Article(id=1304414889766834349, tenantId=1146029695717560320, journalId=1302319053441957962, issueId=1304414858296971266, articleNumber=null, orderNo=null, doi=10.7501/j.issn.0253-2670.2026.06.022, pmid=null, cstr=null, oa=null, hot=0, price=null, onlineType=0, articleFormat=0, articleType=null, articleTypeStr=null, receivedDate=1762099200000, receivedDateStr=2025-11-03, revisedDate=null, revisedDateStr=null, acceptedDate=null, acceptedDateStr=null, onlineDate=1788926344577, onlineDateStr=2026-09-09, pubDate=null, pubDateStr=null, doiRegisterDate=null, doiRegisterDateStr=null, onlineIssueDate=1788926344577, onlineIssueDateStr=2026-09-09, onlineJustAcceptDate=null, onlineJustAcceptDateStr=null, onlineFirstDate=null, onlineFirstDateStr=null, sourceXml=null, magXml=null, createTime=1788926344577, creator=13701087609, updateTime=1788926344577, updator=13701087609, issue=Issue{id=1304414858296971266, tenantId=1146029695717560320, journalId=1302319053441957962, year='2026', volume='57', issue='6', pageStart='2009', pageEnd='2444', issueExtLink='null', onlineDate='null', pubDate='1774627200000', pubDateStr='2026-03-28', beforeIssueId=null, nextIssueId=null, price=null, status=1, issueComplete=1, articleOrder=1, issueType=-1, specialIssue=null, createTime=1788926337074, creator='13701087609', updateTime=1788926665348, updator='13701087609', preIssue=null, nextIssue=null, articleTotal=null, ext={EN=IssueExt(id=1304416235240841997, tenantId=1146029695717560320, journalId=1302319053441957962, issueId=1304414858296971266, language=EN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=), CN=IssueExt(id=1304416235240841998, tenantId=1146029695717560320, journalId=1302319053441957962, issueId=1304414858296971266, language=CN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=)}, issueFiles=null, downloadFileDto=null}, startPage=2278, endPage=2288, ext={EN=ArticleExt(id=1304414890077212847, articleId=1304414889766834349, tenantId=1146029695717560320, journalId=1302319053441957962, language=EN, title=Identification and development of SSR molecular markers in the Platostoma palustre genome and analysis of germplasm genetic diversity, columnId=null, journalTitle=Chinese Traditional and Herbal Drugs, columnName=null, runingTitle=null, highlight=null, articleAbstract=Objective This study aimed to develop SSR molecular markers for Platostoma palustre and analyze the genetic diversity of its germplasm resources, so as to provide theoretical support for the conservation of P. palustre germplasm resources and the breeding of elite varieties. Methods Based on the whole-genome sequence of P. palustre, the distribution characteristics of simple sequence repeats (SSRs) were mined and analyzed, and polymorphic SSR primers were developed to provide a theoretical basis for the evaluation of genetic diversity and analysis of population structure in P. palustre. Results A total of 122,699 SSR loci were identified in the P. palustre genome, with a genomic SSR density of 96.91 loci/Mb and a locus occurrence frequency of 10.32 kb/SSR. Dinucleotide repeat motifs were the dominant type, accounting for 68.3% of all repeat motifs. After polymorphism screening, 15 pairs of SSR primers with good polymorphism were obtained. Their polymorphism information content (PIC) ranged from 0.197 to 0.736, with an average value of 0.425. Genetic diversity analysis of 40 P. palustre germplasms showed that the number of alleles at the 15 SSR loci was higher than the number of effective alleles, and the alleles were unevenly distributed. There were differences in heterozygosity among different loci; the average observed heterozygosity