Characterisation and development of EST-SSR markers in tree peony using transcriptome sequences

Wu, Jing; Cai, Canhui; Cheng, Fangyun; Cui, Huliang; Zhou, Hua

doi:10.1007/s11032-014-0144-x

Cited by 94 publications

(84 citation statements)

References 56 publications

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“…The 21 (35%) polymorphic genic SSR markers were identified among two populations (Table S7). This rate is less than those documented for R. rex (63%) [25] and P. suffruticosa (39.90%) [55] but higher than J. mandshurica Maxim. (30.8%) [57] and E. sibiricus (22.4%) [8].…”

Section: Validation Of Est-ssr Markerscontrasting

confidence: 58%

“…The average of observed heterozygosity and expected heterozygosity was 0.614 and 0.552, respectively. The PIC value is usually used to evaluate the level of genetic information [55]. Our results showed that the PIC value fluctuates from 0.074 and 0.855, and the mean value was 0.504, which is also the middle level.…”

Section: Validation Of Est-ssr Markersmentioning

confidence: 77%

“…(1/3.8 kb) and R. latoucheae [13,42], and higher than Paeonia suffruticosa Andr. (1/9.24 kb) [55]. The frequency of SSRs mainly depends on the mining tool used, database size, the genome structure, and the species differences [56].…”

Section: Ssr Markers In the Transcriptome Of S Japonicusmentioning

confidence: 99%

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De Novo Transcriptomic Analysis and Development of EST–SSRs for Styrax japonicus

Zhang

Jiang

et al. 2018

Forests

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Styrax japonicus sieb. et Zucc. is widely distributed in China with ornamental and medicinal values. However, the transcriptome of S. japonicus has not yet been reported. In this study, we carried out the first transcriptome analysis of S. japonicus and developed a set of expressed sequence tag-simple sequence repeats (EST-SSRs). We obtained 338,570,222 clean reads in total, of which the mean GC content was 41.58%. In total, 136,071 unigenes were obtained having an average length of 611 bp and 71,226 unigenes were favorably annotated in the database. In total, we identified 55,977 potential EST-SSRs from 38,611 unigenes, of which there was 1 SSR per 6.73 kb. The di-nucleotide repeats (40.40%) were the most identified SSRs. One set of 60 primer pairs was randomly selected, and the amplified products in S. japonicus were validated; 28 primer pairs successfully produced clear amplicons. A total of 21 (35%) polymorphic genic SSR markers were identified between two populations. In total, 15 alleles were detected and the average number was 6. The average of observed heterozygosity and expected heterozygosity was 0.614 and 0.552, respectively. The polymorphism information content (PIC) value fluctuated between 0.074 and 0.855, with a mean value of 0.504, which was also the middle level. This study provides useful information for diversity studies and resource assessments of S. japonicus.

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Section: Validation Of Est-ssr Markerscontrasting

confidence: 58%

Section: Validation Of Est-ssr Markersmentioning

confidence: 77%

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De Novo Transcriptomic Analysis and Development of EST–SSRs for Styrax japonicus

Zhang

Jiang

et al. 2018

Forests

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“…Individuals were genotyped using 22 EST‐SSR markers (Table ) distributed over five linkage groups according to the tree peony high‐density genetic linkage map (Cai, ; Peng et al, ). Details of nuclear microsatellite genotyping are described in Wu, Cai, Cheng, Cui, and Zhou (). In addition, three chloroplast (cp) DNA intergenic spacers ( pet B‐ pet D, acc D‐ psa I, and psb E‐ pet L) were sequenced across a subsample of 296 individuals (Table ) using the methods described in Grivet, Heinze, Vendramin, and Petit () and Suo et al ().…”

Section: Methodsmentioning

confidence: 99%

Late Pleistocene speciation of three closely related tree peonies endemic to the Qinling–Daba Mountains, a major glacial refugium in Central China

