The majority of cultivated potato varieties (Solanum tuberosum Grp. Tuberosum 2n=4x=48) are tetraploid. For over a 100 years yield increases have been obtained from improvements in production management rather than through genetic improvement. The goal of this study is to develop diploid germplasm that is self-compatible (SC) that can be used as parental material F1 hybrid variety breeding scheme. Producing true F1 hybrid potato seeds requires first developing SC inbred lines. Wild and cultivated species and dihaploid produced from cultivated tetraploid potato are self-incompatible (SI). We designed our study to develop breeding strategies to generate two germplasm pools using the benefit of having the S-locus inhibitor (Sli) gene from Solanum chacoense (M6).The first goal was to create a SC diploid potato multi-species germplasm pool. The objectives of recurrent selection (RS) are to introgress and improve SC in a multi-species potato germplasm pool that has essential cultivated tuber and canopy traits. SC was increased from 16% to 85% in the progeny over five cycles of RS. Genetic variability analysis based on 4885 single nucleotide polymorphisms (SNPs) was maintained in the germplasm based on heterozygosity, and Neighbor-joining tree (NJ), Principal component analysis (PCA), and Structure analyze. Agronomic trait measurements showed that the RS population has genetic variability for many agronomic traits such as tuber appearance, tuber shape, and average tuber weight, average tuber yield, and tuber specific gravity. SC combined with essential tuber traits, is a valuable germplasm resource for inbred/F1 hybrid variety development.The second goal was to introgress self-compatibility into S. tuberosum dihaploids by crossing SC donor lines to cultivated dihaploids (2n=2x=24) produced from cultivated lines with traits such as chip processing, disease resistance, and virus resistance. A set of three crosses with dihaploid selections was used to select against undesirable traits and reduce the genetic contribution of the SC donor parents. The SC progeny were used in each round of crosses to a set of cultivated dihaploids. This set of three crosses is referred to as S. tuberosum backcross. Genetic diversity analysis based on over 6000 SNPs and agronomic traits measurements showed that the backcross (BC) population has genetic variability for many agronomic traits such as tuber appearance, tuber shape, and average tuber weight, average tuber yield, and specific gravity. The SC germplasm is a valuable resource for the future development of dihaploid F1 hybrid varieties.Third, a study was conducted to examine the results of chloroplast counting in stomatal guard cells, SNP genotyping calling, and flow cytometry to determine ploidy level. All three methods of ploidy determination agreed for evaluating ploidy. Twenty-eight clones with known ploidy level were used as reference samples (14 diploid lines (2n=2x=24), 14 tetraploid varieties and advanced breeding lines (2n=4x=48)) and 102 samples of unknown ploidy level from the RS and the BC populations. These results demonstrate the usefulness of chloroplast counting as an efficient and inexpensive method for breeders to differentiate ploidy between diploid and tetraploid potato.SNP-based heterozygosity, an unweighted pair-group method with arithmetic averages (UGPMA), PCA, and Structure analysis were done using the RS and BC germplasm pools. The NJ tree and PC analysis show the BC2 selections are distinct from the cycle 4 RS selections. The BC2 selections were clustered in one distinct group, and genetic variability was maintained within the group. Developing SC multi-species germplasm pool by using recurrent selection and SC S. tuberosum pool using backcross has led to two germplasm pools that could be tested to identify heterotic combinations. These two germplasm pools may help us develop F1 hybrid diploid potato varieties in the future.
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