Assessment of genetic diversity in Amomum tsao-ko Crevost &amp; Lemarié, an important medicine food homologous crop from Southwest China using SRAP and ISSR markers

Ma, Mingzhu; Wang, Tiantao; Lu, Bingyue

doi:10.1007/s10722-021-01204-6

Cited by 17 publications

(14 citation statements)

References 44 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…A. tsaoko is a high-altitude medicinal crop that grows in humid forests, narrowly distributed in the southern Yunnan Province of China and northern Laos and Vietnam at high altitudes between 1100 and 1800 m in mountainous regions [ 16 , 17 ]. Due to excessive harvesting and the destruction of the original habitat of A. tsaoko , wild resources are almost extinct, and it was listed as a “Nearly Endangered Species” on the IUCN Red List in 2012.…”

Section: Introductionmentioning

confidence: 99%

De novo transcriptome assembly, gene annotation, and EST-SSR marker development of an important medicinal and edible crop, Amomum tsaoko (Zingiberaceae)

Meng

Lei

et al. 2022

BMC Plant Biol

Self Cite

View full text Add to dashboard Cite

Background Amomum tsaoko is a medicinal and food dual-use crop that belongs to the Zingiberaceae family. However, the lack of transcriptomic and genomic information has limited the understanding of the genetic basis of this species. Here, we performed transcriptome sequencing of samples from different A. tsaoko tissues, and identified and characterized the expressed sequence tag-simple sequence repeat (EST-SSR) markers. Results A total of 58,278,226 high-quality clean reads were obtained and de novo assembled to generate 146,911 unigenes with an N50 length of 2002 bp. A total of 128,174 unigenes were successfully annotated by searching seven protein databases, and 496 unigenes were identified as annotated as putative terpenoid biosynthesis-related genes. Furthermore, a total of 55,590 EST-SSR loci were detected, and 42,333 primer pairs were successfully designed. We randomly selected 80 primer pairs to validate their polymorphism in A. tsaoko; 18 of these primer pairs produced distinct, clear, and reproducible polymorphisms. A total of 98 bands and 96 polymorphic bands were amplified by 18 pairs of EST-SSR primers for the 72 A. tsaoko accessions. The Shannon's information index (I) ranged from 0.477 (AM208) to 1.701 (AM242) with an average of 1.183, and the polymorphism information content (PIC) ranged from 0.223 (AM208) to 0.779 (AM247) with an average of 0.580, indicating that these markers had a high level of polymorphism. Analysis of molecular variance (AMOVA) indicated relatively low genetic differentiation among the six A. tsaoko populations. Cross-species amplification showed that 14 of the 18 EST-SSR primer pairs have transferability between 11 Zingiberaceae species. Conclusions Our study is the first to provide transcriptome data of this important medicinal and edible crop, and these newly developed EST-SSR markers are a very efficient tool for germplasm evaluation, genetic diversity, and molecular marker-assisted selection in A. tsaoko.

show abstract

Section: Introductionmentioning

confidence: 99%

De novo transcriptome assembly, gene annotation, and EST-SSR marker development of an important medicinal and edible crop, Amomum tsaoko (Zingiberaceae)

Meng

Lei

et al. 2022

BMC Plant Biol

Self Cite

View full text Add to dashboard Cite

show abstract

“…Currently, ISSR techniques have been widely used in the identification and analysis of Chinese medicines such as A . tsao-ko Crevost & Lemariéand [ 21 ] and Alpinia oxyphylla [ 36 ]. Zhang et al [ 30 ] analysed 23 samples of A .…”

Section: Discussionmentioning

confidence: 99%

“…In recent years, DNA-based molecular markers have become necessary to study the germplasm diversity of certain traditional Chinese medicine, and various molecular markers such as random amplified polymorphic DNA (RAPD) [16,17], simple sequence repeats (SSR) [18,19] and inter-simple sequence repeat (ISSR) [20][21][22] have been used to distinguish between different germplasm of the same herb. Compared with other technologies, ISSR is simple to operate, rich in polymorphism, reproducible and stable [23,24], and has been widely used in plant variety identification, genetic diversity analysis, molecular breeding and other fields [25,26] In this paper, the genetic diversity of A. villosum from different populations of genuine producing area and non-genuine producing area was analyzed using ISSR techniques, and the comprehensive quality of the collected samples was assessed by combining with TOPSIS model, with the aim of providing a theoretical basis for screening out excellent germplasm of A. villosum and expanding the cultivation range of excellent germplasm for the healthy development of A. villosum industry.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Research on germplasm diversity of Amomum villosum. Lour in genuine producing area

