Characterization and novel Est-SSR marker development of an important Chinese medicinal plant, <i>Morinda officinalis</i> How (Rubiaceae)

Liao, Boyong; Lee, Shiou Yih; Meng, Kaikai; Yin, Qianyi; Huang, Cui‐Ying; Fan, Qingxia; Liao, Wenbo; Chen, Sufang

doi:10.1080/13102818.2019.1664322

Cited by 8 publications

(4 citation statements)

References 25 publications

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“…Of the 50 EST-SSR primer pairs that we tested, 14 produced stable and polymorphic bands of the expected size, with an ampli cation e ciency of 28%; this is comparable to Morinda o cinalis How (24%) [39] but higher than pigeon pea [34] and lower than onion (60%) [23], thorn pear (54.76%) [35], and T. chinensis (53.23%) [30]. Using these primer sets, the accessions could be divided into four distinct groups.…”

Section: Discussionmentioning

confidence: 78%

EST-SSR markers identification based on RNA-sequencing and application in Schisandra chinensis

Shi¹,

Wang²,

Dongxiao³

et al. 2020

Preprint

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Background: Schisandra chinensis, a climbing woody vine, is the best-known and representative genus of the Schisandraceae family which is an important plant in Chinese herbal medicine; however, the application of molecular breeding is restricted by the few genetic markers for this species. Results: In this study, we performed transcriptome sequencing of S. chinensis using the Illumina HiSeq platform to establish a library of expressed sequence tag-simple sequence repeat (EST-SSR) markers. A total of 59,786 unigenes were obtained and 6254 putative SSR sites were detected with a frequency of 10.46%. The predominant type of repeat motif was dinucleotide (35.71%), followed by trinucleotide (13.22%), hexanucleotide (0.50%), tetranucleotide (0.06%), and pentanucleotide (0.22%). We randomly selected 50 EST-SSR primer pairs and used 14 of these for genetic diversity analysis in 42 S. chinensis genotypes. All 42 accessions were successfully identified and formed four major clusters, indicating that the SSR markers can be used for genetic diversity analysis and genetic linkage map construction. In addition, using the polymorphic bands associated with 10 markers as DNA fingerprints, we generated a manual cultivar identification diagram that can distinguish between the 42 accessions, with different individuals identifiable based on polymorphic band patterns. Conclusion: S. chinensis transcriptome data is an effective resource for developing SSR markers. These results can provide a basis for the identification of S. chinensis accessions and construction of genetic linkage maps as part of future selective breeding and conservation efforts for this valuable plant.

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Section: Discussionmentioning

confidence: 78%

EST-SSR markers identification based on RNA-sequencing and application in Schisandra chinensis

Shi¹,

Wang²,

Dongxiao³

et al. 2020

Preprint

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“…Liao et al [ 20 ] have described the 22 microsatellite loci used to generate data for the current study ( Table S2 ).…”

Section: Methodsmentioning

confidence: 99%

“…Studies on molecular markers have been carried out on M. officinalis [ 5 , 20 ]. Liao et al in particular developed an SSR marker dataset to serve in further research related to this plant.…”

Section: Introductionmentioning

confidence: 99%

Phylogenetic Analysis Based on DNA Barcoding and Genetic Diversity Assessment of Morinda officinalis How in Vietnam Inferred by Microsatellites

