Analysis of genetic diversity and population structure among cultivated potato clones from Korea and global breeding programs

Abstract

Characterizing the genetic diversity and population structure of breeding materials is essential for breeding to improve crop plants. The potato is an important non-cereal food crop worldwide, but breeding potatoes remains challenging owing to their auto-tetraploidy and highly heterozygous genome. We evaluated the genetic structure of a 110-line Korean potato germplasm using the SolCAP 8303 single nucleotide polymorphism (SNP) Infinium array and compared it with potato clones from other countries to understand the genetic landscape of cultivated potatoes. Following the tetraploid model, we conducted population structure analysis, revealing three subpopulations represented by two Korean potato groups and one separate foreign potato group within 110 lines. When analyzing 393 global potato clones, country/region-specific genetic patterns were revealed. The Korean potato clones exhibited higher heterozygosity than those from Japan, the United States, and other potato landraces. We also employed integrated extended haplotype homozygosity (iHS) and cross-population extended haplotype homozygosity (XP-EHH) to identify selection signatures spanning candidate genes associated with biotic and abiotic stress tolerance. Based on the informativeness of SNPs for dosage genotyping calls, 10 highly informative SNPs discriminating all 393 potatoes were identified. Our results could help understanding a potato breeding history that reflects regional adaptations and distinct market demands.

Figure 1

The 110-line Korean potato germplasm consists of three subgroups which were inferred using three different approaches, STRUCTURE, discriminant analysis of principal components (DAPC), and hierarchical clustering (HC). Most of the Korean potatoes grouped together into two clusters, whereas the foreign potatoes were placed into the third cluster. (a) Proportional membership (Q) of each clone showing three distinct clusters using 6575 SNP markers. (b) DAPC using the adgenet R package confirmed the structured population. The axes represent the first two linear discriminants and the small solid dots and ellipses represent each clone. The numbers in the circles indicate the different subpopulations identified by DAPC analysis. (c) A dendrogram of the 110 clones using HC (method = “ward.D2”). Two major clusters are observable, in which one cluster indicates I and another one consists of two subgroups (II and III). Note that Cluster III is presented in dark khaki, Cluster II in light blue, and Cluster I in dark gray, corresponding to the colors of the subgroups inferred by DAPC. The leaf colors indicate the respective market class of the individual clones.

Figure 2

A potato genetic landscape revealed by DAPC and KLFDAPC. (A) The ringplot shows the percentages of clones belonging to each of the six inferred clusters based on DAPC for an extended 393-line diversity panel. . The world map was downloaded from the Wikipedia (https://en.wikipedia.org/wiki/File:World_Map_Blank_-_with_blue_sea.svg). The percentages were calculated for 188, 14, 73, and 94 potato clones from North America, Europe, Korea, and Japan, respectively. Note that clones with unknown origins were not included in the ringplots. Below the world map are the clusters originating from the seven countries from which only one potato clone was analyzed in this study. The roman numbers represent individual clusters identified by DAPC. CL; Chile, KZ; Kazakhstan, NZ; New Zealand, BR: Brazil, RU; Russia, BE; Belarus, CH; China. (B) Population genetic structure projected by the first two reduced features in KLFDAPC with σ = 2 for the Korean potato clones and potato varieties released from Japan, the United States, and other countries (Table S2). These results confirm that clustering depends on the geographical location (Korea, Japan, and the USA) where the original crossing was carried out. Potato clones from Europe and other countries are placed into the Japanese cluster. The landrace potatoes are highlighted.

Figure 3

A boxplot showing the genome-wide percent heterozygosity for four populations (Korea, Japan, the USA, and landraces). Note: 2 × varieties were excluded in the Japanese population.

Figure 4

Manhattan plot of the genomic regions detected by integrated extended haplotype homozygosity (left) and cross-population extended haplotype homozygosity (XP-EHH, right) as being under putative selection. The solid/dashed lines represent the significant threshold level for − log₁₀ (p-value).