Yang²,

Li³

et al. 2022

PLoS ONE

View full text Add to dashboard Cite

Background Genuine Chinese medicine is produced from medicinal plant cultivated in a specific region and is of better quality and efficacy, more consistently qualified and famous than that from the same medicinal plant cultivated in other regions. The cultivating region of genuine medicinal plant is known as the genuine producing area. Yangchun City, which is in Guangdong Province of China, is a genuine producing area for the famous Chinese medicine Amomi Fructus (also called Sharen). Amomi Fructus is the ripe and dry fruit of the Zingiberaceae plant A. villosum Lour.. A. villosum was introduced from the Persian Gulf region and has been cultivated in China for over 1000 years. Until now there are no reports on screening for good germplasm of A. villosum. Methods The contents of volatile oil and bornyl acetate of Amomi Fructus from 14 populations were determined with GC method, and the relative contents of the main chemical components in the volatile oils were determined with GC-MS method. Evaluation and variance analysis of the comprehensive quality of the 14 samples were conducted by means of a multi-indicator entropy-weight TOPSIS model (Technique for Order Preference by Similarity to an Ideal Solution) combined with OPLS-DA (Orthogonal Partial Least Squares Discrimination Analysis) and HCA (Hierarchical Clustering Analysis). The ISSR (Inter-Simple Sequence Repeat) molecular marker technique and the UPGMA (unweighted pair-group method with arithmetic means) were employed to analyze the genetic relationship among A. villosum populations. Results The contents of volatile oil and bornyl acetate differed significantly among the different populations, but the main chemical component in the volatile oil was the same in all the samples, which was bornyl acetate. OPLS-DA results showed that 9 indicators were the main factors influencing the quality differences among the 14 populations. The entropy-weight TOPSIS results showed that there were significant differences in the comprehensive qualities of the 12 populations from the genuine producing area. The best quality of fruit was found in the genuine producing area of Chunwan Town; the qualities of 33% of genuine fruits were lower than that of non-genuine fruits. Twenty-three DNA fragments were obtained by ISSR-PCR amplification using four ISSR primers, eleven of which were polymorphic loci, which accounted for 47.8%. The similarity coefficients (GS) of different populations of A. villosum ranged from 0.6087 to 0.9565. Conclusion There are significant differences among different populations of A. villosum in terms of the kinds of major chemical components and their contents, comprehensive quality and genetic diversity. The germplasm resources of A. villosum are rich in the genuine producing area. It means superior germplasm could be selected in the area. The comprehensive quality of the fruit of A. villosum from the non-genuine producing area is better than some of that from genuine producing area, proving that the non-genuine producing area can also produce Amomi Fructus with excellent quality.

show abstract

“…Germplasm is the foundation of good variety breeding. Breeding efficiency depends on the number of germplasm resources and the genetic diversity of these resources [14]. As mentioned above, various marker techniques are developed to evaluate genetic diversity [13].…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity and Chemicals Profile of Ginger (Zingiber officinale Roscoe) in Indonesia

Subositi¹,

Widodo²,

Mujahid³

et al. 2022

International Journal on Advanced Science, Engineering and Information Technology

View full text Add to dashboard Cite

Zingiber officinale is a medicinal plant used to treat various ailments by many ethnic groups in Indonesia. Information on genetic variation and chemical profiling of this plant, especially in the traditional herbal formula in Indonesia, is still limited. The objective of this study was to determine genetic variation and chemical profiling of Zingiber officinale accessions to compile database information. Inter-Simple Sequence Repeats (ISSR) were used to evaluate the genetic diversity of Z. officinale, and Fourier transforms infrared (FTIR) was used to analyze chemical profiling. Dice index similarity was used to calculate a similarity index between accessions, and Unweighted Pair Group Method Using Arithmetic Mean (UPGMA) was used to construct a dendrogram. The ISSR method for genetic profiling proved that Z. officinale from 14 selected ethnic groups were divided into three clusters. The similarity index among Z. officinale accessions ranged from 0.567 to 0.971, indicating high genetic diversity. The high degree of genetic variety detected by ISSR markers demonstrated the marker's efficiency in detecting variation in this Z. offcinale germplasm collection. The FTIR technique's phytochemical profile of Z. officinale analysis shows slight differences in spectra and can be grouped into three clusters. There was no correlation of clustering of Z. officinale accessions between geographical origins based on genetic and chemical profiles. Our findings may be valuable information for breeding, conservation, and utilization of Z. officinale.

show abstract

Assessment of genetic diversity in Amomum tsao-ko Crevost & Lemarié, an important medicine food homologous crop from Southwest China using SRAP and ISSR markers

Cited by 17 publications

References 44 publications

De novo transcriptome assembly, gene annotation, and EST-SSR marker development of an important medicinal and edible crop, Amomum tsaoko (Zingiberaceae)

De novo transcriptome assembly, gene annotation, and EST-SSR marker development of an important medicinal and edible crop, Amomum tsaoko (Zingiberaceae)

Research on germplasm diversity of Amomum villosum. Lour in genuine producing area

Genetic Diversity and Chemicals Profile of Ginger (Zingiber officinale Roscoe) in Indonesia

Contact Info

Product

Resources

About