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Breeding Qualitative and Quantitative Traits for Potatoes in the Columbia Basin

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Breeding Qualitative and Quantitative Traits for Potatoes in the Columbia Basin AN ABSTRACT OF THE DISSERTATION OF Ryan C. Graebner for the degree of Doctor of Philosophy in Crop Science presented on March 30, 2018. Title: Breeding qualitative and quantitative traits for potatoes in the Columbia Basin. Abstract approved: ______________________________________________________ Vidyasagar Sathuvalli The cultivated potato (Solanum tuberosum L.) is one of the world’s most important staple crops, ranked fourth after maize, rice, and wheat. While the potato’s success is due largely to its high yield, it also benefits from its broad global acceptance, and its ability to be used by the consumer without prior processing. However, the potato’s success as a crop comes despite an array of pathogens that can cause extreme yield losses, and quality defects that can make the potato essentially unmarketable. While they can be costly and at times devastating, the presence of these pathogens creates an enormous opportunity for the genetic improvement of the potato. For every major pathogen in potato, multiple sources of resistance have been identified in landraces or wild potato species that if combined in a suitable potato cultivar, could reduce or eliminate the damage caused by that pathogen. While the utilization of genes from exotic germplasm is far from trivial, advances in genetics, genomics, and phenomics will certainly accelerate this process. In addition to improved biotic and abiotic stress resistance, a major feat in potato breeding would be to identify an improved system for developing potato clones with superior quantitative traits. The current strategy used to develop new cultivars, which involves planting tens of thousands of seedlings each year from intercrossed heterozygous clones, may be the best strategy for developing new varieties. However, the difficulty of producing superior potato clones using this strategy has prompted some breeding programs to explore how alternative breeding methods might be applied. Nine wild potato species were evaluated for their resistance to Meloidogyne chitwoodi (the Columbia root-knot nematode, CRKN), which can cause serious damage in potato production systems. Greenhouse screening identified fifteen clones from S. hougasii, one clone from S. bulbocastanum, and one clone from S. stenophyllidium, with moderate to high levels of resistance against three isolates of M. chitwoodi. Geographical mapping showed that these newly identified resistance sources are clustered in the states of Jalisco and Michoacán in west-central Mexico. Further, we screened seedlings from nine potato species for their response to Verticillium wilt (Verticillium dahliae), a major soil-borne pathogen of potatoes in many regions of the world. Greenhouse screenings identified two clones from Solanum andreanum and one clone from S. bulbocastanum that had resistance equal to or greater than ‘Ranger Russet’, the moderately resistant check. These new V. dahliae resistance sources have different taxonomic origins from previous V. dahliae sources and will expand our V. dahliae resistant potato germplasm. ‘Castle Russet’ is a newly released variety from the Northwest potato variety development program with improved agronomic performance and resistance to Potato virus Y (PVY) and Corky ringspot (CRS). A mapping population was developed to study segregation of resistance to PVY and CRS and identify single nucleotide polymorphism (SNP) markers linked to these resistances. SNP genotyping identified that the population phenotyped is in fact a mix of two populations. Molecular mapping of the real population of 49 clones identified 31 SNPs linked to PVY resistance, in addition to the markers STM0003 and YES3-3B, which were previously shown to be linked to Rysto. A single marker association analysis for CRS identified a major peak in chromosome 9 and two minor peaks in chromosomes 1 and 10. The identified linked SNPs for PVY and CRS need to be validated in a larger population for effective use in marker assisted breeding. Finally, we investigated crosses between “Russet” and “Chipper” type potato clones (Russet-Chipper crosses), as well as between elite long- day adapted tetraploid clones and clones from an improved population of diploid potatoes derived from Group Phureja and Group Stenotomum (4x-2x crosses) were investigated. In our trials, clones derived from Russet-Chipper crosses had few notable benefits when compared to clones derived from crosses made within the Russet and Chipper groups in our trial. On the other hand, many of the clones derived from 4x-2x crosses clearly out-yielded the highest yielding clones from crosses between elite long-day adapted tetraploid potato clones. While every favorable quality trait