Genome-wide association mapping and genomic prediction for late blight and potato cyst nematode resistance in potato (Solanum tuberosum L.)

Abstract

Potatoes are an important source of food for millions of people worldwide. Biotic stresses, notably late blight and potato cyst nematodes (PCN) pose a major threat to potato production worldwide, and knowledge of genes controlling these traits is limited. A genome-wide association mapping study was conducted to identify the genomic regulators controlling these biotic stresses, and the genomic prediction accuracy was worked out using the GBLUP model of genomic selection (GS) in a panel of 222 diverse potato accessions. The phenotype data on resistance to late blight and two PCN species (Globodera pallida and G. rostochiensis) were recorded for three and two consecutive years, respectively. The potato panel was genotyped using genotyping by sequencing (GBS), and 1,20,622 SNP markers were identified. A total of 7 SNP associations for late blight resistance, 9 and 11 for G. pallida and G. rostochiensis, respectively, were detected by additive and simplex dominance models of GWAS. The associated SNPs were distributed across the chromosomes, but most of the associations were found on chromosomes 5, 10 and 11, which have been earlier reported as the hotspots of disease-resistance genes. The GS prediction accuracy estimates were low to moderate for resistance to G. pallida (0.04-0.14) and G. rostochiensis (0.14-0.21), while late blight resistance showed a high prediction accuracy of 0.42-0.51. This study provides information on the complex genetic nature of these biotic stress traits in potatoes and putative SNP markers for resistance breeding.

Keywords: GBS; GEBV; PCN; association mapping; genomic prediction; late blight; snps.

Figure 1

Frequency distribution of potato accessions for late blight resistance (A) Late blight AUDPC 2018 (B) Late blight AUDPC 2019 (C) Late blight AUDPC 2020.

Figure 2

Frequency distribution of potato accessions for potato cyst nematode resistance (A) Resistance to G. rostochiensis in 2020 (B) Resistance to G. rostochiensis in 2021 (C) Resistance to G. palida in 2020 (D) Resistance to G. palida in 2021.

Figure 3

Statistics of SNPs identified using GBS (A) Distribution of SNPs based on minor allele frequency (MAF) (B) Distribution of SNPs based on polymorphism information content (PIC).

Figure 4

Neighbor-joining (NJ) phylogenetic tree displaying the genetic relationships among the 222 potato accessions in the panel based on 1,20,622 SNP markers. Branch lengths indicate genetic divergence i.e., the longer the branch, the more diverse the accession from other accessions.

Figure 5

Linkage disequilibrium (LD) decay estimated in the potato accessions. The Pearson correlation coefficient was plotted against the physical map distance (Mb) between pairs of SNPs using a reduced marker data set (24000 SNPs across the genome).

Figure 6

Q-Q plots comparing the inflation of p-values for both the traits using the additive and simplex dominance marker model in full vs reduced marker data sets. The black dotted line indicates p-values under the expected normal distribution.

Figure 7

Manhattan plots for different traits in full vs reduced marker data sets. The significance threshold (black dashed line) is based on the genome-wide false positive rate (a = 0.05) for the Bonferroni correction method and the marker-trait associations (MTAs) crossing the set threshold are depicted in triangles and circles.