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

Abstract

Detailed knowledge on genetic parameters such as diversity, structure, and linkage disequilibrium (LD) and identification of duplicates in a germplasm bank and/or breeding collection are essential to conservation and breeding strategies in any crop. Therefore, the potato genetic breeding collection at the Universidad de Nariño in Colombia, which is made up of diploid and tetraploid genotypes in two of the more diverse genebanks in the world, was analyzed with 8303 single nucleotide polymorphisms (SNP) from SolCAP version 1. In total, 144 genotypes from this collection were analyzed identifying an 57.2% of the polymorphic markers that allowed establishing two and three subpopulations that differentiated the diploid genotypes from the tetraploids. These subpopulations had high levels of heterozygosity and linkage disequilibrium. The diversity levels were higher in the tetraploid genotypes, while the LD levels were higher in the diploid genotypes. For the tetraploids, the genotypes from Peru had greater diversity and lower linkage disequilibrium than those from Colombia, which had slightly lower diversity and higher degrees of LD. The genetic analysis identified, adjusted and/or selected diploid and tetraploid genotypes under the following characteristics: 1) errors in classification associated with the level of ploidy; 2) presence of duplicates; and 3) genotypes with broad genetic distances and potential use in controlled hybridization processes. These analyses suggested that the potato genetic breeding collection at the Universidad de Nariño has a genetic base with a potential use in breeding programs for this crop in the Department of Nariño, in southern Colombia.

Phenotypic and molecular analyses in diploid and tetraploid genotypes of Solanum tuberosum L. reveal promising genotypes and candidate genes associated with phenolic compounds, ascorbic acid contents, and antioxidant activity

“…The LD mean value and the genetic diversity (Ho) of diploids contrasted with the values of the mixed and tetraploid populations. The same pattern of high LD and low Ho in diploid potatoes and low LD and high Ho in tetraploids was previously reported ( Berdugo-Cely et al., 2017 ; Berdugo-Cely et al., 2021 ). As reported in other studies ( Gebhardt et al., 2004 ; Simko et al., 2006 ), the LD decayed slowly in all populations, and it is explained by the clonal propagation of potatoes that limits the number of meiotic generations and, in consequence, the recombination events ( Gebhardt et al., 2004 ; Simko et al., 2006 ).…”

“…The CCC has a strong population structure based on the ploidy level; this collection is structured into diploid and tetraploid potatoes ( Berdugo-Cely et al., 2017 ). Ploidy levels have been reported as one of the main factors to explain the population structure in other potato collections ( Stich et al., 2013 ; Hardigan et al., 2015 ; Berdugo-Cely et al., 2021 ). Identifying the genetic structure of panels used in association mapping analyses is essential to eliminate false marker-traits associations influenced by genetic relationships and population structure tendencies.…”

“…The Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA) is responsible for conserving and characterizing the Colombian potato genetic resources (Colombian Central Collection - CCC). This collection is one of the largest and most diverse for this species in South America ( Berdugo-Cely et al., 2017 ; Berdugo-Cely et al., 2021 ; Nagel et al., 2022 ), with more than 2000 accessions that include landraces or native genotypes (materials developed as a product of selection by Colombian farmers), commercial varieties, and wild-relative species of S. tuberosum . In an earlier study ( Berdugo-Cely et al., 2017 ), 809 native genotypes of the CCC collection were analyzed using morphological characters and Single Nucleotide Polymorphism (SNP).…”

Defining a diverse core collection of the Colombian Central Collection of potatoes: a tool to advance research and breeding

“…In different population structure and genetic diversity studies of genebank collections of traditional cultivars and breeding programs germplasm of potato, the material has been discriminated following ploidy, taxonomy, and characteristics of breeding selection ( Hirsch et al., 2013 ; Berdugo-Cely et al., 2017 ; Hardigan et al., 2017 ; Deperi et al., 2018 ; Ellis et al., 2018 ; Pandey et al., 2021 ). In general, it is observed that the genetic diversity studies of germplasm obtained from genebanks have shown that the discrimination among accessions is mainly associated with ploidy and taxonomy ( Berdugo-Cely et al., 2017 ; Hardigan et al., 2017 ; Ellis et al., 2018 ; Berdugo-Cely et al., 2021 ). This discrimination agrees with our results, in which ploidy and taxonomy explained the identified genetic groups.…”

“…We tested if there was population differentiation by calculating the F ST and the percentages of differentiation between and within identified subpopulations using the analysis of molecular variance (AMOVA) in the R-packages dartR ( Mijangos et al., 2022 ) and Poppr ( Kamvar et al., 2014 ), respectively. Finally, we manually estimated the genetic diversity by calculating the observed heterozygosity (Ho) per genotype and genetic group, using the methodology described by Berdugo-Cely et al. (2021) .…”