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

Abstract

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.

Figure 1

Abundance and localization of various SSRs transcription factors in tea: (a) Overall abundance of various SSR repeats; (b) Localisation of SSR repeats in CDS and UTRs; (c) Distribution frequency of major repeat motif types.

Figure 2

Details of transcription factors families harbouring SSRs in tea: (a) Top 20 SSR containing transcription factor families; (b) Distribution and frequency of various repeat types and functional relevance of major transcription factor families.

Figure 3

Gene Ontology (GO) analysis: (a) GO annotation of transcripts harbouring SSR loci’s classified into Biological Process, Cellular Component and Molecular Functions; (b) GO enrichment analysis representing Biological Process; (c) Cellular Component; (d) Molecular Functions.

Figure 4

Chromosomal assignment of transcription factors derived SSR markers in tea CSS genome: (a) Overall assignment of SSR containing transcription factors to the 15 chromosomes; (b) Genome-wide assignment of experimentally validated polymorphic SSR markers to the 15 chromosomes of Tea.

Figure 5

Protein–protein interaction (PPI) network analysis: PPIN prediction of transcription factors harbouring SSRs including polymorphic SSR markers using Cytoscape v3.4 (https://cytoscape.org).

Figure 6

Cluster analysis: Neighbour-joining tree based on genetic distances of 135 tea cultivars using 15 polymorphic TF-SSR markers. Numbers above branches indicate bootstrap values ≥ 50% (1000 bootstrap replicates).