An efficient identification strategy of clonal tea cultivars using long-core motif SSR markers

Abstract

Microsatellites, or simple sequence repeats (SSRs), especially those with long-core motifs (tri-, tetra-, penta-, and hexa-nucleotide) represent an excellent tool for DNA fingerprinting. SSRs with long-core motifs are preferred since neighbor alleles are more easily separated and identified from each other, which render the interpretation of electropherograms and the true alleles more reliable. In the present work, with the purpose of characterizing a set of core SSR markers with long-core motifs for well fingerprinting clonal cultivars of tea (Camellia sinensis), we analyzed 66 elite clonal tea cultivars in China with 33 initially-chosen long-core motif SSR markers covering all the 15 linkage groups of tea plant genome. A set of 6 SSR markers were conclusively selected as core SSR markers after further selection. The polymorphic information content (PIC) of the core SSR markers was >0.5, with ≤5 alleles in each marker containing 10 or fewer genotypes. Phylogenetic analysis revealed that the core SSR markers were not strongly correlated with the trait ‘cultivar processing-property’. The combined probability of identity (PID) between two random cultivars for the whole set of 6 SSR markers was estimated to be 2.22 × 10−5, which was quite low, confirmed the usefulness of the proposed SSR markers for fingerprinting analyses in Camellia sinensis. Moreover, for the sake of quickly discriminating the clonal tea cultivars, a cultivar identification diagram (CID) was subsequently established using these core markers, which fully reflected the identification process and provided the immediate information about which SSR markers were needed to identify a cultivar chosen among the tested ones. The results suggested that long-core motif SSR markers used in the investigation contributed to the accurate and efficient identification of the clonal tea cultivars and enabled the protection of intellectual property.

Genetic Diversity and Genome Size Variability in the Russian Genebank Collection of Tea Plant [Camellia sinensis (L). O. Kuntze]

“…Genetic Diversity, Genetic Structure, and Relationships in Tea Germplasm Collection Based on Simple Sequence Repeat Genetic Data Our results on SSR marker efficiency are largely consistent with those of Wang et al (2016). We observed the highest Ho for TM337 and TM589 and the lowest Ho for TM514, which is in accordance with Wang et al (2016).…”

“…Genetic Diversity, Genetic Structure, and Relationships in Tea Germplasm Collection Based on Simple Sequence Repeat Genetic Data Our results on SSR marker efficiency are largely consistent with those of Wang et al (2016). We observed the highest Ho for TM337 and TM589 and the lowest Ho for TM514, which is in accordance with Wang et al (2016). In terms of the average allele numbers, we observed higher number of alleles for most SSR marker (e.g., TM352; T447) than in the study of Wang et al (2016), possibly due to the broader genetic background of accessions in the Russian tea collection.…”

“…For SSR analysis of the 106 accessions of the tea collection, eight nuclear microsatellite (SSR) primer pairs (Wang et al, 2016) were combined in two multiplexes with four primers in each multiplex (Supplementary Table 2). The forward primers in one multiplex reaction were labeled with four different dyes (ATTO565, ATTO550, ATTO532, and 6-FAM, Eurofins, Germany).…”

“…In numerous studies, SSRs served as excellent markers in genetic analyses of tea plants (Fang et al, 2012;Taniguchi et al, 2014;Zhao et al, 2014;Wambulwa et al, 2016;Wang et al, 2016;Liu et al, 2018;Meegahakumbura et al, 2018;Lee et al, 2019). Due to their codominant inheritance, polymorphism, ease and reliability of evaluation, SSRs may have significant advantages over dominant anonymous markers (e.g., SCoT, RAPD, or AFLP) for many applications in population genetics.…”

A set of tetra-nucleotide core motif SSR markers for efficient identification of potato (<i>Solanum tuberosum</i>) cultivars

“…Long nucleotide repeats are widely adopted for genetic profiling in humans and animals (Butler et al 2004, Butler 2006, Hammond et al 1994, Hellmann et al 2006, Ruitberg et al 2001). Meanwhile, regarding plants, the use of long nucleotide repeats has been limited to the variety identification of a few crops: grape (Cipriani et al 2008, 2010), Eucalyptus (Faria et al 2011), olive (De la Rosa et al 2013), peach (Dettori et al 2015), and tea (Wang et al 2016). …”