Fig. 5: GWAS analysis of perilla leaf color variation.
From: Incipient diploidization of the medicinal plant Perilla within 10,000 years
a Manhattan plot. The strongest associated SNP on chr8 was marked by a red arrow. Dashed horizontal red line indicated significant p-value threshold of 1.04e−8 (calculated as 0.05/n). Leaf (abaxial) phenotypes were shown as inset. b Exon structure of the causal Myb113 gene. Coding exons are shown as red boxes, and UTRs in gray. Positions of three coding variants are marked by vertical black lines. c Schematic representation of LTR insertion in diploid and subsequent 3′ end partial deletion in allotetraploid. Black box on chromosome (gray line) indicated the 5-nt target site that was duplicated upon LTR integration, and red box on chromosome represented the 5-nt micro-homologous sequences that initiated the 9967-bp segment deletion. Drawn not to scale. d A proposed scenario for evolution of perilla leaf color. Note that the 6-bp in-frame deletion in the 2nd exon of Myb113 (white asterisk) first emerged within the crispa clade.
