Fig. 2: Schematic representation of the AMAT locus with major indels.

a AMAT locus in ‘Concord’. The promoter and transcribed regions were respectively colored in green and blue. Based on the RNA-Seq data and cDNA cloning of berry samples, two exons (blue boxes) and one intron (blue line) were defined and their relative positions were marked, with “A” in the ATG start codon as position 1. The 5′ and 3′ untranslated regions were labeled as “5′U” and “3′U”, respectively. A 400-bp (or 426-bp) fragment was absent in ‘Concord’ (purple box) but was present in PN40024 (or other V. vinifera cultivars). A 42-bp fragment from −354 to −313 (red bar) in the promoter region was absent in some V. labrusca accessions. b AMAT locus in the PN40024 reference genome. The structure is similar as in ‘Concord’ except the presence of 400-bp sequence. A 3-kb fragment in the promoter region, indicated with an aqua-colored bracket, was deleted in one AMAT allele in ‘Chardonnay’ clone I10V1 and some other V. vinifera accessions^30,31,33. Two types of insertions (gray boxes) were found in exon 2 at the exact same position, 504 bp (a soloLTR) in ‘Pinot Noir’ clone ENTAV 115¹⁹ and 1188 bp (a TRIM with 5′LTR, internal sequence and 3′LTR) in the second AMAT allele of ‘Chardonnay’ I10V1 and some other accession^29,30,31,32