TeaMiD: a comprehensive database of simple sequence repeat markers of tea

Abstract

Tea is a highly cross-pollinated, woody, perennial tree. High heterozygosity combined with a long gestational period makes conventional breeding a cumbersome process. Therefore, marker-assisted breeding is a better alternative approach when compared with conventional breeding. Considering the large genome size of tea (~3 Gb), information about simple sequence repeat (SSR) is scanty. Thus, we have taken advantage of the recently published tea genomes to identify large numbers of SSR markers in the tea. Besides the genomic sequences, we identified SSRs from the other publicly available sequences such as RNA-seq, GSS, ESTs and organelle genomes (chloroplasts and mitochondrial) and also searched published literature to catalog validated set of tea SSR markers. The complete exercise yielded a total of 935 547 SSRs. Out of the total, 82 SSRs were selected for validation among a diverse set of tea genotypes. Six primers (each with four to six alleles, an average of five alleles per locus) out of the total 27 polymorphic primers were used for a diversity analysis in 36 tea genotypes with mean polymorphic information content of 0.61–0.76. Finally, using all the information generated in this study, we have developed a user-friendly database (TeaMiD; http://indianteagenome.in:8080/teamid/) that hosts SSR from all the six resources including three nuclear genomes of tea and transcriptome sequences of 17 Camellia wild species. Database URL: http://indianteagenome.in:8080/teamid/

Comparative chloroplast genome s: insights into the evolution of the chloroplast genome of Camellia sinensis and the phylogeny of Camellia

“…In addition to nucleotide substitutions, 671 SSRs (simple repeat) were identi ed (another 32, 31, 31 and 30 SSRs occurred in compound formations for CSS, CSA, CIA and CWN, respectively). The number of SSRs was consistent with a previous study [75]. In addition, a total of 270 long repeats and 100 indels also were identi ed.…”

Comparative chloroplast genomes: insights into the evolution of the chloroplast genome of Camellia sinensis and the phylogeny of Camellia 

“…In addition to nucleotide substitutions, 671 SSRs (simple repeat) were identi ed (another 32, 31, 31 and 30 SSRs occurred in compound formations for CSS, CSA, CIA and CWN, respectively). The number of SSRs was consistent with a previous study [71]. In addition, a total of 270 long repeats and 100 indels also were identi ed.…”

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

“…Likewise, SSR containing with AAG/CTT and AAAG/CTTT were most abundant among tri and tetra-repeats, respectively. Repeat frequency analysis stipulates the low abundance of GC repeats in TFs and similar patterns has been reported in tea genome, indicates that GC repeats are rare in both coding (TFs genes) and non-coding regions of tea genome [8,35]. It is noteworthy that in both coding (TFs genes) and non-coding region of tea genome, di-nucleotide repeats viz.…”

“…Nevertheless, microsatellite maker resource in tea is limited with availability of approximately 2000 experimentally validated SSR markers in various earlier studies [14][15][33][34]. Therefore, enriching functionally relevant experimentally validated polymorphic SSR markers will expedite efforts for high density linkage map construction, comparative genomic, and association studies [34][35].…”

“…It is noteworthy that in both coding (TFs genes) and non-coding region of tea genome, di-nucleotide repeats viz. AG/CT was among the most abundant repeat types [35].…”