Characteristics of Microsatellites Mined from Transcriptome Data and the Development of Novel Markers in Paeonia lactiflora

Wan, Yingling; Zhang, Min; Hong, Aiying; Zhang, Yixuan; Liu, Yan

doi:10.3390/genes11020214

Cited by 10 publications

(8 citation statements)

References 54 publications

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“…We also found that the microsatellites located in CDS regions were dominated by tri-nucleotides, while other SSR motifs accounted for a small proportion. This was common in many plants, such as Phoenix dactylifera L. (Zhao et al, 2013), Tetraena mongolica (Dang et al, 2020), and Paeonia lactiflora (Wan et al, 2020). Compared to other repeat types, tri-nucleotide is less likely to frame-shift mutations in coding regions (Metzgar et al, 2000).…”

Section: Microsatellite Distribution In Different Genic Regionsmentioning

confidence: 99%

Characterization and Development of Microsatellite Markers in Pseudotaxus chienii (Taxaceae) Based on Transcriptome Sequencing

Wang

et al. 2020

Front. Genet.

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Pseudotaxus chienii (Taxaceae) is an endangered conifer species endemic to China. However, a lack of suitable molecular markers hinders the genomic and genetic studies on this species. Here, we characterized and developed the microsatellite markers from a newly sequenced P. chienii transcriptome. A total of 21,835 microsatellite loci were detected from 161,131 non-redundant unigene sequences, and the frequency of SSRs was 13.55%, with an average of one SSR loci per 9.18 kb. Mono-nucleotide, dinucleotide, and tri-nucleotide were the dominant repeat types, accounting for 50.06, 13.49, and 29.39% of the total SSRs, respectively. In terms of distribution location, the coding regions (CDS) with few microsatellites and mainly consisted of tri-nucleotides. There were significant differences in the length of microsatellite among genic regions and motif types. Functional annotation showed that the unigenes containing microsatellites had a wide range of biological functions, most of which were related to basic metabolism, and a few might be involved in expression regulation of gene and response to environmental stress. In addition, 375 primer pairs were randomly selected and synthesized for the amplification and validation of microsatellite markers. Seventyseven primer pairs were successfully amplified and 40 primer pairs were found to be polymorphic. Finally, 20 pairs of primers with high polymorphism were selected to assess the genetic diversity in four P. chienii populations. In addition, the newly developed microsatellite markers exhibited high transferability (70%) in Amentotaxus argotaenia. Our study could enable further genetic diversity analysis and functional gene mining on Taxaceae.

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Section: Microsatellite Distribution In Different Genic Regionsmentioning

confidence: 99%

Characterization and Development of Microsatellite Markers in Pseudotaxus chienii (Taxaceae) Based on Transcriptome Sequencing

Wang

et al. 2020

Front. Genet.

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“…polymorphism and specific function in a species (Lebedev et al, 2020), where for example SSRs in the 5'UTR are more polymorphic compared to those in the 3'UTR (Wan et al, 2020). SSRs found in the 5'UTR have an effect on gene transcription and regulation, whereas SSRs found in the 3'UTR are involved in gene silencing and transcription slippage (Li et al, 2004;Varshney et al, 2005).…”

Section: P R E S Smentioning

confidence: 99%

Oil Palm SSR Resource Interface (Opsri) – Web-Based Bioinformatic Analysis Pipeline for SSR Mining

Rosli¹

2022

JOPR

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Co-dominant simple sequence repeat (SSRs) are popular DNA markers, widely applied in oil palm genetic studies, especially in genetic mapping, marker-trait association, diversity analysis and detecting illegitimacy.A repository having detailed information on SSRs and their inheritance profiles in specific breeding lines is lacking in Malaysia. Such a database enables prioritising polymorphic SSRs for screening, identification of which otherwise can be expensive and time consuming. As such, to facilitate and accelerate development of informative SSRs, oil palm SSR resource interface (OPSRI) was established and currently contains information on 1983 markers that were genotyped successfully across several oil palm breeding lines. OPSRI is a well-structured database that can expedite marker development and reduce redundancy in the on-going efforts at developing DNA markers for genetic analysis of oil palm. The system has been integrated with MISA, Primer3, ORF search script and BLAST to enable SSR identification. This study also characterised a large number of expressed sequence tags (EST)-SSRs using an in-silico approach. The information within the OPSRI database can help accelerate research in oil palm as well as in crops such as coconut and date palm which have a high level of synteny and marker-transferability with oil palm.

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“…Simple sequence repeat markers (SSRs, microsatellites) were developed for tree peonies (Gai et al 2012;Gao et al 2013;Guo et al 2017;Homolka et al 2010;Hou et al 2011a, b;Wang et al 2009;Wu et al 2014;Yu et al 2013;Zhang et al 2011Zhang et al , 2012 and to a lesser extent for P. lactiflora Pall. (Cheng et al 2011;Gilmore et al 2013;Ji et al 2014;Li et al 2011;Wan et al 2020). In addition to identifying cultivars and species, DNA markers can be used to identify hybrid origin, to study genetic diversity and relationships, and for linkage mapping.…”

Section: Introductionmentioning

confidence: 99%

Dear old peonies–for gene banks and gardeners; microsatellite fingerprinting of herbaceous peonies in Fennoscandia

Tanhuanpää

Juhanoja

Oskarsson

et al. 2021

Genet Resour Crop Evol

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The genetic diversity of 334 herbaceous peonies from Fennoscandia was analysed using 18 microsatellites (simple sequence repeats, SSRs). The samples included peonies mostly from Finnish home gardens (284) and nurseries (5) as well as from Norwegian (20) and Swedish (25) peony collections. The study focused on the following species and hybrids: Paeonia anomala L., P. × hybrida Pall., P. officinalis ‘Nordic Paradox’ (Marstein 2015), P. tenuifolia L., and P. × festiva Tausch. The 18 microsatellites amplified a total of 249 alleles and were used to calculate genetic distances between samples and to build a dendrogram. In the dendrogram, samples formed clear groups according to their species. The outcome from the genetic analysis was mainly confirmed by preliminary morphological observations of the Finnish home garden samples performed within the project and the previous morphological study of peonies in Norwegian clone archives. The results of the study will be used to create a Finnish genetic resources collection of the most diverse and vigorous peonies, and to update the Norwegian and Swedish collections.

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Characteristics of Microsatellites Mined from Transcriptome Data and the Development of Novel Markers in Paeonia lactiflora

Cited by 10 publications

References 54 publications

Characterization and Development of Microsatellite Markers in Pseudotaxus chienii (Taxaceae) Based on Transcriptome Sequencing

Characterization and Development of Microsatellite Markers in Pseudotaxus chienii (Taxaceae) Based on Transcriptome Sequencing

Oil Palm SSR Resource Interface (Opsri) – Web-Based Bioinformatic Analysis Pipeline for SSR Mining

Dear old peonies–for gene banks and gardeners; microsatellite fingerprinting of herbaceous peonies in Fennoscandia

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