Vidyasagar R. Sathuvalli

Development and mapping of microsatellite markers from transcriptome sequences of European hazelnut ( Corylus avellana L.) and use for germplasm characterization

Microsatellite markers, also known as simple sequence repeat (SSR) markers, are useful in genetics and plant breeding for marker-assisted selection, cultivar fingerprinting, and kinship studies. They were previously developed for European hazelnut (Corylus avellana L.) from enriched libraries, inter-simple sequence repeat (ISSR) fragments, and bacterial artificial chromosome (BAC) sequences. This study utilized the ‘Jefferson’ transcriptome sequence to develop microsatellite markers for hazelnut. Microsatellites were mined from the transcriptome sequence and aligned with the corresponding genomic sequence using a BLASTN search, and primers were designed from the genomic sequence. From a total of 1432 identified microsatellites, 382 primer pairs were designed for repeats with motifs of three base pairs or longer and at least five repeats, and a few di-repeat sequences. The primers were initially screened for polymorphism with a set of 24 C. avellana accessions, and those that were polymorphic were characterized using a set of 63 accessions. One hundred nine polymorphic microsatellite markers that generated one or two fragments per accession were characterized, with AAG, AGC, and ACT being the most common motifs. Two additional SSR primer pairs generated three PCR products in a few accessions. Of the 109 loci, 53 were placed on the linkage map of the mapping population OSU 252.146 × OSU 414.062, and 22 were assigned to linkage groups using alternate segregating populations. A dendrogram constructed from the SSR fingerprints at the 109 new marker loci mostly showed clustering of accessions from similar geographic origins and confirmed the tremendous amount of genetic diversity present within C. avellana. These markers will be useful for fingerprinting, marker-assisted selection, and genetic studies in hazelnut.

Genetic Fingerprinting of Potato Varieties from the Northwest Potato Variety Development Program

The Northwest Potato Variety Development (NWPVD) Program has released 45 improved potato varieties since 1985. Thirty-four potato varieties, four breeding clones and two advanced selections from NWPVD Program, and six commonly-grown potato varieties were fingerprinted using 32 simple sequence repeat (SSR) markers and 12,808 single nucleotide polymorphism (SNP) markers. Of 32 SSR markers, 29 exhibited significant polymorphism across all the 46 potato clones studied. A total of 143 alleles were observed with an average of 4.6 alleles per SSR marker. These markers span all 12 chromosomes of potato, with a maximum of five markers from chromosome VIII and minimum of one marker from chromosome VI. The polymorphic information content (PIC) and expected heterozygosity (He) of the SSR markers ranges between 0.18 to 0.75 and 0.20 to 0.78, respectively. Based on PIC, He, and ease of scoring, we recommend a set of eight SSR markers: STG0016, STI0004, STI0012, STI0023, STI0030, STI0033, STM1016 and STM1104 for fingerprinting NWPVD varieties. Out of 12,808 SNPs, 88.8% resulted in reliable three cluster diploid calling of which 87.8% were polymorphic. Tetraploid calling resulted in 44.2% of SNPs of which 94.5% were polymorphic. Our study provided fingerprinting resources for the NWPVD varieties and can be used in issues related to intellectual property rights, ownership, trademark and diversity analysis.ResumenEl Programa de Desarrollo de Variedades de Papa Noroccidental (NWPVD, por sus siglas en inglés), ha liberado 45 variedades mejoradas de papa desde 1985. Se le obtuvo la huella digital molecular a 34 variedades de papa, cuatro clones para mejoramiento, y a dos selecciones avanzadas del Programa NWPVD, así como a seis variedades de papa de cultivo común, utilizando 32 marcadores de repeticiones de secuencias simples (SSR en inglés) y 12,808 marcadores de polimorfismo de nucleótidos simples (SNP). De los 32 marcadores SSR, 29 exhibieron polimorfismo significativo en todos los 46 clones de papa estudiados. Se observó un total de 143 alelos, con un promedio de 4.6 alelos por marcador SSR. Estos marcadores abarcaron los 12 cromosomas de la papa, con un máximo de cinco marcadores del cromosoma VIII y un mínimo de un marcador del cromosoma VI. El contenido de información polimórfica (PIC) y la heterocigocidad esperada (He) de los marcadores SSR fluctúa entre 0.18 a 0.75 y 0.20 a 0.78 respectivamente. Con base en el PIC, He, y las calificaciones, recomendamos un juego de ocho marcadores SSR: STG0016, STI0004, STI0012, STI0023, STI0030, STI0033, STM1016 y STM1104 para obtener la huella molecular digital de las variedades del NWPVD. De 12,808 SNPs, el 88.8% resultó en tres agrupamientos confiables de diploides identificados, de los cuales 87.8% fueron polimórficos. La identificación de tetraploides resultó en 44.2% de SNPs, de los cuales 94.5% fueron polimórficos. Nuestro estudio proporciona recursos de huellas moleculares para las variedades de NWPVD, y puede usarse en temas relacionados con derechos de propiedad intelectual, pertenencia, marcas registradas y análisis de diversidad.