Pham

Nguyen

Tran

et al. 2022

Genes

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Morinda officinalis How. is well-known as a valuable medicinal plant found in some regions of Vietnam. This species is mainly used for treating male impotence, irregular menstruation, and rheumatoid arthritis. This study aimed to identify the species of and genetic diversity in three M. officinalis populations: one each in Quang Binh (QB), Thua Thien Hue (TTH), and Quang Nam (QN). In this study, four DNA barcoding markers (ITS1, ITS2, matK, and rbcL) were used to identify the species and 22 microsatellite markers were applied for population structure and diversity analyses. The results showed that the sequences of gene regions studied in M. officinalis had a high similarity (>95%) to the ITS1, ITS2, matK, and rbcL sequences of M. officinalis on BLAST. Of the four DNA barcoding markers used, ITS1 and ITS2 showed higher efficiency in DNA amplification of M. officinalis. From this study, 27 GenBank codes were published on BLAST. The results also revealed high levels of genetic diversity in populations. The average observed and expected heterozygosity values were HO = 0.513 and HE = 0.612, respectively. The average FST value was 0.206. Analysis of molecular variance (AMOVA) showed 70% variation within populations and 30% among populations. The population structure of M. officinalis inferred in STRUCTURE revealed that the optimum number of genetic groups for the admixture model was K = 2. These findings provided vital background information for future studies in the conservation of M. officinalis in both ex situ and in situ plans.

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“…Among the 50 EST-SSR primer pairs tested, 40 were successfully amplified, whereas 14 produced stable and polymorphic bands of the expected size (Table 5), with a polymorphic amplification efficiency of 28%, which is comparable to Chinese bajitian (Morinda officinalis) (24%) [40], higher than pigeonpea (Cajanus cajan) (12.9%) [26] but lower than onion (Allium cepa) (60%) [15], thorn pear (Rosa roxburghii) (54.76%) [27] and Chinese yew (Taxus chinensis) (53.23%) [22]. A total of 38 alleles were detected by 7 pairs of primers, with an average of 2.71.…”

Section: Development Of S Chinensis Est-ssr Primer Pairs and Detectimentioning

confidence: 97%

EST-SSR markers development and application in an important medicinal plant, Schisandra chinensis (Schisandraceae)

Shi

Wang

et al. 2020

Biotechnology & Biotechnological Equipment

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Schisandra chinensis, classed as a climbing woody vine, is representative of the Schisandraceae family regarded as a significant plant in Chinese herbal medicine. However, the application of molecular breeding is constrained by the fact that the number of genetic markers is small for this species. In this study, transcriptome sequencing of S. chinensis was performed using the Illumina HiSeq platform to construct a library of expressed sequence tag-simple sequence repeat (EST-SSR) markers. A total of 59,786 unigenes were obtained on the basis of 8.57 Gbp clean data. A total of 3460 putative SSR sites were detected with a frequency of 5.79%. The predominant type of repeat markers was dinucleotide (64.54%), followed by trinucleotide (23.87%), hexanucleotide (0.90%), tetranucleotide (0.12%) and pentanucleotide (0.40%). Besides, 50 pairs of EST-SSR primers were randomly selected for verification, among which 14 pairs (28%) showed polymorphism in 42 different types of S. chinensis accessions. The mean values of Na, Ne, PIC, Ho, He and SI were 2.71, 1.7642, 0.4295, 0.6016, 0.3934 and 0.6078, respectively. All of the 42 accessions were successfully identified and formed four major clusters, indicating that the EST-SSR markers are applicable for genetic diversity analysis and identification in S. chinensis. According to the result, the transcriptome data are an effective resource for developing SSR markers. These markers can provide a basis for the identification of S. chinensis accessions, genetic diversity analysis, the conservation and construction of genetic linkage maps as part of selective breeding and the conservation efforts for this valuable plant.

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Characterization and novel Est-SSR marker development of an important Chinese medicinal plant, Morinda officinalis How (Rubiaceae)

Cited by 8 publications

References 25 publications

EST-SSR markers identification based on RNA-sequencing and application in Schisandra chinensis

EST-SSR markers identification based on RNA-sequencing and application in Schisandra chinensis

Phylogenetic Analysis Based on DNA Barcoding and Genetic Diversity Assessment of Morinda officinalis How in Vietnam Inferred by Microsatellites

EST-SSR markers development and application in an important medicinal plant, Schisandra chinensis (Schisandraceae)

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