AtSNP_TATAdb: Candidate Molecular Markers of Plant Advantages Related to Single Nucleotide Polymorphisms within Proximal Promoters of Arabidopsis thaliana L

• Published in: International journal of molecular sciences Vol. 25; no. 1; p. 607
• Main Authors: Bogomolov, Anton, Zolotareva, Karina, Filonov, Sergey, Chadaeva, Irina, Rasskazov, Dmitry, Sharypova, Ekaterina, Podkolodnyy, Nikolay, Ponomarenko, Petr, Savinkova, Ludmila, Tverdokhleb, Natalya, Khandaev, Bato, Kondratyuk, Ekaterina, Podkolodnaya, Olga, Zemlyanskaya, Elena, Kolchanov, Nikolay A, Ponomarenko, Mikhail
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 03-01-2024; MDPI
• Subjects: estimates in silico; Gene expression; genome-wide analysis; Genomes; noncoding polymorphism; Proteins; Statistical analysis; TATA box; TATA-binding protein; estimates in silico; target-assisted breeding; TATA-binding protein; genome-wide analysis; TATA box; noncoding polymorphism; verification in vivo; gene expression
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms25010607

The mainstream of the post-genome target-assisted breeding in crop plant species includes biofortification such as high-throughput phenotyping along with genome-based selection. Therefore, in this work, we used the Web-service Plant_SNP_TATA_Z-tester, which we have previously developed, to run a uniform in silico analysis of the transcriptional alterations of 54,013 protein-coding transcripts from 32,833
L. genes caused by 871,707 SNPs located in the proximal promoter region. The analysis identified 54,993 SNPs as significantly decreasing or increasing gene expression through changes in TATA-binding protein affinity to the promoters. The existence of these SNPs in highly conserved proximal promoters may be explained as intraspecific diversity kept by the stabilizing natural selection. To support this, we hand-annotated papers on some of the Arabidopsis genes possessing these SNPs or on their orthologs in other plant species and demonstrated the effects of changes in these gene expressions on plant vital traits. We integrated in silico estimates of the TBP-promoter affinity in the AtSNP_TATAdb knowledge base and showed their significant correlations with independent in vivo experimental data. These correlations appeared to be robust to variations in statistical criteria, genomic environment of TATA box regions, plants species and growing conditions.