was higher than the average expected heterozygosity with a certain gap between them, indicating that the tested population deviated from the Hardy-Weinberg equilibrium (HWE), with genetic variation and favorable overall genetic diversity, and the genotype frequencies of some loci in the population changed. Fixation index (F) analysis showed that F > 0 at 3 loci and F < 0 at 12 loci, indicating that the number of heterozygous individuals was higher than that of homozygous individuals in the population. The Shannon’s information index (I) ranged from 0.449 (TDF191) to 1.628 (TDF166), with an average of 0.887. A phylogenetic tree of the 40 P. palustre germplasms was constructed using Phylip software based on the UPGMA method, which divided the germplasms into two subgroups. A “0/1” DNA fingerprint was successfully constructed by digital assignment coding. Conclusion The abundant SSR loci information obtained in this study can provide important theoretical and technical support for the development of whole-genome SSR markers, molecular marker-assisted breeding, and genetic diversity research of P. palustre., authors=LI Jingchun, QUAN Changqian, XU Meihua, WEI Fan, HUANG Shasha, TANG Danfeng, authorsList=LI Jingchun, QUAN Changqian, XU Meihua, WEI Fan, HUANG Shasha, TANG Danfeng, authorCompany=null, correspAuthors=null, authorNote=null, correspAuthorsNote=null, copyrightStatement=null, copyrightOwner=null, extLink=null, articleAbsUrl=null, sourceXml=null, magXml=null, pdfUrl=null, pdf=null, pdfFileSize=null, pdfExtLink=null, richHtmlUrl=null, mobilePdfUrl=null, reviewReport=null, pdfFirstPage=null, abstractGraph=null, abstractGraphContent=null, abstractVideo=null, citation=null, cebUrl=null, magXmlContent=null, mapNumber=null, fund=null), CN=ArticleExt(id=1304414889993326766, articleId=1304414889766834349, tenantId=1146029695717560320, journalId=1302319053441957962, language=CN, title=凉粉草基因组SSR分子标记开发与种质遗传多样性分析, columnId=1304140203967410414, journalTitle=中草药, columnName=药材与资源, runingTitle=null, highlight=null, articleAbstract=目的 开发凉粉草（Platostoma palustre）SSR分子标记，分析其种质资源的遗传多样性，为凉粉草种质资源保护与优良品种选育提供理论支撑。方法 基于凉粉草全基因组序列，挖掘并分析简单重复序列（simple sequence repeats，SSRs）的分布特征，开发多态性SSR引物，为凉粉草遗传多样性评价和群体结构解析提供理论依据。结果 凉粉草基因组中共鉴定出122 699个SSR位点，基因组SSR密度为96.91个/Mb，位点发生频率为10.32 kb/SSR，其中二核苷酸重复基序为优势类型，占总重复基序的68.3%。经过多态性筛选，获得15对多态性较好的SSR引物，其多态性信息指数（polymorphism information content，PIC）介于0.197～0.736，平均值为0.425。对40份凉粉草种质的遗传多样性分析显示，15个SSR位点的等位基因数高于有效等位基因数，等位基因分布呈不均匀分布特征；各位点杂合度存在差异，平均观测杂合度高于平均期望杂合度，二者平均值存在一定差距，表明供试群体偏离了哈迪-温伯格平衡（Hardy-Weinberg equilibrium，HWE），存在遗传变异，整体遗传多样性较好，且群体内部分基因型频率发生改变。固定指数（F）分析结果表明，3个位点的F＞0，12个位点的F＜0，说明种群内杂合个体数量多于纯合个体。香农指数（I）的数值范围为0.449（TDF191）～1.628（TDF166），平均值为0.887。基于UPGMA法，利用Phylip软件构建40份凉粉草种质的系统发育树，可将其划分为2个亚群；通过数字赋值编码，成功构建“0/1”型DNA指纹图谱。结论 获得的大量SSR位点信息，可为凉粉草全基因组SSR标记开发、分子标记辅助育种以及遗传多样性研究提供重要的理论与技术支撑。, authors=李静纯1,2, 全昌乾1, 徐梅华1, 韦范1, 黄莎莎1, 汤丹峰1,2, authorsList=李静纯, 全昌乾, 徐梅华, 韦范, 黄莎莎, 汤丹峰, authorCompany=1 广西壮族自治区药用植物园, 广西药用资源保护与遗传改良重点实验室, 广西 南宁 530023; 2 中国药科大学中药学院, 江苏 南京 211198, correspAuthors=null, authorNote=李静纯: 李静纯(2001-),女,广东普宁人,硕士研究生,主要从事中药质量评价与资源开发方面研究。