Exploring Folate Diversity in Wild and Primitive Potatoes for Modern Crop Improvement

Malnutrition is one of the world’s largest health concerns. Folate (also known as vitamin B9) is essential in the human diet, and without adequate folate intake, several serious health concerns, such as congenital birth defects and an increased risk of stroke and heart disease, can occur. Most people’s folate intake remains sub-optimal, even in countries that have a folic acid food fortification program in place. Staple crops, such as potatoes, represent an appropriate organism for biofortification through traditional breeding based on their worldwide consumption and the fact that modern cultivars only contain about 6% of the daily recommended intake of folate. To start breeding potatoes with enhanced folate content, high folate potato material must be identified. In this study, 250 individual plants from 77 accessions and 10 Solanum species were screened for their folate content using a tri-enzyme extraction and microbial assay. There was a 10-fold range of folate concentrations among individuals. Certain individuals within the species Solanum tuberosum subsp. andigenum, Solanum vernei and Solanum boliviense have the potential to produce more than double the folate concentrations of commercial cultivars, such as Russet Burbank. Our results show that tapping into the genetic diversity of potato is a promising approach to increase the folate content of this important crop.

Yukon Nugget: a Mid-Season Yellow Skin, Yellow Flesh Specialty Potato with Extreme Resistance to Potato Virus X

Yukon Nugget is a mid-season specialty potato with yellow flesh, yellow skin and distinct red eyes. Yukon Nugget was developed to provide the potato industry with an alternative to Yukon Gold. The overall tuber size profile of Yukon Nugget is smaller and more uniform than Yukon Gold and it typically produces an average of four more tubers per plant than Yukon Gold. Yukon Nugget tubers are ideal for boiling, baking, and microwaving, and have culinary and nutritional qualities generally similar to Yukon Gold. Yukon Nugget has extreme resistance to Potato Virus X due to presence of PVX resistance allele Rx1. It also has moderate resistance to powdery scab and tuber late blight. Yukon Nugget has less vascular and stem end discoloration and less hollow heart than Yukon Gold. Yukon Nugget is similar to Yukon Gold in terms of susceptibility to several major potato diseases, such as PVY, PLRV, and foliage late blight. It was released in 2013 by the Agricultural Experiment Stations of Oregon, Idaho and Washington and the USDA-ARS, and is a product of the Pacific Northwest (Tri-State) Potato Variety Development Program.ResumenYukon Nugget es una papa de especialidad de ciclo intermedio, con pulpa amarilla y ojos rojos evidentes. Esta variedad se desarrolló para suministrar a la industria de la papa una alternativa a Yukon Gold. El perfil general del tamaño del tubérculo de Yukon Nugget es más pequeño y uniforme que Yukon Gold, y típicamente produce un promedio de cuatro tubérculos más por planta que Yukon Gold. Los tubérculos de Yukon Nugget son ideales para hervir, cocinar, para el horno de microondas, y tiene cualidades culinarias y nutricionales generalmente similares a las de Yukon Gold. Yukon Nugget tiene resistencia extrema al Virus X de la papa debido a la presencia del alelo Rx1 de resistencia al PVX. También tiene resistencia moderada a la roña polvorienta y al tizón tardío en el tubérculo. Yukon Nugget tiene menos decoloración vascular y en el extremo del tallo, y menos corazón hueco que Yukon Gold. Yukon Nugget es similar a Yukon Gold en términos de susceptibilidad a varias enfermedades importantes de la papa, tales como el PVY, PLRV y al tizón tardío del follaje. Se liberó en el 2013 por las Estaciones Agrícolas Experimentales de Oregon, Idaho y Washington y el USDA-ARS, y es un producto del Programa de desarrollo de Variedades Triestatal del Pacifico Nor-Occidental.

