Volume 11, Issue 3, Pages 473-484 (March 2018) Genomic Analyses Yield Markers for Identifying Agronomically Important Genes in Potato  Yangping Li, Christophe Colleoni, Junjie Zhang, Qiqi Liang, Yufeng Hu, Holly Ruess, Reinhard Simon, Yinghong Liu, Hanmei Liu, Guowu Yu, Eric Schmitt, Chloé Ponitzki, Guangjian Liu, Huanhuan Huang, Feilong Zhan, Lin Chen, Yubi Huang, David Spooner, Binquan Huang  Molecular Plant  Volume 11, Issue 3, Pages 473-484 (March 2018) DOI: 10.1016/j.molp.2018.01.009 Copyright © 2018 The Authors Terms and Conditions

Figure 1 Geographic Distribution and Population Structure of 167 Potato Accessions. (A) The geographic distribution of 167 accessions. Each dot represents one accession. (B) Principal component analysis (PCA) of the first two components of 167 accessions. Different colors represent different clades as described in the text. (C) Neighbor-joining tree of 167 accessions inferred from whole-genome SNPs with 1000 bootstrap replications. S. chomatophilum Bitter was used as the outgroup. The main clades are designated in color. (D) Decay of linkage disequilibrium (LD) indicated by r2 in wild and cultivated species. Molecular Plant 2018 11, 473-484DOI: (10.1016/j.molp.2018.01.009) Copyright © 2018 The Authors Terms and Conditions

Figure 2 Whole-Genome Screening and Functional Annotation of Selective Sweeps. The horizontal dashed line indicates the threshold for defining the top 5% πw/πc values or the top 5% XP-CLR scores. Genes with both πw/πc values and XP-CLR scores at the top 5% were considered to be under selection. A total of 609 genes under selection were identified in the whole genome of potato. The arrows indicate the chromosome location of QTLs related to tuber glycoalkaloid content (TGC), tuber length (TL), tuber width (TW), tuber number (TN), and late blight resistance (LB). The numbers in brackets indicate the number of selective sweeps in the QTL interval. The top diagram is the distribution of πw/πc values (genetic diversity in cultivated potatoes compared with wild potatoes) in the whole genome of potato. The bottom diagram is the distribution of XP-CLR scores in the whole genome of potato. Molecular Plant 2018 11, 473-484DOI: (10.1016/j.molp.2018.01.009) Copyright © 2018 The Authors Terms and Conditions

Figure 3 Genetic Variation in R Genes of Potato. The putative R genes were divided into two major groups: CC-NBS-LRR (CNL) and TIR-NBS-LRR (TNL). (A) Higher polymorphism levels in regions containing R genes than non-R gene regions. The bars represent the mean θw in 50 kb windows. Windows with less than 10 SNPs were removed. (B) Higher polymorphism levels in regions containing R genes in wild potato than in cultivated potato. (C) Major-effect mutations in potato R genes. (D) The 14 R pseudogenes in the wild species, S. commersonii; the red regions represent deletions in the S. tuberosum group Phureja. Molecular Plant 2018 11, 473-484DOI: (10.1016/j.molp.2018.01.009) Copyright © 2018 The Authors Terms and Conditions

Figure 4 The Phylogenetic Relationship of All Clades of Section Petota as Determined by SVD Quartets Analysis. The nodes with black dots are supported by bootstrap support values ≥90%. The circles indicate bootstrap support values for the designated clades. SVD, singular value decomposition. Molecular Plant 2018 11, 473-484DOI: (10.1016/j.molp.2018.01.009) Copyright © 2018 The Authors Terms and Conditions