E-mail:2476598059@qq.com, correspAuthorsNote=null, copyrightStatement=null, copyrightOwner=null, extLink=null, articleAbsUrl=null, sourceXml=null, magXml=null, pdfUrl=null, pdf=twsglxaSAVmn5NwZC67jcQ==, pdfFileSize=1397686, pdfExtLink=null, richHtmlUrl=null, mobilePdfUrl=null, reviewReport=null, pdfFirstPage=null, abstractGraph=null, abstractGraphContent=null, abstractVideo=null, citation=null, cebUrl=null, magXmlContent=null, mapNumber=null, fund=广西重点研发计划 (桂科AB24010015); 国家自然科学基金资助项目 (82460754); 国家自然科学基金资助项目 (82260750); 广西药用资源保护与遗传改良重点实验室自主课题 (KL2025ZZ05))}, authors=null, keywords=[Keyword(id=1304414890270150832, tenantId=1146029695717560320, journalId=1302319053441957962, articleId=1304414889766834349, language=CN, orderNo=1, keyword=凉粉草), Keyword(id=1304414890362425521, tenantId=1146029695717560320, journalId=1302319053441957962, articleId=1304414889766834349, language=CN, orderNo=2, keyword=SSR), Keyword(id=1304414890446311602, tenantId=1146029695717560320, journalId=1302319053441957962, articleId=1304414889766834349, language=CN, orderNo=3, keyword=种质资源), Keyword(id=1304414890513420467, tenantId=1146029695717560320, journalId=1302319053441957962, articleId=1304414889766834349, language=CN, orderNo=4, keyword=遗传多样性), Keyword(id=1304414890588917940, tenantId=1146029695717560320, journalId=1302319053441957962, articleId=1304414889766834349, language=CN, orderNo=5, keyword=指纹图谱), Keyword(id=1304414892308582581, tenantId=1146029695717560320, journalId=1302319053441957962, articleId=1304414889766834349, language=EN, orderNo=1, keyword=Platostoma palustre (Blume) A. 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Integrating LC-MS and HS-GC-MS for the metabolite characterization of the Chinese medicinal plant Platostoma palustre under different processing methods[J]. Front Nutr, 2023, 10: 1181942. Huang S H, Chen Z N, Chen H, et al. Widely targeted metabolomics reveals the phytoconstituent changes in Platostoma palustre leaves and stems at different growth stages[J]. Front Plant Sci, 2024, 15: 1378881. Li X F, Wei F, Quan C Q, et al. Identification of key modules and genes in response to high-temperature stress in Platostoma palustre based on WGCNA[J]. BMC Plant Biol, 2025, 25(1): 695. 林丽华, 黄莉鑫, 谢建华. 凉粉草功能活性成分及其生物活性研究进展[J]. 食品工业科技, 2016, 37(20): 356-359. 汤丹峰, 韦范, 谢锦祥, 等. 广西仙草保育关键技术及问题分析[J]. 中国现代中药, 2022, 24(3): 407-411. 李博, 谢欢, 钟国跃, 等. 仙草质量控制的研究进展[J]. 广州中医药大学学报, 2016, 33(5): 755-758. Zhong L A, Zou X, Wu S Q, et al. Volatilome and flavor analyses based on e-nose combined with HS-GC-MS provide new insights into ploidy germplasm diversity in Platostoma palustre[J]. Food Res Int, 2024, 183: 114180. Reed D H, Frankham R. Correlation between fitness and genetic diversity[J]. Conserv Biol, 2003, 17(1): 230-237. Cruse-Sanders J M, Hamrick J L. Genetic diversity in harvested and protected populations of wild American ginseng, Panax quinquefolius L. (Araliaceae)[J]. Am J Bot, 2004, 91(4): 540-548. 张桂芳, 关杰敏, 林吉, 等. 凉粉草RAPD指纹图谱的构建及遗传相似性研究[A] // 2010年中国药学大会暨第十届中国药师周论文集[C]. 北京: 中国药学大会, 2010: 2046-2052. 陈菁瑛, 刘萍, 黄颖桢, 等. 不同仙草种源间遗传关系的ISSR分析[J]. 中国野生植物资源, 2011, 30(5): 46-50. Zhang G F, Guan J M, Lai X P, et al. RAPD fingerprint construction and genetic similarity of Mesona chinensis (Lamiaceae) in China[J]. Genet Mol Res, 2012, 11(4): 3649-3657. 李晓晖, 黎颖菁, 黄荣韶, 等. 凉粉草遗传多样性的SCoT和ISSR分析[J]. 西南农业学报, 2012, 25(5): 1834-1840. 师玉华, 马定乾, 张景景, 等. 凉茶药材凉粉草与混伪品的ITS2条形码鉴定[J]. 中国药学杂志, 2015, 50(15): 1282-1285. 夏微. 基于SLAF-seq技术的凉粉草居群遗传多样性分析[D]. 广州: 华南农业大学, 2018. 兰秀, 阮丽霞, 马仙花, 等. 基于主要农艺性状的25份凉粉草种质资源遗传多样性分析与综合评价[J]. 山东农业科学, 2023, 55(11): 57-64. Huang S H, Wei X M, Quan C Q, et al. Genetic diversity evaluation and germplasm identification of Mesona chinensis Benth from plant morphology, cytology, and EST-SSR molecular markers[J]. Acta Physiol Plant, 2024, 46(11): 98. Parthiban S, Govindaraj P, Senthilkumar S. Comparison of relative efficiency of genomic SSR and EST-SSR markers in estimating genetic diversity in sugarcane[J]. 3 Biotech, 2018, 8(3): 144. 吴仕蔓, 娄兵海, 陈传武, 等. 应用SSR荧光标记法构建22个柚类品种的分子身份证[J]. 果树学报, 2023, 40(4): 605-614. Luo L T. Correlation analysis of microsatellite DNA markers with some substantial economic traits in high quality fine wool strain of Gansu alpine fine-wool sheep[D]. Lanzhou: Gansu Agricultural University. 