Genome-wide identification and characterization of functionally relevant microsatellites from putative transcription factor genes of tea for efficient genotyping.

Abstract Background: SSR markers derived from coding region and non-coding un-translated regions (UTRs) act as potential “functional genetic markers”. Tea, one among the most popular herbal drink with multiple medicinal properties is greatly suffered due to several bottlenecks of self-incompatibility, genome heterozygosity and long gestation period. Despite the huge genomic resources, experimentally validated functionally relevant SSR markers are still scarce in tea. Transcription factors (TFs) accounts for larger proportion of plant genomes regulating expression of various desirable traits have not been explored for development of functional marker resource in tea.Results: In current study, putative 2776 transcripts encoding TFs were identified harbouring 3687 SSR loci. High abundance of repeats in ORF (44.37%), UTRs (5'UTR: 32.57%; 3'UTR: 23.0%) suggests significant functional and regulatory relevance of novel SSR loci in trait dissection. 589 polymorphic novel experimentally validated SSR markers (ORF: 297; 5’UTR: 211; 3'UTR: 81) amplified 2864 alleles with allele numbers (Na) of 2 to 17 per locus. Interestingly, repetitive pattern of tri/hexa-repeats in coding region revealed single amino acid repeats reiteration of serine, glycine and proline, leucine in TFs of tea. Moreover, high representation of TF derived polymorphic SSR markers in bHLH (53), WRKY (37), C3H (32), and Myb-related (31) can be utilised for candidate-gene based mapping in tea. Successful utilization of polymorphic SSR makers for genetic diversity characterization of 115 tea cultivars suggests their wider utility in arge-scale fingerprinting studies. Furthermore, 185 SSR markers representing hk x hk, lm x ll, nn x np, ab x cd and ef x eg segregating patterns in selective genotyping of bi-parental mapping population can be potentially employed in genome mapping studies in tea. Conclusion: SSR repeats in regulatory genes influencing normal activity and function of the gene due to the repeat length (expansion and contraction) causing phenotypic variation in plants. Therefore, identification of first set of 1843 novel putative TFs derived microsatellite markers resource with experimentally validated potential polymorphic markers stipulates their importance in various genotyping studies in tea. Interestingly, SSRs retrieved in important TFs may have direct implications for molecular dissection desirable in tea. Genic functional markers developed in the study are powerful tools and can be potentially utilized to accelerate molecular breeding and trait dissection efforts for implantation of marker-asserted selection in tea.