Knowledge regarding genetic diversity and population structure of breeding materials is essential for crop improvement. The Texas A&M University Potato Breeding Program has a collection of advanced clones selected and maintained in-vitro over a 40-year period. Little is known about its genetic makeup and usefulness for the current breeding program. In this study, 214 potato clones were genotyped with the Infinium Illumina 22 K V3 Potato Array. After filtering, a total of 10,106 single nucleotide polymorphic (SNP) markers were used for analysis. Heterozygosity varied by SNP, with an overall average of 0.59. Three groups of tetraploid clones primarily based on potato market classes, were detected using STRUCTURE software and confirmed by discriminant analysis of principal components. The highest coefficient of differentiation observed between the groups was 0.14. Signatures of selection were uncovered in genes controlling potato flesh and skin color, length of plant cycle and tuberization, and carbohydrate metabolism. A core set of 43 clones was obtained using Core Hunter 3 to develop a sub-collection that retains similar genetic diversity as the whole population, minimize redundancies, and facilitates long-term conservation of genetic resources. The comprehensive molecular characterization of our breeding clone bank collection contributes to understanding the genetic diversity of existing potato resources. This analysis could be applied to other breeding programs and assist in the selection of parents, fingerprinting, protection, and management of the breeding collections.

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In potato breeding, morphological tuber traits are important selection targets to meet the demands of the fresh and processing markets. Understanding the genetic basis of tuber traits should guide selection and improve breeding efficiencies. However, this is challenging in potato due to the complexity of the traits and the polyploid nature of the potato genome. High-throughput affordable molecular markers and new software specific for polyploid species have the potential to unlock previously unattainable levels of understanding of the genetic basis of tuber traits in tetraploid potato. In this study, we genotyped a diversity panel of 214 advanced clones with the 22 K SNP potato array and phenotyped it in three field environments in Texas. We conducted a genome-wide association study using the GWASpoly software package to identify genomic regions associated with tuber morphological traits. Some of the QTLs discovered confirmed prior studies, whereas others were discovered for the first time. The main QTL for tuber shape was detected on chromosome 10 and explained 5.8% of the phenotypic variance. GWAS analysis of eye depth detected a significant QTL on chromosome 10 and explained 3.9% of the phenotypic variance. Another QTL peak for eye depth on chromosome 5 was located near the CDF1 gene, an important regulator of maturity in potato. Our study found that multiple QTLs govern russeting in potato. A major QTL for flesh color on chromosome 3 that explained 26% of the phenotypic variance likely represents the Y locus responsible for yellow flesh in potato tubers. Several QTLs were detected for purple skin color on chromosome 11. Furthermore, genomic estimated breeding values were obtained, which will aid in the early identification of superior parental clones that should increase the chances of producing progenies with higher frequencies of the desired tuber traits. These findings will contribute to a better understanding of the genetic basis of morphological traits in potato, as well as to identifying parents with the best breeding values to improve selection efficiency in our potato breeding program.

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