2009. Qin Y, Sun D Q, Xu T J, et al. Genetic diversity and population genetic structure of the miiuy croaker, Miichthys miiuy, in the East China Sea by microsatellite markers[J]. Genet Mol Res, 2014, 13(4): 10600-10606. Botstein D, White R L, Skolnick M, et al. Construction of a genetic linkage map in man using restriction fragment length polymorphisms[J]. Am J Hum Genet, 1980, 32(3): 314-331. 申屠圆玥, 吴昀, 周泓, 等. SSR分子标记在百合中的研究现状与展望[J]. 分子植物育种, 1-8[2025-05-23].http://kns.cnki.net/kcms/detail/46.1068.S.20241101.1338.004.html. 李春花, 陈蕤坤, 王艳青, 等. 利用SSR标记构建云南苦荞种质资源分子身份证[J]. 分子植物育种, 2019, 17(5): 1575-1582. 刘更森. 苹果SSR和SNP标记开发及在遗传图谱构建和品种鉴定中的应用[D]. 长沙: 湖南农业大学, 2018. Kalia R K, Rai M K, Kalia S, et al. Microsatellite markers: An overview of the recent progress in plants[J]. Euphytica, 2011, 177(3): 309-334. 郑长远. 黄缨菊SSR分子标记开发及遗传多样性研究[D]. 西宁: 青海师范大学, 2023. Kalia R K, Rai M K, Kalia S, et al. Microsatellite markers: An overview of the recent progress in plants[J]. Euphytica, 2011, 177(3): 309-334. 杨路存, 周国英, 聂学敏. 濒危植物宽叶羌活天然居群cpDNA非编码区多态性分析[J]. 西北植物学报, 2013, 33(8): 1535-1543.)
Objective This study aimed to develop SSR molecular markers for Platostoma palustre and analyze the genetic diversity of its germplasm resources, so as to provide theoretical support for the conservation of P. palustre germplasm resources and the breeding of elite varieties. Methods Based on the whole-genome sequence of P. palustre, the distribution characteristics of simple sequence repeats (SSRs) were mined and analyzed, and polymorphic SSR primers were developed to provide a theoretical basis for the evaluation of genetic diversity and analysis of population structure in P. palustre. Results A total of 122,699 SSR loci were identified in the P. palustre genome, with a genomic SSR density of 96.91 loci/Mb and a locus occurrence frequency of 10.32 kb/SSR. Dinucleotide repeat motifs were the dominant type, accounting for 68.3% of all repeat motifs. After polymorphism screening, 15 pairs of SSR primers with good polymorphism were obtained. Their polymorphism information content (PIC) ranged from 0.197 to 0.736, with an average value of 0.425. Genetic diversity analysis of 40 P. palustre germplasms showed that the number of alleles at the 15 SSR loci was higher than the number of effective alleles, and the alleles were unevenly distributed. There were differences in heterozygosity among different loci; the average observed heterozygosity was higher than the average expected heterozygosity with a certain gap between them, indicating that the tested population deviated from the Hardy-Weinberg equilibrium (HWE), with genetic variation and favorable overall genetic diversity, and the genotype frequencies of some loci in the population changed. Fixation index (F) analysis showed that F > 0 at 3 loci and F < 0 at 12 loci, indicating that the number of heterozygous individuals was higher than that of homozygous individuals in the population. The Shannon’s information index (I) ranged from 0.449 (TDF191) to 1.628 (TDF166), with an average of 0.887. A phylogenetic tree of the 40 P. palustre germplasms was constructed using Phylip software based on the UPGMA method, which divided the germplasms into two subgroups. A “0/1” DNA fingerprint was successfully constructed by digital assignment coding. Conclusion The abundant SSR loci information obtained in this study can provide important theoretical and technical support for the development of whole-genome SSR markers, molecular marker-assisted breeding, and genetic diversity research of P. palustre.
