Two EST-derived marker systems for cultivar identification in tree peony

Zhang, J. J.; Shu, Q. Y.; Liu, Z. A.; Hong, Ren; Wang, L. S.; Keyser, Ellen De

doi:10.1007/s00299-011-1164-1

Cited by 38 publications

(26 citation statements)

References 28 publications

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“…Cultivars ‘Huai Nian’ (14), ‘Ju Yuan Shao Nv’ (15), and ‘Xin Xing’ (16) from the Xibei cultivar group clustered together, reflecting their close inter-relationships, and formed another branch in the UPGMA dendrogram (Figure 9). The results of cluster analysis of these SSR genotypes, consistent with known genetic relationships, are similar to results obtained using EST-SSR, TRAP, and SRAP markers [17,18], and confirm the usefulness of the SSR markers developed in this study.…”

Section: Resultssupporting

confidence: 87%

Rapid microsatellite development for tree peony and its implications

Gao

Liu

et al. 2013

BMC Genomics

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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.

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Section: Resultssupporting

confidence: 87%

Rapid microsatellite development for tree peony and its implications

Gao

Liu

et al. 2013

BMC Genomics

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“…Luo et al (2015) developed 91 combinations of TRAP primers (13 fixed and 7 arbitrary) for mango, of which 72.5% were consistent, and Kumar et al (2014) reported 262 TRAP combinations for chickpea, of which 42% of the markers were valid. Similar combination percentage of fixed and arbitrary TRAP primers (49%) was found by Zhang et al (2012) for the ornamental species Paeonia suffruticosa.…”

Section: Selecting the Trap Combinationssupporting

confidence: 74%

Development of TRAP primers for Ricinus communis L.

et al. 2017

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ABSTRACT. The objective of this article was to develop TRAP (target region amplification polymorphism) primers for castor bean, with the goal of making functional markers available for genetic studies about the species. To do this, oligonucleotides were designed based on ESTs, obtained from the NCBI (National Center for Biotechnology Information) databank, which code enzymes involved in metabolic routes of fatty acid synthesis, ricin synthesis, and resistance to castor bean pathogens. The forward primers were designed with the help of the Primer3 software and, for the reverse, six arbitrary primers were used. To standardize the amplification reactions, the following criteria were used to select the primers: sizes between 18 and 20 bp, guanine/ cytosine (GC) in the range of 40 to 60%, and average annealing temperature between 55° and 62°C. The design quality of the primers was verified using the Net Primer application. Fifty-six primers were designed, which had an average GC percentage of 53.2%. A total of 336 combinations were obtained using the 56 fixed and 6 arbitrary primers. Based on polymerase chain reaction, 330 combinations (89%) presented good amplification patterns for the genomic DNA of castor bean. The size of the fragments amplified varied between 50 and 2072 bp. The TRAP primers designed and validated in this study are the first for castor bean and represent a significant increase in the molecular markers for this species.

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“…Similar weak bootstraps have been reported for avocado ( Persea americana Mill.) [50] and tree peony ( Paeonia suffruticosa Andrews) [51]; these low values were hypothesized to result from the large number of hybrid genotypes in the data set and possible recombination among cultivar groups, respectively. This hypothesis is further supported by the observation of a slight excess of heterozygotes.…”

Section: Discussionmentioning

confidence: 99%

Isolation and Characterization of Microsatellite Markers and Analysis of Genetic Diversity in Chinese Jujube (Ziziphus jujuba Mill.)

Wang

Liu

et al. 2014

PLoS ONE

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Chinese jujube (Ziziphus jujuba Mill, 2n = 2× = 24, Rhamnaceae) is an economically important Chinese native species. It has high nutritional value, and its medicinal properties have led to extensive use in traditional oriental medicine. The characterization of genotypes using molecular markers is important for genetic studies and plant breeding. However, few simple sequence repeat (SSR) markers are available for this species. In this study, 1,488 unique SSR clones were isolated from Z. jujuba ‘Dongzao’ using enriched genomic libraries coupled with a three-primer colony PCR screening strategy, yielding a high enrichment rate of 73.3%. Finally, 1,188 (80.87%) primer pairs were amplified successfully in the size expected for ‘Dongzao’. A total of 350 primer pairs were further selected and evaluated for their ability to detect polymorphisms across a panel of six diverse cultivars; among these, 301 primer pairs detected polymorphisms, and the polymorphism information content (PIC) value across all loci ranged from 0.15 to 0.82, with an average of 0.52. An analysis of 76 major cultivars employed in Chinese jujube production using 31 primer pairs revealed comparatively high genetic diversity among these cultivars. Within-population differences among individuals accounted for 98.2% of the observed genetic variation. Neighbor-joining clustering divided the cultivars into three main groups, none of which correspond to major geographic regions, suggesting that the genetics and geographical origin of modern Chinese jujube cultivars might not be linked. The current work firstly reports the large-scale development of Chinese jujube SSR markers. The development of these markers and their polymorphic information represent a significant improvement in the available Chinese jujube genomic resources and will facilitate both genetic and breeding applications, further accelerating the development of new cultivars.

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Two EST-derived marker systems for cultivar identification in tree peony

Cited by 38 publications

References 28 publications

Rapid microsatellite development for tree peony and its implications

Rapid microsatellite development for tree peony and its implications

Development of TRAP primers for Ricinus communis L.

Isolation and Characterization of Microsatellite Markers and Analysis of Genetic Diversity in Chinese Jujube (Ziziphus jujuba Mill.)

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