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Development and characterization of novel EST-SSR markers for Gentiana straminea Maxim., a traditional Tibetan herb in China and cross-amplification in related species

Published online by Cambridge University Press:  09 May 2024

Tingfeng Cheng ,
Pengcheng Lin ,
Dangwei Zhou Open the ORCID record for Dangwei Zhou [Opens in a new window] ,
Huan Wang ,
Shengbo Shi ,
Jianwei Shen ,
Jing Meng ,
Xing Ye ,
Kun Zheng  and
Xingqiang Hu
...Show all authors
Tingfeng Cheng
Affiliation:
Key Laboratory of Qinghai-Tibetan Plateau Biological Resource Diversity and Protection, State Commission of Nationalities and Religions, Xining 810007, China Key Laboratory of Adaptation and Evolution of Plateau Biota (AEPB), Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
Pengcheng Lin
Affiliation:
Key Laboratory of Qinghai-Tibetan Plateau Biological Resource Diversity and Protection, State Commission of Nationalities and Religions, Xining 810007, China
Dangwei Zhou*
Affiliation:
Key Laboratory of Qinghai-Tibetan Plateau Biological Resource Diversity and Protection, State Commission of Nationalities and Religions, Xining 810007, China Key Laboratory of Adaptation and Evolution of Plateau Biota (AEPB), Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
Huan Wang
Affiliation:
Key Laboratory of Adaptation and Evolution of Plateau Biota (AEPB), Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
Shengbo Shi
Affiliation:
Key Laboratory of Adaptation and Evolution of Plateau Biota (AEPB), Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
Jianwei Shen
Affiliation:
Key Laboratory of Adaptation and Evolution of Plateau Biota (AEPB), Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
Jing Meng
Affiliation:
Key Laboratory of Qinghai-Tibetan Plateau Biological Resource Diversity and Protection, State Commission of Nationalities and Religions, Xining 810007, China
Xing Ye
Affiliation:
Key Laboratory of Qinghai-Tibetan Plateau Biological Resource Diversity and Protection, State Commission of Nationalities and Religions, Xining 810007, China
Kun Zheng
Affiliation:
Key Laboratory of Qinghai-Tibetan Plateau Biological Resource Diversity and Protection, State Commission of Nationalities and Religions, Xining 810007, China
Xingqiang Hu
Affiliation:
Key Laboratory of Qinghai-Tibetan Plateau Biological Resource Diversity and Protection, State Commission of Nationalities and Religions, Xining 810007, China
Yuanwen Zhuang
Affiliation:
Key Laboratory of Qinghai-Tibetan Plateau Biological Resource Diversity and Protection, State Commission of Nationalities and Religions, Xining 810007, China
*
Corresponding author: Dangwei Zhou; Email: dangweizhou@sina.com
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Abstract

Gentiana straminea Maxim. (Gentianaceae) is an important traditional Tibetan herb that is mainly distributed on the Qinghai-Tibetan Plateau. Despite its agricultural and pharmacological importance, there remains a paucity of microsatellite markers, particularly expressed sequence tag-simple sequence repeat (EST-SSR) markers, available for this local endemic species. In this study, based on previous Illumina transcriptome data of G. straminea, a total of 96 EST-SSR markers were initially designed and tested. Thirty-two of 96 loci (33.33%) were successfully amplified and verified for validation. Among them, 10 were polymorphic and had clear bands. The polymorphism information content values were 0.09–0.799, the number of alleles per locus ranged from 3 to 14, and the levels of observed and expected heterozygosity were 0.078–0.722 and 0.238–0.884, respectively, which suggested a high level of information. Moreover, cross-amplification was successful for 10 loci in two other related species, Gentiana macrophylla Pallas and Gentiana dahurica Fischer. These EST-SSR markers provide a valuable tool for investigating the genetic diversity related to quantitative traits and population genetic studies on G. straminea and related species in sect. Cruciata Gaudin.

Keywords

cross-speciesEST-SSR markerGentiana straminea Maximpolymorphismsect. Cruciata Gaudin
Type
Short Communication
Information
Plant Genetic Resources , Volume 22 , Issue 4 , August 2024 , pp. 258 - 263
Copyright
Copyright © The Author(s), 2024. Published by Cambridge University Press on behalf of National Institute of Agricultural Botany

