segregation ratios were unique to each population with blocks on chromosomes 9 and 12 in DRH and 3, 4, 6 and 8 in D84. Chromosome assignment of markers based on linkage mapping differed from sequence alignment with the Potato Genome Sequencing Consortium (PGSC) pseudomolecules for 1% of the mapped markers with some disconcordant markers attributable to paralogs. In total, 126 (DRH) and 226 (D84) mapped markers were not anchored to the pseudomolecules and provide new scaffold anchoring data to improve the potato genome assembly. The high degree of concordance between the linkage maps and the pseudomolecules demonstrates both the quality of the potato genome sequence and the functionality of the Infinium 8303 Potato Array. The broad genome coverage of the Infinium 8303 Potato Array compared to other marker sets will enable numerous downstream applications.

Retrospective View of North American Potato (Solanum tuberosum L.) Breeding in the 20th and 21st Centuries

Cultivated potato (Solanum tuberosum L.), a vegetatively propagated autotetraploid, has been bred for distinct market classes, including fresh market, pigmented, and processing varieties. Breeding efforts have relied on phenotypic selection of populations developed from intra- and intermarket class crosses and introgressions of wild and cultivated Solanum relatives. To retrospectively explore the effects of potato breeding at the genome level, we used 8303 single-nucleotide polymorphism markers to genotype a 250-line diversity panel composed of wild species, genetic stocks, and cultivated potato lines with release dates ranging from 1857 to 2011. Population structure analysis revealed four subpopulations within the panel, with cultivated potato lines grouping together and separate from wild species and genetic stocks. With pairwise kinship estimates clear separation between potato market classes was observed. Modern breeding efforts have scarcely changed the percentage of heterozygous loci or the frequency of homozygous, single-dose, and duplex loci on a genome level, despite concerted efforts by breeders. In contrast, clear selection in less than 50 years of breeding was observed for alleles in biosynthetic pathways important for market class-specific traits such as pigmentation and carbohydrate composition. Although improvement and diversification for distinct market classes was observed through whole-genome analysis of historic and current potato lines, an increased rate of gain from selection will be required to meet growing global food demands and challenges due to climate change. Understanding the genetic basis of diversification and trait improvement will allow for more rapid genome-guided improvement of potato in future breeding efforts.

Susceptibility of potato (Solanum tuberosum L.) foliage and tubers to the US8 genotype ofPhytophthora infestans

Late blight is an important disease of potato(Solanum tuberosum L.) worldwide, and therefore, many potato-breeding programs have prioritized the development of late blight-resistant potato cultivars. Although the emphasis has been to enhance foliar resistance, it is also necessary to evaluate tuber late blight resistance in new breeding lines and new sources of late blight resistance. We report here on the assessment of foliar and tuber resistance and the correlation between these aspects of resistance in a sample of Michigan State University potato breeding lines. Two MSU breeding lines had significantly less infected foliage than the susceptible check cultivars. Tuber susceptibility was significantly different (P < 0.05) only between the most susceptible and the least susceptible breeding lines/cultivars. Foliar and tuber susceptibility to potato late blight were not correlated as low tuber susceptibility was associated both with extremely low (e.g., MSG274-3) and high (e.g., MSE202-3Rus) foliar susceptibility.

Evaluation of wildSolanum species for resistance to the US-8 genotype ofPhytophthora infestans utilizing a fine-screening technique

