Extrapolative microRNA precursor based SSR mining from tea EST database in respect to agronomic traits

Abstract

Tea (Camellia sinensis, (L.) Kuntze) is considered as most popular drink across the world and it is widely consumed beverage for its several health-benefit characteristics. These positive traits primarily rely on its regulatory networks of different metabolic pathways. Development of microsatellite markers from the conserved genomic regions are being worthwhile for reviewing the genetic diversity of closely related species or self-pollinated species. Although several SSR markers have been reported, in tea, the trait-specific Simple Sequence Repeat (SSR) markers, leading to be useful in marker assisted breeding technique, are yet to be identified. Micro RNAs are short, non-coding RNA molecules, involved in post transcriptional mode of gene regulation and thus effects on related phenotype. Present study deals with identification of the microsatellite motifs within the reported and predicted miRNA precursors that are effectively followed by designing of primers from SSR flanking regions in order to PCR validation. In addition to the earlier reports, two new miRNAs are predicting here from tea expressed tag sequence database. Furthermore, 18 SSR motifs are found to be in 13 of all 33 predicted miRNAs. Trinucleotide motifs are most abundant among all followed by dinucleotides. Since, miRNA based SSR markers are evidenced to have significant role on genetic fingerprinting study, these outcomes would pave the way in developing novel markers for tagging tea specific agronomic traits as well as substantiating non-conventional breeding program.

Sequence variation in genes encoding miRNAs/targets and other related approaches for possible use in crop improvement

“…In M. truncatula, a total of 169 primer pairs were successfully designed from 130 miRNA genes (Min et al, ); (b) in lotus ( Nelumbo nucifera ), 1,000 bp sequences (500 bp flanking 5′ and 3′ ends) each in 106 pre‐miRNAs were screened for the presence of miR‐SSRs using MISA; 45 miR‐SSRs were identified in 36 genotypes (Wang, Gui, Pan, Hu, & Ding, ). (c) In tea ( Camellia sinensis ), using an online program WebSat, 18 SSRs were identified in 13 of 33 predicted miRNAs that were located in ESTs; primer pairs flanking each SSR were designed with the help of BatchPrimer3 server (Hazra, Dasgupta, Sengupta, & Das, ). In a reverse approach, SSR signatures were also used for the identification of 208 miRNAs (including 201 novel miRNAs) in Phaseolus vulgaris (Nithin et al, ).…”

NCodR: A multi-class support vector machine classification to distinguish non-coding RNAs in Viridiplantae

“…The ND measures the base pair distance for all the pairs of structures (Huynen et al, 1997;Moulton et al, 2000). Previous reports have suggested that repeats of length one to six nucleotides play significant roles in functions of ncRNAs (Chen et al, 2010;Hazra et al, 2017;Jaiswal et al, 2020;Joy et al, 2013;Joy & Soniya, 2012;Mondal & Ganie, 2014;Sharma et al, 2021;Tabkhkar et al, 2020). The RNA folding measures and di-nucleotide compositions were previously employed to develop classifiers for ncRNAs (Barik & Das, 2018;Panwar et al 2014).…”

NCodR: A multi-class SVM classification to distinguish between non-coding RNAs in Viridiplantae

“…The normalized base-pairing distance (ND) measures the base pair distance for all the pairs of structures [5,6]. Previous reports have suggested that repeats of length one to six nucleotides play significant roles in functions of ncRNAs [7][8][9][10][11][12][13]. The RNA folding measures and di-nucleotide compositions were previously employed to develop classifiers for noncoding RNAs [14,15].…”