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References

Cai, K, Zhu, LF, Zhang, KK, Li, L, Zhao, ZY, Zeng, W and Lin, XC (2019) Development and characterization of EST-SSR markers from RNA-Seq data in Phyllostachys violascens. Frontier in Plant Sciences 10, 50.10.3389/fpls.2019.00050CrossRefGoogle ScholarPubMed
Cao, XY (2010) Study on ‘Qinjiao’ germplasm resource (Dissertation). ShannXi Normal University.Google Scholar
Chapman, MA (2019) Optimizing depth and type of high-throughput sequencing data for microsatellite discovery. Application in Plant Sciences 7, e11298.10.1002/aps3.11298CrossRefGoogle ScholarPubMed
Cheng, TF, Wang, H, Zhou, DW, Chen, SL, Wang, JL, Shi, SB, Shen, JW and Lei, TX (2019) Advance of genetic diversity studies on the Chinese traditional herb ‘Qinjiao’. Chinese Traditional Herbal and Drugs 50, 3720–3728.Google Scholar
Chinese Pharmacopoeia Commission (2015) Pharmacopoeia of People's Republic of China. Beijing: China Medical Science Press.Google Scholar
Collard, BCY and Mackill, DJ (2008) Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Philosophical Transactions – Royal Society. Biological Sciences 363, 557–572.10.1098/rstb.2007.2170CrossRefGoogle ScholarPubMed
Čortan, D, Krak, K, Vít, P and Mandák, B (2019) Development, characterization, and cross-amplification of 17 microsatellite markers for Filipendula vulgaris. Applications in Plant Sciences 7, e11307.10.1002/aps3.11307CrossRefGoogle ScholarPubMed
Deng, TX, Pang, CY, Lu, XR, Zhu, P, Duan, AQ, Tan, ZZ, Huang, J, Li, H, Chen, MT and Liang, XW (2016) De novo transcriptome assembly of the Chinese swamp buffalo by RNA sequencing and SSR marker discovery. PLoS ONE 11, e0147132.10.1371/journal.pone.0147132CrossRefGoogle ScholarPubMed
Doyle, JJ and Doyle, JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bulletin 19, 11–15.Google Scholar
Ho, TN and Liu, SW (2001) A Worldwide Monograph of Gentiana. Beijing: Science Press.Google Scholar
Kalia, RK, Rai, MK, Kalia, S, Singh, R and Dhawan, AK (2011) Microsatellite markers: an overview of the recent progress in plants. Euphytica 177, 309–334.10.1007/s10681-010-0286-9CrossRefGoogle Scholar
Kalinowski, ST, Taper, ML and Marshall, TC (2007) Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Molecular Ecology 16, 1099–1106.10.1111/j.1365-294X.2007.03089.xCrossRefGoogle ScholarPubMed
Koelliker, R, Enkerli, JÜR and Widmer, F (2006) Characterization of novel microsatellite loci for red clover (Trifolium pratense L.) from enriched genomic libraries. Molecular Ecology Notes 6, 50–53.10.1111/j.1471-8286.2005.01133.xCrossRefGoogle Scholar
Li, Y, Li, LF, Chen, GQ and Ge, XJ (2007) Development of ten microsatellite loci for Gentiana crassicaulis (Gentianaceae). Conservation Genetics 8, 1499–1501.10.1007/s10592-007-9313-3CrossRefGoogle Scholar
Li, X, Yang, H and Liu, J (2008) Genetic variation within and between populations of the Qinghai-Tibetan Plateau endemic Gentiana straminea (Gentianaceae) revealed by RAPD markers. Belgian Journal of Botany 141, 95–102.Google Scholar
Liu, J, Yan, HF and Ge, XJ (2016) The use of DNA barcoding on recently diverged species in the genus Gentiana (Gentianaceae) in China. PLoS ONE 11, e0153008.10.1371/journal.pone.0153008CrossRefGoogle ScholarPubMed
Luo, K, Ma, P, Yao, H, Xin, T, Hu, Y, Zheng, S, Huang, LF, Liu, J and Song, J (2012) Identification of Gentianae macrophyllae radix using the ITS2 barcodes. Acta Pharmacologica Sinica 47, 1710–1717.Google ScholarPubMed
Malhotra, EV, Jain, R and Bansal, S (2021) Development of a new set of genic SSR markers in the genus Gentiana: in silico mining, characterization and validation. 3 Biotech 11, 430.10.1007/s13205-021-02969-4CrossRefGoogle ScholarPubMed
Meng, J, Chen, XF, Song, JH, Yao, RY, Li, ZF, Zeng, Y, Li, Y and Cheng, T (2013) Research progress in classification and identification of Sect. Cruciata Gaudin in Gentiana (Tourn.) L. Chinese Traditional Herbal and Drugs 44, 330–2335.Google Scholar