A Real-Time PCR Assay for Early Detection of Eastern Filbert Blight

Eastern filbert blight (EFB) is a devastating disease of European hazelnut, Corylus avellana, which causes economic losses in Oregon, where 99% of the U.S. crop is produced. The causal fungus, Anisogramma anomala, is native to eastern North America, where it is found associated with the American hazelnut (C. americana). Although C. americana is tolerant, EFB causes cankers, branch dieback, and death of C. avellana. Detection and identification of A. anomala is time consuming using conventional methods because the fungus can only be cultured from sporulating perithecia and the disease symptoms and signs only show 12 to 16 months after infection. In this study, a TaqMan real-time polymerase chain reaction (PCR) assay based on a ribosomal DNA internal transcribed spacer was developed for A. anomala. The assay was validated with multiple isolates of A. anomala, closely related species, common environmental microorganisms, and over 100 C. avellana samples. The real-time PCR assay detected as low as 0.12 pg of A. anomala genomic DNA, and positively diagnosed EFB on 82% of asymptomatic plants as early as 15 weeks from infection. The real-time PCR assay is more sensitive and faster than traditional diagnostic methods. It can facilitate hazelnut breeding and disease management by early and accurate diagnosis of EFB.

High-Resolution Genetic and Physical Mapping of the Eastern Filbert Blight Resistance Region in ‘Jefferson’ Hazelnut ( Corylus avellana L.)

Resistance to EFB from ‘Gasaway’ hazelnut is controlled by a single dominant locus. Map‐based cloning is a feasible approach for gene identification in tree crops. Chromosome walking results in high‐resolution genetic and physical mapping.

Single Nucleotide Polymorphism (SNP) markers associated with high folate content in wild potato species.

Micronutrient deficiency, also known as the hidden hunger, affects over two billion people worldwide. Potato is the third most consumed food crops in the world, and is therefore a fundamental element of food security for millions of people. Increasing the amount of micronutrients in food crop could help alleviate worldwide micronutrient malnutrition. In the present study, we report on the identification of single nucleotide polymorphism (SNP) markers associated with folate, an essential micronutrient in the human diet. A high folate diploid clone Fol 1.6 from the wild potato relative Solanum boliviense (PI 597736) was crossed with a low/medium folate diploid S. tuberosum clone USW4self#3. The resulting F1 progeny was intermated to generate an F2 population, and tubers from 94 F2 individuals were harvested for folate analysis and SNP genotyping using a SolCap 12K Potato SNP array. Folate content in the progeny ranged from 304 to 2,952 ng g-1 dry weight. 6,759 high quality SNPs containing 4,174 (62%) polymorphic and 2,585 (38%) monomorphic SNPs were used to investigate marker-trait association. Association analysis was performed using two different approaches: survey SNP-trait association (SSTA) and SNP-trait association (STA). A total of 497 significant SNPs were identified, 489 by SSTA analysis and 43 by STA analysis. Markers identified by SSTA were located on all twelve chromosomes while those identified by STA were confined to chromosomes 2, 4, and 6. Eighteen of the significant SNPs were located within or in close proximity to folate metabolism-related genes. Forty two SNPs were identical between SSTA and STA analyses. These SNPs have potential to be used in marker-assisted selection for breeding high folate potato varieties.

