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Table 6 Missense single nucleotide polymorphisms between Sangiovese (SG) and Corinto Nero (CN) that were detected in the RNA-Seq dataset described by [52] and confirmed by Sanger sequencing. For each variant allele (highlighted in bold), somatic line specificity in comparison with the PN40024 (PN) reference genome, position, locus affected, locus functional annotation, genotype of each cultivar, and predicted effect in the protein sequence and function are shown.

From: Somatic variants for seed and fruit set in grapevine

Variant type Variant position Gene ID Functional annotation Genotype Variant allele effect on protein sequence Variant amino acid effect on protein function PROVEAN scorea
PN SG CN
SG specific Chr2:2,837,618 VIT_02s0025g03330 H(+)-ATPase 4 AHA4 A:A A:G A:A Y274C Deleterious -7.74
CN specific Chr6:4,776,574 VIT_06s0004g03800 DNA-binding protein C:C C:C C:T T1383M Neutral -1.06
CN specific Chr11:2,940,013 VIT_11s0016g03590 Transducing protein A:A A:A A:G I1114V Neutral 0.48
CN specific Chr11:5,363,589 VIT_11s0016g05820 CCR4-NOT transcription complex subunit 10 G:G G:G A:G V317M Neutral -0.76
SG specific Chr14: 23,114,120 VIT_14s0083g00910 Auxin-independent growth promoter C:C C:T C:C R536C Deleterious -2.71
  1. aVariants with a PROVEAN score equal to or below -2.5 were considered "deleterious," variants with a score above -2.5 were considered "neutral"