Greenhouse assays were carried out to characterizeSolanum accessions previously reported to be late blight resistant and to identify individuals within the accessions with high levels of resistance to late blight. Foliage of wildSolanum species accessions or hybrid cultivated potato x wild species (diploid or tetraploid) from Mexico, Russia, or South America was inoculated withPhytophthora infestans (US-8) and was scored for severity of foliar symptoms at 7 and 14 days after inoculation (DAI). Mexican accessions (S. brachycarpum,S. pinnatisectum,S. guerreroense, andS.fendleri) were significantly more resistant (1.1% infection at 14 DAI) than either Russian (59.1% infection at 14 DAI) or South American (53.4% infection at 14 DAI) accessions. Moreover, the genotypes within the Mexican accessions tended to be more uniformly resistant whereas genotypes within the Russian and South American accessions tended to segregate for resistance. The more resistant genotypes of Russian and South American accessions (176/546) were retested, and 56 genotypes were identified as having potential for use in potato breeding programs for resistance to late blight. Fifty percent of the selected genotypes were fromS. microdontum accessions PI498124, PI595510, and PI595511. The potential of these species for incorporation into breeding programs for late blight resistance is discussed.ResumenUn experimente fue conducido en invernadero para la seleción de genoti.pos entre accesiones deSolanum previamente identificados como resistentes al tizón tardÌo de la papa (Phytophthora infestans). El foliaje de accesiones de especies silvestres o hibridos entre cultivares de papa y especies silvestres (diploide y tetraploide) de MÈxico, Rusia y America del Sur fue inoculado con el genotipo US-8 de P.infestans. El porcentaje del foliage infectado fue evaluado a los 7 y 14 dias despues de la inoculación. Las accesiones de MÈxico (S. brachycarpum,S. pinnatisectum,S. guerreroense yS. fendleri) fueron significativamente mas resistentes al tizón tardÌo a los 14 dias depues de la inoculación (1,1%) que las accesiones de Rusia (59,1% ) o de America der Sur (53,4% ). Tambien, la resistencia al tizón tardÌo fue uniformemente distribuida al nivel de genotipo en las accesiones de MÈxico, pero segregación para resistancia ocurrio en accesiones de Rusia y de America del Sur. Selecciones hechas en las accesiones de Rusia y de America del Sur (176/546) fueron reevaluadas en 1998 y resultarón en 56 genotipos que pueden ser utilizados en un programa de mejoramiento para resistencia ai tizón tardÌo de la papa. Un total de 50% de los genotipos seleccionados sonSolanum microdontum accesiones PI 498124, PI 595510 y PI 595511. Tambien se discuten las posibilidades del uso y las estrategias de mejoramiento para la utilizatión de estas especies en un programa de resistencia al tizón tardÌo de la papa.

Missaukee: A Round White Potato Variety Combining Chip-Processing With Resistance to Late Blight, Verticillium Wilt and Golden Cyst Nematode

Previously identified as breeding line MSJ461-1, Missaukee is a round white chip processing potato variety resulting from a cross between Tollocan and NY88 and has foliar resistance to potato late blight (Phytophthora infestans de Bary). This variety has an attractive round shape and mildly netted, bright skin. Seven years of field testing in Michigan indicate that the yield of total marketable tubers in Missaukee is similar to that of Snowden. However, Missaukee has a lower incidence of internal defects than Snowden. Specific gravity ranged from 1.069 to 1.086 in Michigan trials and out-of-the-field chip scores were similar to those of Snowden. Missaukee showed some resistance to Verticillium wilt in 2-years of trials. DNA marker and greenhouse tests indicate that Missaukee is also resistant to the golden cyst nematode (Globodera rostochiensis Woll) pathotype Ro1.ResumenPreviamente identificada como la línea de mejoramiento MSJ461-1, Missaukee es una variedad de papa redonda, blanca, para proceso de fritura, como resultado de la cruza entre Tollocan y NY88 y tiene resistencia foliar al tizón tardío de la papa (Phytophthora infestans de Bary). Esta variedad tiene una forma redonda atractiva y piel brillante, ligeramente con red. Siete años de pruebas de campo en Michigan indican que el rendimiento total de tubérculos comerciales en Missaukee es similar al de Snowden. No obstante, Missaukee tiene mas baja incidencia de defectos internos que Snowden. La gravedad específica fluctuó entre 1.069 a 1.086 en los ensayos de Michigan y fuera del campo los valores de fritura fueron similares a los de Snowden. Missaukee mostró alguna resistencia al marchitamiento por Verticillium en ensayos de dos años. Los marcadores de DNA y las pruebas de invernadero indican que Missaukee también es resistente al nematodo dorado de quiste (Globodera rostochiensis Woll) patotipo Ro1.

Evaluations of Transgenic Potatoes for Resistance to Potato Tuberworm in the Laboratory and Field

The potato variety ‘Spunta’ was previously transformed to constitutively express the cry1Ia1 gene from Bacillus thuringiensis from which three transgenic lines (SpuntaG2, SpuntaG3 and Spunta6a3) were chosen to evaluate for resistance to potato tuberworm (Phthorimaea operculella Zeller). Because potato tuberworm is becoming a serious pest in the Pacific Northwest of the United States, ‘SpuntaG2’, ‘SpuntaG3’ and ‘Spunta6a3’ were evaluated in Washington State through laboratory and field experiments. In the laboratory, both choice and no-choice experiments demonstrated that the transgenic ‘Spunta’ lines were completely resistant (100% mortality) to potato tuberworm. Potato tuberworm resistance was further supported by choice, field-cage studies in which the transgenic ‘Spunta’ lines harbored no potato tuberworm larvae at any sampling date while the controls were heavily infested (averaging 6.4 to as many 17.0 larvae per stem). These results indicate that the cry1Ia1 gene could be an effective component of potato tuberworm management in the Pacific Northwest as well as the international venues where it has already been proven effective.ResumenSe transformó previamente a la variedad de papa “Spunta” para que expresara constitutivamente el gen cry1Ia1 de Bacillus thuringiensis, de la cual se seleccionaron tres líneas transgénicas (SpuntaG2, SpuntaG3, y Spunta6a3) para evaluarles su resistencia a la palomilla de la papa (Phthorimaea operculella Zeller). Considerando que la palomilla de la papa se está convirtiendo en una plaga seria en el Pacífico Noroeste de los Estados Unidos, “SpuntaG2”, “SpuntaG3”, y “Spunta6a3” se evaluaron en el Estado de Washington en experimentos de laboratorio y campo. En el laboratorio, ambos, experimentos seleccionados y no seleccionados, demostraron que las líneas transgénicas de Spunta fueron completamente resistentes (100% de mortalidad) a la palomilla de la papa. La resistencia fue posteriormente respaldada por estudios de selección, en jaulas de campo, en donde las líneas transgénicas de Spunta no mantuvieron a las larvas de la palomilla en ninguna de las fechas de muestreo, mientras que los testigos estuvieron fuertemente infestados (promediando de 6.4 a tanto como 17.0 larvas por tallo). Estos resultados indican que el gen cry1Ia1 pudiera ser un componente efectivo en el manejo de la palomilla de la papa en el Pacífico Noroeste, así como a nivel internacional donde ya se ha probado que es efectivo.