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.

Targhee Russet: A High Yielding, Dual Purpose Potato Variety with High Protein and Vitamin C Content and Resistance to Tuber Soft Rot

Targhee Russet is a darker-skinned russet potato variety that has shown higher total and marketable yields than Russet Burbank in most yield trials conducted in the western United States. A major strength of Targhee Russet is resistance to tuber soft rot, and it also has moderate resistance to common scab, Verticillium wilt, and net necrosis associated with Potato leafroll virus. Targhee Russet also has exhibited resistance to hollow heart and blackspot bruise. Analyses have shown Targhee Russet to have significantly higher tuber protein and Vitamin C content than Russet Burbank and Ranger Russet. It produces lighter colored fries out of storage than standard processing varieties, indicating its high potential for the production of premium quality frozen and fresh-cut fries. High merit scores for fresh use are also indicative of it having excellent potential as a dual-purpose russet variety, suitable for both processing and fresh-pack operations.ResumenTarghee Russet es una variedad de papa de piel más oscura y corrugada que ha mostrado más rendimiento total y comercial que Russet Burbank en la mayoría de los ensayos de rendimiento desarrollados en el occidente de los Estados Unidos. Una fortaleza mayor de Targhee Russet es su resistencia a la pudrición blanda del tubérculo, y también tiene resistencia moderada a la roña común, a la marchitez por Verticillium y a la necrosis asociada con el virus del enrollamiento de la hoja de la papa. Targhee Russet también ha mostrado resistencia al corazón hueco y a la mancha oscura por daño mecánico. Los análisis también han mostrado que Targhee Russet tiene significativamente más proteína en el tubérculo y contenido de vitamina C que Russet Burbank y que Ranger Russet. Produce hojuelas más ligeramente pigmentadas al salir del almacén que las variedades estándar para proceso, lo que indica su alto potencial para la producción de papa frita congelada de calidad Premium y para corte en fresco. Las altas calificaciones para uso en fresco también son indicativas de tener excelente potencial como una variedad russet de doble propósito, apropiada tanto para operaciones de proceso como para paquetes en fresco.

Evaluation of genetic diversity among Russet potato clones and varieties from breeding programs across the United States

DNA fingerprinting is a powerful tool for plant diversity studies, cultivar identification, and germplasm conservation and management. In breeding programs, fingerprinting and diversity analysis provide an insight into the extent of genetic variability available in the breeding material, which in turn helps breeders to maintain a pool of highly diverse genotypes by avoiding the selection of closely related parents. Oblong-long tubers with russeting skin characterize Russet potato, a primary potato market class in the United States, and especially in the western production regions. The aim of this study was to estimate the level of genetic diversity within this market class potato, utilizing clones and varieties from various breeding programs across the United States. A collection of 264 Russet and non-Russet breeding clones and varieties was fingerprinted using 23 highly polymorphic genome-wide simple sequence repeat (SSR) markers, resulting in 142 polymorphic alleles. The number of alleles produced per SSR varied from 2 to 10, with an average of 6.2 alleles per marker. The polymorphic information content and expected heterozygosity of SSRs ranged from 0.37 to 0.89 and 0.50 to 0.89 with an average of 0.77 and 0.81, respectively. Out of these 23 markers, we propose nine SSR markers best suited for fingerprinting Russet potatoes based on polymorphic information content, heterozygosity and ease of scoring. Diversity analysis of these clones suggest that there is significant diversity across the breeding material and the diversity has been evenly distributed among all the regional breeding programs.