Genetic diversity analysis of Korean peanut germplasm using 48 K SNPs 'Axiom_Arachis' Array and its application for cultivar differentiation

Abstract

Cultivated peanut (Arachis hypogaea) is one of the important legume oilseed crops. Cultivated peanut has a narrow genetic base. Therefore, it is necessary to widen its genetic base and diversity for additional use. The objective of the present study was to assess the genetic diversity and population structure of 96 peanut genotypes with 9478 high-resolution SNPs identified from a 48 K 'Axiom_Arachis' SNP array. Korean set genotypes were also compared with a mini-core of US genotypes. These sets of genotypes were used for genetic diversity analysis. Model-based structure analysis at K = 2 indicated the presence of two subpopulations in both sets of genotypes. Phylogenetic and PCA analysis clustered these genotypes into two major groups. However, clear genotype distribution was not observed for categories of subspecies, botanical variety, or origin. The analysis also revealed that current Korean genetic resources lacked variability compared to US mini-core genotypes. These results suggest that Korean genetic resources need to be expanded by creating new allele combinations and widening the genetic pool to offer new genetic variations for Korean peanut improvement programs. High-quality SNP data generated in this study could be used for identifying varietal contaminant, QTL, and genes associated with desirable traits by performing mapping, genome-wide association studies.

Figure 1

(A) Pseudomolecule-wise SNP distribution on the array and the distribution of polymorphic SNPs in the ‘Korean Set’ of genotypes, (B) Species-wise representation of SNPs (%), (C) Heat map of genome-wide distribution SNP calling pattern and genome density, (D) Heterozygosity distribution of genotype used for analysis (deep blue: A Homo; mid Blue: Hetero; light Blue: B Homo; white: blank).

Figure 2

Population structure analyses of 96 peanut genotypes in the Korean set based on high-resolution SNPs assessed by STRUCTURE (http://pritch.bsd.uchicago.edu/structure.html). (A) Determining delta K values for different numbers of populations (K = 2) or 3 clusters (K = 3). (B) Bar plot for the K value = 2 or 3. The population structure analysis was performed with admixture 1.3. Color segments represent different groups inferred by STRUCTURE analysis.

Figure 3

Population structure analyses of 207 genotypes in the Merge set based on the high-resolution 4475 SNPs assessed by STRUCTURE (http://pritch.bsd.uchicago.edu/structure.html). (A) Determining delta K values for different populations (K = 2) or 3 clusters (K = 3). (B) Bar plot for the K value 2 or 3. Population structure analysis was performed using admixture 1.3. Color segments represent different groups inferred by STRUCTURE analysis.

Figure 4

Phylogenetic tree of the Korean set of peanut genotypes (n = 96) constructed using MEGA X software (http://www.megasoftware.net/.) with a neighbor-joining method. These genotypes were clustered into two major clusters. The second cluster was subdivided into CIIa and CIIb, with each colored branch representing respective clusters (CI, red; CIIa, purple; CIIb, green). The leaf node symbol represents the respective country mentioned in the legend.

Figure 5

Phylogenetic tree of Merge set of peanut genotypes (n = 207) constructed using MEGA X software (http://www.megasoftware.net/.) with the neighbor-joining method. These genotypes were clustered into two major clusters. The second cluster was subdivided into CIIa and CII, with each colored branch representing respective cluster (CI, red; CIIa, purple; CIIb, green).

Figure 6

Principal component analysis (PCA) of Korean set and Merge set of peanut genotypes. (A) Korean set was classified according to the origin of genotypes (AR- Argentina, CN- China, IN- India, KR- Korea, TW-Taiwan, US- United State of America, and ZW-Zimbabwe). (B) Merge set classified according to the data set (KRS- Korean set of genotypes and MCS- Merged set of genotypes).

Figure 7

Validation of KASP marker and identification of 17 Korean peanut genotypes based on newly designed KASP markers. Results were visualized based on fluorescence signals emitted by the marker set (Cv_1—5). The number represents the designated genotype name (1: Daekwang, 2: Daepung, 3: Palkwang, 4: Akwang, 5: Baekjung, 6: Pungan, 7: Sangan, 8: Sinpalkwang, 9: Ami, 10: K-Ol, 11: Daan, 12: Heuksaeng, 13: Tamsil, 14: Sewon, 15: Haeol, 16: Milyang, 79, 17: Milyang, 75).