Fig. 5
From: Genomic insights into the evolutionary history and diversification of bulb traits in garlic
Selection signatures for the clove number in CG1. a Genomic regions with the top 5% of πOG/πCG1 values. Horizontal dashed lines indicate the genome-wide thresholds of the selection signals from the analysis of πOG/πCG1 values. Candidate genes/genetic loci identified in this study and overlapped with selective sweeps are marked. In the top right position of figure, bulbs from left to right represent the one from accession of OG, CG1, and CG2, respectively. b Phylogenetic tree of garlic TB1 homologs and AtBRC1 (Arabidopsis), OsTB1 (rice), and ZmTB1 (maize). c Distribution of the ratio of nucleotide diversity (πOG/πCG1) and FST values in the region of 112.0–114.0 Mb on chromosome 2, where Asa2G000245.1 is located (green line). d Important variations of Asa2G00245.1 and their allelic frequency in three garlic groups. Two variations in the promoter region (site of −703 and −692 bp, respectively) and one deleterious mutation (site of 12,217 bp) generated a termination codon are shown by red vertical lines. At the site of −703 bp, blue, grey, and orange part in each pie graph indicated the allelic frequency of GG, AA, and AG in corresponding garlic group, and at the site of −692 bp, they represented the allelic frequency of AA, TT, and AT, whereas at the site of 12,217 bp, blue and orange part in each pie graph indicate the allelic frequency of CC and CA in corresponding garlic group. e Clove number of accessions with different allele of Asa2G000245.1. f Expression level of Asa2G000245.1 in the enlarging bulbs of three garlic groups based on the estimation of FPKM value. ns indicates no significant difference, and ** and *** indicate the significant difference at the level of 0.01 and 0.001, respectively. g Local Manhattan plot showing the 160–170-Mb regions on chromosomes 2. The red dot represents the SNP associated with the clove number trait, and the green arrow indicates the position of Asa2G00253.1. Distribution of the ratio of nucleotide diversity (πOG/πCG1) and FST values in the region of 163.5–165.5 Mb indicate the associated signal and Asa2G00253.1 are in the sweep region of CG1. h Frequency of three haplotypes identified in the AXR1-like Asa2G00253.1. i Clove number of accessions with different haplotypes in Asa2G00253.1. The y-axis in the e and i figure indicates the trait value of clove number