Miah, G, Rafii, MY, Ismail, MR, Puteh, AB, Rahim, HA, Islam, KN and Latif, MA (2013) A review of microsatellite markers and their applications in rice breeding programs to improve blast disease resistance. International Journal of Molecular Sciences 14, 22499–22528.10.3390/ijms141122499CrossRefGoogle ScholarPubMed
Rozen, S and Skaletsky, H (2000) Primer3 on the WWW for general users and for biologist programmers. In Misener, S and Krawetz, SA (eds), Methods in Molecular Biology, 132, Bioinformatics: Methods and Protocols. Totowa, New Jersey: Humana Press, pp. 365–386.Google Scholar
Wang, YM, Xu, M, Wang, D, Yang, CR, Yang, Z and Zhang, YJ (2013) Anti-inflammatory compounds of ‘Qin-Jiao’, the roots of Gentiana dahurica (Gentianaceae). Journal of Ethnopharmacology 147, 341–348.10.1016/j.jep.2013.03.016CrossRefGoogle ScholarPubMed
Wang, YP, Ahmad, B, Duan, BZ, Zeng, R and Huang, LF (2016) Chemical and genetic comparative analysis of Gentiana crassicaulis and Gentiana macrophylla. Chemistry and Biodiversity 13, 776–781.10.1002/cbdv.201500247CrossRefGoogle ScholarPubMed
Wang, L, Zhao, ZL, Ni, LH, Gaawe, D and Mi, M (2017) Assessment of genetic diversity on Gentiana straminea based on ISSR markers. Chinese Traditional Herbal and Drugs 15, 3168–3174.Google Scholar
Wu, LH, Bligh, SWA, Leon, CJ, Li, XS, Wang, ZT, Branford-White, CJ and Simmonds, MSJ (2012) Chemotaxonomically significant roburic acid from section Cruciata of Gentiana. Biochemical Systematics and Ecology 43, 152–155.10.1016/j.bse.2012.03.008CrossRefGoogle Scholar
Xie, K, Wang, Z, Guo, Y, Zhang, C, Zhu, W and Hou, F (2022) Gentiana straminea supplementation improves feed intake, nitrogen and energy utilization, and methane emission of Simmental calves in northwest China. Animal Bioscience 35, 838–846.10.5713/ab.21.0263CrossRefGoogle ScholarPubMed
Yang, SP, Zhong, QW, Tian, J, Wang, LH, Zhao, ML, Li, L and Sun, XM (2018) Characterization and development of EST-SSR markers to study the genetic diversity and populations analysis of Jerusalem Artichoke (Helianthus Tuberosus L.). Genes & Genomics 40, 1023–1032.10.1007/s13258-018-0708-yCrossRefGoogle Scholar
Yeh, FC, Yang, RC, Boyle, TBJ, Ye, ZH and Mao, JX (1997) POPGENE, the User-Friendly Shareware for Population Genetic Analysis. Edmonton, Canada: University of Alberta.Google Scholar
Yu, K, Park, SJ, Poysa, V and Gepts, P (2000) Integration of Simple Sequence Repeat (SSR) markers into a molecular linkage map of common bean (Phaseolus vulgaris L.). Journal of Heredity 91, 429–434.10.1093/jhered/91.6.429CrossRefGoogle ScholarPubMed
Yuan, YM (1993) Karyological studies on Gentiana section Cruciata Gaudin (Gentianaceae) from China. Caryologia 46, 99–114.10.1080/00087114.1993.10797252CrossRefGoogle Scholar
Zheng, X, Cheng, T, Yang, L, Xu, J, Tang, J, Xie, K, Huang, X, Bao, Z, Zheng, X, Diao, Y, You, Y and Hu, Z (2019) Genetic diversity and DNA fingerprints of three important aquatic vegetables by EST-SSR markers. Scientific Reports 9, 14074.10.1038/s41598-019-50569-3CrossRefGoogle ScholarPubMed
Zhou, DW, Gao, S, Wang, H, Chen, SL, Shen, JW, Gao, J, Lei, TX, Yin, J and Liu, JQ (2016) De novo sequencing transcriptome of endemic Gentiana straminea (Gentianaceae) to identify genes involved in the biosynthesis of active ingredients. Gene 575, 160–170.10.1016/j.gene.2015.08.055CrossRefGoogle ScholarPubMed
Zhou, DW, Lv, DJ, Zhang, H, Cheng, TF, Wang, H, Lin, PC, Shi, SB, Chen, SL and Shen, JW (2021) Quantitative analysis of the profiles of twelve major compounds in Gentiana straminea Maxim. Roots by LC-MS/MS in an extensive germplasm survey in the Qinghai-Tibetan plateau. Journal of Ethnopharmacology 280, 114068.10.1016/j.jep.2021.114068CrossRefGoogle Scholar
Zhou, T, Zhao, YM, Zhou, LP, Chen, XD, Jia, Y and Bai, GQ (2023) Comparative transcriptome analyses of three Gentiana species provides signals for the molecular footprints of selection effects and the phylogenetic relationships. Molecular Genetics and Genomics 298, 399–411.10.1007/s00438-022-01991-2CrossRefGoogle ScholarPubMed
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