Cheng

Sun

et al. 2019

Ecology and Evolution

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Determining the factors promoting speciation is a major task in ecological and evolutionary research and can be aided by phylogeographic analysis. The Qinling–Daba Mountains (QDM) located in central China form an important geographic barrier between southern subtropical and northern temperate regions, and exhibit complex topography, climatic, and ecological diversity. Surprisingly, few phylogeographic analyses and studies of plant speciation in this region have been conducted. To address this issue, we investigated the genetic divergence and evolutionary histories of three closely related tree peony species ( Paeonia qiui , P. jishanensis , and P. rockii ) endemic to the QDM. Forty populations of the three tree peony species were genotyped using 22 nuclear simple sequence repeat markers (nSSRs) and three chloroplast DNA sequences to assess genetic structure and phylogenetic relationships, supplemented by morphological characterization and ecological niche modeling (ENM). Morphological and molecular genetic analyses showed the three species to be clearly differentiated from each other. In addition, coalescent analyses using DIYABC conducted on nSSR variation indicated that the species diverged from each other in the late Pleistocene, while ecological niche modeling (ENM) suggested they occupied a larger area during the Last Glacial Maximum (LGM) than at present. The combined genetic evidence from nuclear and chloroplast DNA and the results of ENM indicate that each species persisted through the late Pleistocene in multiple refugia in the Qinling, Daba, and Taihang Mountains with divergence favored by restricted gene flow caused by geographic isolation, ecological divergence, and limited pollen and seed dispersal. Our study contributes to a growing understanding of the origin and population structure of tree peonies and provides insights into the high level of plant endemism present in the Qinling–Daba Mountains of Central China.

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“…Among its numerous applications, it has significantly advanced the development of transcriptomederived SSR markers in a number of plant and animal species, including tree peony and yellow catfish (Wu et al, 2014;Zhang et al, 2014). In this study, using the Illumina Hiseq-2000 platform, we were able to analyze transcriptome ESTs, generate 142,950 contigs, and design a higher number of potential SSR primers (12,208) compared to previous studies of D. involucrata (Du et al, 2012;Li et al, 2012b;Tao et al, 2012).…”

Section: Discussionmentioning

confidence: 96%

Development of EST-SSR markers in the relict tree Davidia involucrata (Davidiaceae) using transcriptome sequencing

et al. 2016

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ABSTRACT. Davidia involucrata, reputed to be a "living fossil" in the plant kingdom, is a relict tree endemic to China. Extant natural populations are diminishing due to anthropogenic disturbance. In order to understand its ability to survive in a range of climatic conditions and to design conservation strategies for this endangered species, we developed genic simple sequence repeats (SSRs) from mRNA transcripts. In total, 142,950 contigs were assembled. Of these, 30,411 genic SSR loci were discovered and 12,208 primer pairs were designed. Dinucleotides were the most common (77.31%) followed by trinucleotides (16.44%). Thirteen randomly selected primers were synthesized and validated using 24 individuals of D. involucrata. The markers displayed high polymorphism with the number of alleles per locus ranging from 3 to 12 and the observed and expected heterozygosities ranging from 0.083 to 1.0 and 0.102 to 0.69, respectively. This large expressed sequence tag dataset and the novel SSR markers will be key tools in comparative studies that may reveal the adaptive evolution, population structure, and resolve the genetic diversity in this endangered species.

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Characterisation and development of EST-SSR markers in tree peony using transcriptome sequences

Cited by 94 publications

References 56 publications

De Novo Transcriptomic Analysis and Development of EST–SSRs for Styrax japonicus

De Novo Transcriptomic Analysis and Development of EST–SSRs for Styrax japonicus

Late Pleistocene speciation of three closely related tree peonies endemic to the Qinling–Daba Mountains, a major glacial refugium in Central China

Development of EST-SSR markers in the relict tree Davidia involucrata (Davidiaceae) using transcriptome sequencing

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