measured was present in at least several clones derived from 4x-2x crosses, the frequency of many of these favorable quality traits was lower than was observed in crosses between elite long-day adapted tetraploid potato clones. Therefore, continued selection of parental clones in 4x and 2x populations would likely be required before a high yielding clone with acceptable or superior quality characteristics could be expected from these 4x-2x crosses. When evaluating the 4x-2x crosses, we found that 61.5% of the resulting clones were triploid, compared to a previously reported frequency of 0.0-7.6%. Tubers of these triploids are generally intermediate between the two parental groups, indicating that there are no pronounced tuber characteristics associated with triploid potato clones. This finding opens the possibility of using triploid potatoes in potato variety development programs and in genetic and genomic studies. ©Copyright by Ryan C. Graebner March 30, 2018 All Rights Reserved Breeding qualitative and quantitative traits for potatoes in the Columbia basin by Ryan C. Graebner A DISSERTATION submitted to Oregon State University in partial fulfillment of the requirements for the degree of Doctor of Philosophy Presented Defense Date March 30, 2018 Commencement June 2018 Doctor of Philosophy dissertation of Ryan C. Graebner presented on March 30, 2018 APPROVED: Vidyasagar Sathuvalli, representing Crop Science Head of the Department of Crop and Soil Science Dean of the Graduate School I understand that my dissertation will become part of the permanent collection of Oregon State University libraries. My signature below authorizes release of my dissertation to any reader upon request. Ryan C. Graebner, Author ACKNOWLEDGEMENTS I would like to thank my major advisor, Dr. Sathuvalli, for contributing countless hours towards my education, and providing me with invaluable advice and support along the way. I’d also like to thank the department head, Dr. Noller, my committee members, the members of the OSU potato breeding program, and all of the other researchers who lent time, advice, and expertise, allowing these projects to be at the level they are. I would also like to thank my family and friends, who supported and encouraged me throughout my education. Most of all, I’d like to thank my wife Christina, who has given me endless love, support and inspiration. CONTRIBUTION OF AUTHORS Chapter 2. Dr. Brown and Dr. Mojtahedi assisted with the experimental design, and the interpretation of results. Dr. Ingham assisted with the experimental design, and with writing the manuscript. Dr. Hagerty assisted with the nematode extractions and quantifications, and with writing the manuscript. Mr. Quick, Ms. Hamlin, and Ms. Wade assisted with the experimental design, and with maintaining plants during testing. Dr. Bamberg helped select germplasm to evaluate. Dr. Sathuvalli secured the funding and assisted with the experimental design, interpretation of results, and writing the manuscript. Chapter 3. Dr. Bamberg helped select germplasm to evaluate. Dr. Frost assisted with the experimental design, and with phenotypic evaluations. Dr. Johnson assisted with the selection of isolates to screen. Dr. Hagerty assisted with inoculation preparation and application. Dr. Sathuvalli secured the funding and assisted with the experimental design, interpreting the results, and writing the manuscript. Chapter 4. Dr. Bali assisted with the genetic characterization of these clones and the mapping of resistance. Dr. Brown assisted with the population development, and the experimental design. Ms. Hamlin and Mr. Quick conducted the phenotypic evaluation for corky ringspot resistance and assisted with the phenotypic evaluation for Potato virus Y resistance. Dr. Sathuvalli assisted with all stages of this experiment. Chapter 5. Mr. Chen assisted with root squashes. Dr. Contreras assisted with flow cytometry and the interpretation of results. Dr. Haynes provided the diploid germplasm and assisted with the experimental design. Dr. Sathuvalli assisted in all stages of this experiment. Chapter 6. Dr. Haynes provided the diploid germplasm and assisted with the experimental design. Mr. Charlton assisted with the management of potatoes grown in Klamath Falls. Mr. Yilma assisted with crossing the parental clones. Dr. Sathuvalli assisted in all stages of this experiment. TABLE OF CONTENTS 1 Introduction ...................................................................................................................... 1 1.1 Potato’s role in global food security ................................................................. 1 1.2 Potato production in the Columbia Basin of Oregon and Washington ............. 1 1.3 Progress of germplasm improvement efforts in temperate growing regions .... 4 1.4 Clean introgression of major genes ..................................................................
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