Fig. 3: Candidate loci associated with agronomic traits and their genomic footprints of artificial selection.
From: Grapevine pangenome facilitates trait genetics and genomic breeding
a, Integrated GWAS map for 29 grape agronomic traits. The ordinate represents the PVE of the trait. b–d, Three significant SVs for BL1 (b), SN6 (c) and Suc1 (d) GWAS loci and their populational frequencies. Left, Gene models with coding regions and transcription direction. The corresponding deletions and insertions are highlighted. Right, Proportions of different genotypes in three populations. e,f, The GWAS results and linkage for SSC7 (e) and BeWi9 (f) loci. Statistical significance was determined by generalized least squares F-test. g, The nucleotide diversity (π) and FST around this candidate region. The vertical dashed lines indicate the combined GWAS loci of BeWi or SSC traits, VL represents V. labrusca. h, Proportions of different genotypes at significant SNP sites in BeWi (nGT0/0 = 272, nGT0/1 = 51) and SSC (nGT0/0 = 288, nGT0/1 = 58) in 2016 (center line, median; box limits, first and third quartiles; whiskers, 1.5× interquartile range). nGT0/0 and nGT0/1 refer to the counts of different genotypes at significant SNP sites. Statistical significance was determined by two-sided Student’s t-tests. i, Gene annotation in candidate region (upper) and expression level (transcripts per kilobase of exon model per million mapped reads) of genes in the candidate region in different grape cultivars (lower).
