Rapid microsatellite development for tree peony and its implications

Abstract

BackgroundMicrosatellites are ubiquitous in genomes of various organisms. With the realization that they play roles in developmental and physiological processes, rather than exist as ‘junk’ DNA, microsatellites are receiving increasing attention. Next-generation sequencing allows acquisition of large-scale microsatellite information, and is especially useful for plants without reference genome sequences.ResultsIn this study, enriched DNA libraries of tree peony, a well-known ornamental woody shrub, were used for high-throughput microsatellite development by 454 GS-FLX Titanium pyrosequencing. We obtained 675,221 reads with an average length of 356 bp. The total size of examined sequences was 240,672,018 bp, from which 237,134 SSRs were identified. Of these sequences, 164,043 contained SSRs, with 27% featuring more than one SSR. Interestingly, a high proportion of SSRs (43%) were present in compound formation. SSRs with repeat motifs of 1–4 bp (mono-, di-, tri-, and tetra-nucleotide repeats) accounted for 99.8% of SSRs. Di-nucleotide repeats were the most abundant. As in most plants, the predominant motif in tree peony was (A/T)n, with (G/C)n less common. The lengths of SSRs were classified into 11 groups. The shortest SSRs (10 bp) represented 1% of the total number, whereas SSRs 21–30 and 101–110 bp long accounted for 26% and 29%, respectively, of all SSRs. Many sequences (42,111) were mapped to CDS (coding domain sequence) regions using Arabidopsis as a reference. GO annotation analysis predicted that CDSs with SSRs performed various functions associated with cellular components, molecular functions, and biological processes. Of 100 validated primer pairs, 24 were selected for polymorphism analysis among 23 genotypes; cluster analysis of the resulting data grouped genotypes according to known relationships, confirming the usefulness of the developed SSR markers.ConclusionsThe results of our large-scale SSR marker development using tree peony are valuable for investigating plant genomic structural evolution and elucidating phenotypic variation in this species during its evolution and artificial selection. The newly identified SSRs should be useful for genetic linkage map construction, QTL mapping, gene location and cloning, and molecular marker-assisted breeding. In addition, the genome-wide marker resources generated in this study should aid genomic studies of tree peony and related species.

Genetic Divergence and Relationship Among Opisthopappus Species Identified by Development of EST-SSR Markers

“…Among the mononucleotide repeats, A/T repeats (95.08%) were far more prevalent than G/C repeats (4.92%), which was consistent with most plants (Gao et al, 2013;Yue et al, 2016;Feng et al, 2017;Taheri et al, 2019). The most abundant dinucleotide repeat was the AC/GT motif (65.37%), followed by AG/CT (22.93%) and AT/TA (10.73%), which was similar to previous findings in other Chrysanthemum species Chrysanthemum indicum (Han et al, 2018).…”

Identification and molecular mapping of Flowering Date1 (FD1), a major photoperiod insensitivity gene in the adzuki bean (Vigna angularis)

“…, available at http://viggs.dna.affrc.go.jp/) using SSR finder (Gao et al. , available from http://www.fresnostate.edu/ssrfinder/). Four SSR motifs, located at positions 15–16 Mb, 20–21 Mb, 25–26 Mb, 30–31 Mb, 35–36 Mb and 37–38 Mb, and 12 SSR motifs, located at 40–41 Mb, were identified for the development of SSR markers.…”

“…Analysis of simple sequence repeats: Using the F 5 population of #0626 and 196 simple sequence repeat (SSR) markers (Wang et al 2004, Han et al 2005, 81 polymorphic SSRs were detected between 'Shumari' and Acc2265 and used to construct a molecular linkage map (Horiuchi et al 2015). To saturate the gap in a target region between CEDG108 and CEDG275 on linkage group 2 (>50 cM) with molecular markers, novel SSR motifs were obtained from the whole-genome sequence on the Vigna Genome Server (Sakai et al 2016, available at http:// viggs.dna.affrc.go.jp/) using SSR finder (Gao et al 2013, available from http://www.fresnostate.edu/ssrfinder/). Four SSR motifs, located at positions [15][16][20][21][25][26][30][31][35][36]and 12 SSR motifs, Mb, were identified for the development of SSR markers.…”

Genetic diversity and population structure of the endangered endemic speciesPaeonia decompositafrom China and implications for its conservation

“…Primers previously documented and developed for tree peonies were selected for screening. These primers were screened on representative samples and after initial screening, 16 polymorphic microsatellite primer pairs (Wang et al ., 2009; Homolka et al ., 2010; Hou et al ., 2011; Hou et al ., 2011; Zhang et al ., 2012; Gao et al ., 2013; Gilmore et al ., 2013; Wang et al ., 2013; Cai 2015) (Table 2) producing a high degree of polymorphism and high level of amplification were selected for subsequent analysis.…”