Genomic Characterization of the Ruby Locus

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Genomic Characterization of the Ruby Locus Genomic Characterization of the Ruby Locus.(A) DNA gel blot of genomic DNA from different blood and blond orange varieties and from hybrids between Tarocco and mandarin (OTA) and Moro and mandarin (OMO) digested with AseI and probed with a 32P-labeled probe... Genomic Characterization of the Ruby Locus.(A) DNA gel blot of genomic DNA from different blood and blond orange varieties and from hybrids between Tarocco and mandarin (OTA) and Moro and mandarin (OMO) digested with AseI and probed with a 32P-labeled probe of the Ruby gene from 465 bp upstream of the ATG to the stop codon of the gene. Varieties: C, Cadenera; DS, Doppio Sanguigno; J, Jingxian; M (I), Moro from CRA; N, Navelina; O, Oroval Clementine; T (UK), Tarocco from Reeds (UK); T (I), Tarocco from CRA, Italy. OTA hybrids 3, 9, 14, and 20 are pigmented with anthocyanin; OMO hybrids 28 and 31 are pigmented with anthocyanin. Band 1 is the AseI fragment at the 5′ end of the Ruby gene with the full retroelement insertion (Tcs1 for Tarocco and Doppio Sanguigno and Tcs2 for Jingxian). Band 2 is the AseI fragment at the 5′ end of the Ruby gene containing the solo LTR insertion. Band 3 is the AseI fragment at the 5′ end of the Ruby gene without any insertion (i.e., the wild-type R allele) present in blond oranges.(B) DNA gel blot of genomic DNA from different blood and blond orange varieties. Genomic DNA was digested with AseI and probed with a 32P-labeled probe of the Ruby gene from 465 bp upstream of the ATG to the stop codon of the gene. The gel was run for longer than that shown in Figure 2A so that only the 5′ fragments of the Ruby gene with insertions remained on the gel. Varieties: J, Jingxian; MS, Maltaise Sanguine; N, Navelina; O, Oroval; S, Sanguinelli; T, Tarocco (Reeds, UK). The presence of DNA containing only the solo LTR (band 2) as well as DNA containing the full Tcs1 retroelement (band 1) is apparent in Sanguinelli and Maltaise Sanguine accessions. Eugenio Butelli et al. Plant Cell 2012;24:1242-1255 ©2012 by American Society of Plant Biologists