Broadening Genetic Diversity of the Japanese Potato Gene Pool

Abstract

Newly developed potato varieties in Japan have never replaced existing old varieties, indicating genetic poverty in our gene pool. To broaden the genetic diversity, Andean primitive cultivated potatoes (Andigena) were used to create parental clones. A total of 184 Andigena accessions and 10 tetraploid Solanum tarijense-Andigena hybrid clones were crossed with a breeding clone 10H17. From 6939 F 1 hybrid clones, 287 were selected as long-day-adapted F 1 clones. From progeny evaluation using these as pollen parents crossed with Atlantic, 95 male-fertile and high-yielding F 1 clones were selected (PGEL clones). The genetic relationship was evaluated using 17,947 single nucleotide polymorphism (SNP) markers, which disclosed their distinctiveness, with larger mean Euclidean distances between PGEL clones and Japanese, foreign, or all tetraploid varieties (48.0, 49.9 or 49.4, respectively) than between Japanese and foreign varieties (47.2). Thus, these PGEL clones can be used to expand genetic diversity in Japanese potato breeding populations. Resumen Las nuevas variedades de papa desarrolladas en Japón nunca han reemplazado a las viejas variedades en existencia, indicando pobreza genética en nuestro grupo de genes. Para ampliar la diversidad genética, se usaron papas cultivadas primitivas Andinas (Andigena) para crear clones parentales. Se cruzaron un total de 184 accesiones de Andigena y 10 clones híbridos tetraploides de Solanum tarijense-Andigena, con el clon 10H17. De 6939 clones híbridos de F1, se seleccionaron 287 como clones F1 adaptados a día largo. De la evaluación de la progenie usando polen parental cruzado con Atlantic, se seleccionaron 95 clones androfértiles y de alto rendimiento de F1 (clones PGEL). Se evaluó la relación genética usando 17,947 marcadores de polimorfismo de nucleótido simple (SNP), que exhibieron sus diferencias, con promedios de distancias Euclideanas mas grandes entre los clones PGEL y las variedades japonesas, extranjeras, o todas las tetraploides (48.0, 49.9 o 49.4, respectivamente) que entre variedades japonesas y extranjeras (47.2). De aqui que estos clones PGEL pueden usarse para expandir la diversidad genética en las poblaciones del mejoramiento genético de papa japonés. Keywords Andigena. Long-day-adapted F 1 hybrid clones. PGEL clones. Single nucleotide polymorphism (SNP). Marker-assisted selection. Cytoplasmic genome diversity This paper is dedicated to Mr. Masahiko Matsuo, the former President of Calbee Inc., who endowed the Potato Germplasm Enhancement Laboratory at Obihiro University of Agriculture and Veterinary Medicine to initiate the prebreeding program presented in this paper but suddenly died at the age of 76 on February 12, 2018.

Genetic analysis of a potato (Solanum tuberosum L.) breeding collection for southern Colombia using Single Nucleotide Polymorphism (SNP) markers

“…The analysis of the population structure of the potato genetic breeding collection at the Universidad de Nariño based on the Bayesian analyses of the STRUCTURE and PCA program identified two and three possible subpopulations associated with the ploidy level, where diploid genotypes separated from tetraploids, and, according to the geographical origin, the tetraploid genotypes of Colombia separated from those of Peru. Multiple studies have described the use of molecular markers to classify and separate potato genetic materials conserved in germplasm banks according to their ploidy level [ 17 – 19 , 42 , 43 ] and the degree of genetic breeding to discriminate materials according to the varieties, cultivars, elite materials, wild species and/or related species [ 17 , 42 , 44 – 46 ].…”

Statistical considerations for applying genomic prediction to potato

“…However, the Euclidean distance was the most reliable, as the other distance measures sometimes showed a decrease in prediction accuracy as sample size increased, which is not expected. Other tetraploid studies have used the Euclidean distance as a tool to measure sub-population distinction, including potato (Hosaka and Sanetomo, 2020;Selga et al, 2022) and marram grass (Hol et al, 2008).…”

Evolutionary Fixed Potential Agronomic Traits in Polysomic Polyploidy Plants with Special Reference to Potato

“…Moreover, with the biological features making hereditary improvement in potato was more complexity than in other staple crops, a powerful and effective approach conducted by potato breeders was the unique capacity of among ploidy and wild relative potato to cross as a way to introgress favorable agronomic traits derived from their genetic pools into the aim of the potato breeding strategies [110] [111]. For instance, the genetic diversity of Japanese potato cultivar was broadened by breeding with Andigena [112]. In another study, QTL associated with disease such Early Blight in tetraploid potato was identified in specific chromosomes [113].…”