Study of the Myb-factor polymorphism based on comparative genomics of vegetable Solanaceae crops (tomato, pepper, eggplant) to search for DNA markers that differentiate samples by the anthocyans accumulation

Anthocyanins are high-value plant antioxidants; they also determine biotic and abiotic stress resistance. The aim of our research was to study the allelic polymorphism of Antocyanin 1 orthologs in the vegetable Solanaceae crops of C. annuum and S. melongena. The search revealed the following closest genes in C. annuum: Myb113-like1 TF and Myb113like2 transcription factors and Myb1 in S. melongena. Exon amplicons of those genes were obtained and then sequenced in the pepper and eggplant samples with contrasting anthocyanin fruit coloration. Primers to the identified polymorphisms were developed and their correlation with the anthocyanin accumulation in fruits was studied. A close correlation was found between a minimum accumulation or the complete absence of anthocyanin synthesis in fruits with a single nucleotide deletion (Myb113-like1), and in the pepper samples, 2 SNP (Myb113-like2) was detected using the CAPS marker Myb 113-AccI. In the eggplant samples, the deletions of 6 and 26 bp were detected using the SCAR marker MybMel and the CAPS marker MybmelPst1. The disturbance of anthocyanin synthesis in pepper forms with 1Indel in Myb113-like1 TF was determined by a shift in the reading frame and SNPs in Myb113-like2 TF lead to amino acid substitutions: Lys → Arg and Thr → Lys. In the eggplant, a deletion of 6 bp leads to the loss of ala and arg in the protein; a deletion of 26 bp causes disorder during the mRNA maturation. The developed markers allow identifying the Myb-like TF alleles under study, resulting in anthocyanin synthesis disturbance in fruits. C. annuum and S. melongena samples with different alleles were selected for a further study and new varieties in agriculture. 

1. Liu Y., Tikunov Y., Schouten R. E., Marcelis L., Visser R., Bovy A. Anthocyanin biosynthesis and degradation mechanisms in Solanaceous Vegetables: a review. Frontiers in Chemistry, 2018, vol. 6, art. 52, pp. 1–17. https://doi.org/10.3389/fchem.2018.00052

2. Sapir M., Oren-Shamir M., Ovadia R., Reuveni M., Evenor D., Tadmor Y., Nahon S., Shlomo H., Chen L., Meir A., Levin I. Molecular Aspects of Anthocyanin fruit Tomato in Relation to high pigment-1. Journal of Heredity, 2008, vol. 99, no. 3, pp. 292–303. https://doi.org/10.1093/jhered/esm128

3. GenBank. Available at: https://www.ncbi.nlm.nih.gov/genbank/ (accessed 1 August 2019).

4. Solgenomics. Available at: https://solgenomics.net/ (accessed 1 August 2019).

5. Stommel J. R., Dumm J. M. Coordinated regulation of biosynthetic and regulatory genes coincides with anthocyanin accumulation in developing eggplant fruit. Journal of the American Society for Horticultural Science, 2015, vol. 140, no. 2, pp. 129–135. https://doi.org/10.21273/jashs.140.2.129

6. Lightbourn G. J., Stommel J. R., Griesbach R. J. Epistatic interactions influencing anthocyanin gene expression in Capsicum annuum. Journal of the American Society for Horticultural Science, 2007, vol. 132, no. 6, pp. 824–829. https://doi.org/10.21273/jashs.132.6.824

7. Jung S., Venkatesh J., Kang M.-Y., Kwon J.-K., Kang B.-C. A non-LTR retrotransposon activates anthocyanin biosynthesis by regulating a MYB transcription factor in Capsicum annuum. Plant Science, 2019, vol. 287, pp. 110181. https://doi.org/10.1016/j.plantsci.2019.110181

8. Ye J., Coulouris G., Zaretskaya I., Cutcutache I., Rozen S., Madden T. Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics, 2012, vol. 13, no. 1, art. 134, pp. 1–11. https://doi.org/10.1186/1471-2105-13-134