Genome-wide identification and characterization of functionally relevant microsatellite markers from transcription factor genes of Tea (Camellia sinensis (L.) O. Kuntze)

• Published in: Scientific reports Vol. 12; no. 1; p. 201
• Main Authors: Parmar, Rajni, Seth, Romit, Sharma, Ram Kumar
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 07-01-2022; Nature Publishing Group; Nature Portfolio
• Subjects: 631/114; 631/208; 631/337; 631/449; 631/61; Amino acid sequence; Amino acids; Aroma; Beverages; Camellia sinensis - genetics; Camellia sinensis - metabolism; Chromosomes; Cultivars; Gene Expression Regulation, Plant; Gene Regulatory Networks; Genes, Plant; Genetic diversity; Genetic improvement; Genetic markers; Genetic Variation; Genome, Plant; Genomes; Genotyping; Humanities and Social Sciences; Hydrophobicity; Microsatellite Repeats; Microsatellites; multidisciplinary; Plant breeding; Plant Proteins - genetics; Plant Proteins - metabolism; Protein Interaction Maps; Regulatory sequences; Science; Science (multidisciplinary); Tea; Transcription factors; Transcription Factors - genetics; Transcription Factors - metabolism; Transcriptomes
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-021-03848-x

Tea, being one of the most popular beverages requires large set of molecular markers for genetic improvement of quality, yield and stress tolerance. Identification of functionally relevant microsatellite or simple sequence repeat (SSR) marker resources from regulatory “Transcription factor (TF) genes” can be potential targets to expedite molecular breeding efforts. In current study, 2776 transcripts encoding TFs harbouring 3687 SSR loci yielding 1843 flanking markers were identified from traits specific transcriptome resource of 20 popular tea cultivars. Of these, 689 functionally relevant SSR markers were successfully validated and assigned to 15 chromosomes (
Chr
) of CSS genome. Interestingly, 589 polymorphic markers including 403 core-set of TF-SSR markers amplified 2864 alleles in key TF families (bHLH, WRKY, MYB-related, C2H2, ERF, C3H, NAC, FAR1, MYB and G2-like). Their significant network interactions with key genes corresponding to aroma, quality and stress tolerance suggests their potential implications in traits dissection. Furthermore, single amino acid repeat reiteration in CDS revealed presence of favoured and hydrophobic amino acids. Successful deployment of markers for genetic diversity characterization of 135 popular tea cultivars and segregation in bi-parental population suggests their wider utility in high-throughput genotyping studies in tea.