Fig. 2: The patterns of genetic diversity and linkage disequilibrium in the Pgt panel. | Nature Communications

Fig. 2: The patterns of genetic diversity and linkage disequilibrium in the Pgt panel.

From: Population genomics of Puccinia graminis f.sp. tritici highlights the role of admixture in the origin of virulent wheat rust races

Fig. 2: The patterns of genetic diversity and linkage disequilibrium in the Pgt panel.

a Classification of SNPs based on their effect and location relative to gene models (intergenic, 5 kb upstream and downstream of a gene, UTRs, first and last exons, and introns). b MAF (minor allele frequency) of nonsynonymous and synonymous SNPs. A two-sided Kolmogorov–Smirnov test was applied to compare MAF spectra between these two types of SNPs. SEM strong effect mutations include stop codon gain and splice site disruption. c MAF of synonymous and nonsynonymous SNPs located within predicted effectors and non-effectors. d The rate of LD decay in the Pgt samples from the US (15 isolates) and outside of the US (22 isolates) was modeled as a function of the physical distance between SNPs.

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