Segregation and Efficacy of the cry1Ia1 Gene for Control of Potato Tuberworm in Four Populations of Cultivated Potato

ABSTRACT The potato (Solanum tuberosum L.) cultivar ‘SpuntaG2’ contains a single copy of the Bacillus thuringiensis (Bt) cry1Ia1 gene and controls potato tuberworm (Phthorimaea operculella Zeller, Lepidoptera: Gelechiidae). Two potato cultivars and two breeding lines were crossed with SpuntaG2 creating four populations used to study cry1Ia1 segregation and efficacy. The cry1Ia1 gene segregated in each of the four populations with a 1:1 ratio. All progeny that were polymerase chain reaction positive for the cry1Ia1 gene had no surviving larvae and no leaf mining in detached leaf assays after 72 h. These results support previous evidence that SpuntaG2 carries a single copy of the cry1Ia1 gene and that transmission of the transgene from parent to progeny is not restricted and follows expected Mendelian segregation ratios. Based on detached leaf assays, the efficacy of the cry1Ia1 gene is retained through sexual transmission. If the SpuntaG2 cry1Ia1 insertion event is deregulated for commercial use, SpuntaG2 could be used for conventional breeding and the progeny carrying the SpuntaG2 event would also be available for commercial use.

Comparing Host Plant Resistance, Engineered Resistance, and Insecticide Treatment for Control of Colorado Potato Beetle and Potato Leafhopper in Potatoes

The Colorado potato beetle, Leptinotarsa decemlineata (Say) Order Coleoptera and the potato leafhopper, Empoasca fabae (Harris) Order Homoptera, are the major insect pests of potato in eastern North America. In two years of field trials, we compared the effectiveness of three pest management options for the control of Colorado potato beetle and potato leafhopper: natural host plant resistance (glandular trichomes), engineered resistance (Bacillus thuringiensis [Bt] Berliner cry3A gene) and a susceptible potato cultivar (Superior) with an at-planting application of the insecticide thiamethoxam. Similar and acceptable control of the Colorado potato beetle larvae was obtained with the Bt-cry3A lines and the thiamethoxam treated “Superior” variety. The glandular trichome cultivar had significantly less Colorado potato beetle damage than did the untreated “Superior” in 2004, although damage was significantly greater than in the Bt-cry3A lines and the insecticide-treated potatoes for both years, and was the only treatment that consistently had very little potato leafhopper damage. These data demonstrate that although each type of host plant resistance mechanism (Bt-cry3A or glandular trichomes) was as effective as the chemical control against one of the insects, neither provides adequate resistance to both Colorado potato beetle and potato leaf hopper.

Michigan Purple: A Purple-Skinned Tablestock Variety

Michigan Purple is a purple-skinned tablestock variety. The tubers have an attractive round-ovoid shape and a strong iridescent purple skin. It has a medium set of bright purple-skinned tubers similar in shape to Norland. The tuber flesh is white; it has few internal defects and does not darken after cooking. Under irrigated conditions the yield is high and specific gravity intermediate. Michigan Purple has mid-early vine maturity.ResumenMichigan Purple es una nueva variedad morada de papa para consumo fresco. Los tubérculos tienen forma redonda, muy atractivos y piel morada brillante. Michigan Purple produce números promedio de tubérculos de coloración morada brillante y forma parecida a la variedad Norland. Los tubérculos tienen pulpa blanca, reducido nivel de defectos y no se negrean despues de cocinarlos. Michigan Purple tiene altos redimientos en cultivo irrigado y maduración media temprana.