The origin and germplasm collection for cultivated Dendrobium officinale K. Kimura &amp; Migo individuals revealed by EST-SSR markers

Xie, Jiankun; Zuo, Junhua; Huang, Yunhong; Li, Changsheng; Chen, Yaling

doi:10.1007/s10722-020-00906-7

Cited by 9 publications

(9 citation statements)

References 34 publications

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“…Xie et al [ 28 ] indicated that the origin of market individuals were derived from Shenglan8 , and our previous observation showed that Shenglan8 and Longhu1 had high seed setting rate of cross-pollination. So, we selected Shenglan8 for self-pollination and Shenglan8 cross-pollination with Longhu1 to explore cytological and transcriptome comparative phenomena of self-pollination and cross-pollination in D. officinale.…”

Section: Methodsmentioning

confidence: 95%

Cytological Observation and Transcriptome Comparative Analysis of Self-Pollination and Cross-Pollination in Dendrobium Officinale

Chen

Zhang

et al. 2021

Genes

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Dendrobium officinale is a rare and traditional medicinal plant with high pharmacological and nutritional value. The self-incompatibility mechanism of D. officinale reproductive isolation was formed in the long-term evolution process, but intraspecific hybridization of different germplasm resources leads to a large gap in the yield, quality, and medicinal value of D. officinale. To investigate the biological mechanism of self-incompatibility in D. officinale, cytological observation and the transcriptome analysis was carried out on the samples of self-pollination and cross-pollination in D. officinale. Results for self-pollination showed that the pollen tubes could grow in the style at 2 h, but most of pollen tubes stopped growing at 4 h, while a large number of cross-pollinated pollen tubes grew along the placental space to the base of ovary, indicating that the self-incompatibility of D. officinale may be gametophyte self-incompatibility. A total of 63.41 G basesum of D. officinale style samples from non-pollinated, self-pollination, and cross-pollination by RNA-seq were obtained, and a total of 1944, 1758, and 475 differentially expressed genes (DEGs) in the comparison of CK (non-pollinated) vs. HF (cross-pollination sample), CK vs. SF (self-pollination sample) and SF vs. HF were identified, respectively. Forty-one candidate genes related to self-incompatibility were found by function annotation of DEGs, including 6 Ca2+ signal genes, 4 armed repeat containing (ARC) related genes, 11 S-locus receptor kinase (SRK) related genes, 2 Exo70 family genes, 9 ubiquitin related genes, 1 fatty acid related gene, 6 amino acid-related genes, 1 pollen-specific leucine-rich repeat extensin-like protein (LRX) related gene and 1 lectin receptor-like kinases (RLKs) related gene, showed that self-incompatibility mechanism of D. officinale involves the interaction of multiple genes and pathways. The results can provide a basis for the study of the self-incompatibility mechanism of D. officinale, and provide ideas for the preservation and utilization of high-quality resources of D. officinale.

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Section: Methodsmentioning

confidence: 95%

Cytological Observation and Transcriptome Comparative Analysis of Self-Pollination and Cross-Pollination in Dendrobium Officinale

Chen

Zhang

et al. 2021

Genes

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“…In addition, the categories of volatile compounds and the content of medicinal components in JA1 from Jiangxi were also high. Xie [29] showed that the origin of market-collected individuals was derived from Zhejiang and the germplasm resources from Jiangxi were well preserved, so the germplasm resources from Jiangxi should be exploited efficiently for breeding superior D. officinale individuals.…”

Section: Discussionmentioning

confidence: 99%

“…Our previous results showed that genetic diversity of D. officinale varies between different regions, most of the D. officinale in the market were derived from Zhejiang and the germplasm resources from Jiangxi were well preserved [29], so D. officinale germplasm resources from Zhejiang, Yunnan, Jiangxi and Fujian were collected as experimental materials. All the experimental materials were cultivated in the greenhouse.…”

Section: Plant Materialsmentioning

confidence: 99%

Variability of Volatile Compounds in the Medicinal Plant Dendrobium officinale from Different Regions

