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.

Genome-wide association study and selective sweeps reveal genetic variations associated with Chip Processing clones selected over sixty years in global potato breeding programs

“…In fact, the Chip Processing phenotype is determined primarily by considering properties such as chip color, dry matter content, speci c gravity or starch content. Through breeding efforts over sixty years, a set of chip processing potato varieties/clones designated as the Chip Processing market class (Hirsch et al 2013;Igarashi et al 2019;Jo et al 2022) have been created to make great contributions to potato chip production industry. Our results were replicated using internal replication that shared individual clones with the discovery cohort but was ancestrally matched (Uffelmann et al 2021).…”

“…This panel included 69 Korean potato clones (43 commercial varieties and 26 advanced breeding lines) selected over 40 years by a local potato breeding program, and 290 potato collections from various countries (Japan, North America, the Netherlands, Germany, Chile, New Zealand, and Austria) (Supplementary Table 1). Market class designations for potato clones of study were based on the previous papers (Hirsh et al 2013;Igarashi et al 2019;Jo et al 2022).…”

“…We performed case-control GWAS in the genetic diversity panel using the ltered high quality 3977 SNPs based on the dosage genotyping model described in Jo et al (2022), to identify loci associated with the chip processing characteristics (Supplementary Table 3). The case consisted of 95 chip processing clones, while the control 264 non-chip processing clones including the French fry processing, Pigmented, Table , Starch processing and Yellow.…”

“…The potato chips, invented in the 1850s, form the largest snack food sector in all markets (Riaz 2016). With growing chip-processing industry after World War II, intensive potato breeding for chip processing clones over the past 60 years has dramatically increased chip processing performance which speci cally match industry requirements for the production of chips, resulting in divergence of a distinct market class called Chip Processing clones from all other non-chip processing lines including Table, French fry Processing, Pigmented, Starch Processing and Yellow (Hirsch et al 2013;Igarashi et al 2019;Jo et al 2022). The stringent market requirements for chip processing varieties include light chip color, low defects, high starch content, and resistance to cold-sweetening.…”

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Key message A Chip Processing phenotype in potato was characterized using both the case-control genome-wide association study and selective sweep approaches, pinpointing the associated genetic variants on chromosome 10, as well as nding variants under selection across the genome.Although with booming potato chip industry, distinct chip processing clones have been released over the past 60 years, the genetic architecture of their chip processing characteristics remains largely unknown. The case-control genome-wide association studies (GWAS) using SolCAP SNP array data for Chip Processing clones versus all other market classes in the 359-line potato diversity panel (Jo et al 2022) were performed to detect signi cant signals on chromosome 10. The signals were redetected in the GWAS test using the strata-corrected 190-line panel and also genomic scans employing selective sweep approaches such as the cross-population composite likelihood ratio method (XP-CLR) and PCAdapt.

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