"Cultivated potato (Solanum tuberosum L.) is a clonally propagated autotetraploid (2n=4x=48) with high potential for genetic improvement due to the expansive genetic diversity of its related germplasm. This diversity includes high levels of heterozygosity but also deleterious genetic load in cultivated clones, multiple groups of genetically distinct landrace sub-species, and over 100 related tuber-bearing species that can introduce heterosis and adaptation. To generate a better understanding of the landscape of potato genetic diversity, studies were conducted to (1) explore the genetic relationships between tuber-bearing Solanum species, landraces, and cultivars, (2) investigate the role of structural variation in cultivated potato genome evolution and diversity, and (3) identify key loci that were selected during domestication of potato. Phylogenetic analysis of tuber-bearing Solanum species was examined in the first application of genome-wide nuclear single nucleotide polymorphism (SNP) markers with a diversity panel of potato species from the USDA Potato Gene Bank core collection. Genotyping a panel of 75 accessions representing 25 species and 213 cultivated tetraploid clones using 5,023 polymorphic SNPs supported previous taxonomic placement of wild potato germplasm, while reinforcing the theory of a Peruvian domestication origin for potato. Several genes involved in carbohydrate metabolism or with potential roles in tuber development were found to contain diverging allele frequencies in the wild and cultivated potato groups suggesting they may have been key loci involved in domestication. A comprehensive analysis of genomic variation (sequence and structural variation) using 30- 70x sequence coverage in a panel of 12 monoploid/doubled monoploid potatoes derived from primitive South American diploid landraces was performed. Extensive copy number variation (CNV) was found to impact over 30% of the potato genome and nearly 30% of genes, with widespread deletion affecting lowly expressed sequences, and enriched duplication within gene families that function in adaptation and environmental response. This study revealed CNV is equally relevant to sequence-level variation (SNPs, insertions/deletions) in its contribution to deleterious mutation load and gene evolution in the potato genome. The study also demonstrated that the extensive structural heterogeneity present in tetraploid genotypes is present in their diploid progenitors, and thus, is not the result of polyploidy alone. A diversity panel was sequenced at 8x to 16x coverage to enable genome-wide comparison of allele composition in 23 tetraploid potato cultivars, 20 wild species and 20 landrace progenitors. Analysis of selection signatures including FST, Tajima's D, reduced nucleotide diversity and allele frequency differences yielded a set of domestication candidate genes including several regulating carbohydrate pathways, glycoalkaloid biosynthesis and stress responses. Comparable levels of total sequence diversity were present in elite cultivars and South American landraces, yet significant genetic variance between landrace populations was repartitioned as single-clone heterozygosity in cultivars, confirming the hypothesis that elite varieties represent a highly heterozygous group lacking significant population structure. These findings may assist the ability of potato breeders to exploit key performance-related loci and heterosis in the future."--Pages ii-iii.
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