Huang

Zhang

et al. 2020

Molecules

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Dendrobium officinale Kimura et Migo, a rare and traditional medicinal plant, contains many nutrients such as polysaccharides, alkaloids, amino acids and so on. Different growth environment and intraspecific hybridization of different germplasm resources lead to large differences in the yield, quality and medicinal value of D. officinale. Here, the volatile compounds of D. officinale from four producing regions (Zhejiang, Fujian, Yunnan and Jiangxi) were analyzed to provide a certain reference value for the selection of a specific medicinal component in D. officinale breeding. Fresh stems of D. officinale germplasm resources were collected, and the chemical constituents were determined by gas chromatography-mass spectrometry. A total of 101 volatile compounds were identified, of which esters and alcohols accounted for 23 and 22. Hexacosane is the highest relative content of all volatile components. The highest content of hexacosane was observed in YA1 from Yunnan was 34.41%, and the lowest (23.41%) in JA1 from Jiangxi. Moreover, 5-10 unique substances were determined in different regions. A total of 17 medicinal components were detected, and three unique medicinal components were detected only in YA1, revealing that YA1 can provide raw materials for the application of specific medicinal substances extraction. A total of four toxic components were detected, but no toxic components were detected in JA1 from Jiangxi, suggested that the germplasm resources from Jiangxi could be exploited efficiently for breeding superior D. officinale specimens. The results provide a theoretical basis for the collection, protection and utilization of D. officinale germplasm resources in different regions.

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“…We recognized functional annotations matching each unique transcript by searching NR [17], NT, Protein families (Pfam) (http://pfam.xfam.org) KOG (http://www.ncbi. nlm.nih.gov/COG/) [18], Swiss-prot (http://www.ebi.ac.uk/uniprot/) [19], KEGG (http: //www.genome.jp/kegg/) [20] and GO [21]. We used BLAST software (with "1e-10" e-value) in the NT database using Diamond BLASTX v2.7.1 (ftp://ftp.ncbi.nlm.nih.gov/ blast/executables/blast+/LATEST/).…”

Section: Functional Annotation Of Transcriptsmentioning

confidence: 99%

“…All 726,846 unique SMRT transcripts were functionally annotated by seven data storages, such as gene ontology (GO), eukaryotic ortholog groups (KOG), Protein family (Pfam), Swissport (15), COG (17), COG (18) and KEGG (20) by using BLAST (7) software (version 2.2.26) (Table 3). By comparing the transcript sequence to NR with homologous species, among them are Vitis vinifera (12,056), Sesamum indicum (2559), Coffea canephora (2431) and Theobroma cacao (2319), which were the top four distributed species of transcripts, as shown in Figure 5.…”

Section: Functional Annotation Of Transcriptsmentioning

confidence: 99%

Functional Annotation of a Full-Length Transcriptome and Identification of Genes Associated with Flower Development in Rhododendron simsii (Ericaceae)

Liu

Liaquat

et al. 2021

Plants

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Rhododendronsimsii is one of the top ten famous flowers in China. Due to its historical value and high aesthetic, it is widely popular among Chinese people. Various colors are important breeding objectives in Rhododendron L. The understanding of the molecular mechanism of flower color formation can provide a theoretical basis for the improvement of flower color in Rhododendron L. To generate the R. simsii transcriptome, PacBio sequencing technology has been used. A total of 833,137 full-length non-chimeric reads were obtained and 726,846 high-quality full-length transcripts were found. Moreover, 40,556 total open reading frames were obtained; of which 36,018 were complete. In gene annotation analyses, 39,411, 18,565, 16,102 and 17,450 transcriptions were allocated to GO, Nr, KEGG and COG databases, correspondingly. To identify long non-coding RNAs (lncRNAs), we utilized four computational methods associated with Protein families (Pfam), Cooperative Data Classification (CPC), Coding Assessing Potential Tool (CPAT) and Coding Non Coding Index (CNCI) databases and observed 6170, 2265, 4084 and 1240 lncRNAs, respectively. Based on the results, most genes were enriched in the flavonoid biosynthetic pathway. The eight key genes on the anthocyanin biosynthetic pathway were further selected and analyzed by qRT-PCR. The F3′H and ANS showed an upward trend in the developmental stages of R. simsii. The highest expression of F3′5′H and FLS in the petal color formation of R. simsii was observed. This research provided a huge number of full-length transcripts, which will help to proceed genetic analyses of R. simsii. native, which is a semi-deciduous shrub.

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The origin and germplasm collection for cultivated Dendrobium officinale K. Kimura & Migo individuals revealed by EST-SSR markers

Cited by 9 publications

References 34 publications

Cytological Observation and Transcriptome Comparative Analysis of Self-Pollination and Cross-Pollination in Dendrobium Officinale

Cytological Observation and Transcriptome Comparative Analysis of Self-Pollination and Cross-Pollination in Dendrobium Officinale

Variability of Volatile Compounds in the Medicinal Plant Dendrobium officinale from Different Regions

Functional Annotation of a Full-Length Transcriptome and Identification of Genes Associated with Flower Development in Rhododendron simsii (Ericaceae)

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