Key words
Platostoma palustre (Blume) A. J. Paton
/
SSR
/
germplasm resources
/
genetic diversity
/
DNA fingerprinting
LI Jingchun, QUAN Changqian, XU Meihua, WEI Fan, HUANG Shasha, TANG Danfeng.
Identification and development of SSR molecular markers in the Platostoma palustre genome and analysis of germplasm genetic diversity[J].
Chinese Traditional and Herbal Drugs,
2026
, 57
(6)
: 2278
-2288
.
DOI: 10.7501/j.issn.0253-2670.2026.06.022
Tang D F, Quan C Q, Huang S H, et al. Integrating LC-MS and HS-GC-MS for the metabolite characterization of the Chinese medicinal plant Platostoma palustre under different processing methods[J]. Front Nutr, 2023, 10: 1181942. Huang S H, Chen Z N, Chen H, et al. Widely targeted metabolomics reveals the phytoconstituent changes in Platostoma palustre leaves and stems at different growth stages[J]. Front Plant Sci, 2024, 15: 1378881. Li X F, Wei F, Quan C Q, et al. Identification of key modules and genes in response to high-temperature stress in Platostoma palustre based on WGCNA[J]. BMC Plant Biol, 2025, 25(1): 695. 林丽华, 黄莉鑫, 谢建华. 凉粉草功能活性成分及其生物活性研究进展[J]. 食品工业科技, 2016, 37(20): 356-359. 汤丹峰, 韦范, 谢锦祥, 等. 广西仙草保育关键技术及问题分析[J]. 中国现代中药, 2022, 24(3): 407-411. 李博, 谢欢, 钟国跃, 等. 仙草质量控制的研究进展[J]. 广州中医药大学学报, 2016, 33(5): 755-758. Zhong L A, Zou X, Wu S Q, et al. Volatilome and flavor analyses based on e-nose combined with HS-GC-MS provide new insights into ploidy germplasm diversity in Platostoma palustre[J]. Food Res Int, 2024, 183: 114180. Reed D H, Frankham R. Correlation between fitness and genetic diversity[J]. Conserv Biol, 2003, 17(1): 230-237. Cruse-Sanders J M, Hamrick J L. Genetic diversity in harvested and protected populations of wild American ginseng, Panax quinquefolius L. (Araliaceae)[J]. Am J Bot, 2004, 91(4): 540-548. 张桂芳, 关杰敏, 林吉, 等. 凉粉草RAPD指纹图谱的构建及遗传相似性研究[A] // 2010年中国药学大会暨第十届中国药师周论文集[C]. 北京: 中国药学大会, 2010: 2046-2052. 陈菁瑛, 刘萍, 黄颖桢, 等. 不同仙草种源间遗传关系的ISSR分析[J]. 中国野生植物资源, 2011, 30(5): 46-50. Zhang G F, Guan J M, Lai X P, et al. RAPD fingerprint construction and genetic similarity of Mesona chinensis (Lamiaceae) in China[J]. Genet Mol Res, 2012, 11(4): 3649-3657. 李晓晖, 黎颖菁, 黄荣韶, 等. 凉粉草遗传多样性的SCoT和ISSR分析[J]. 西南农业学报, 2012, 25(5): 1834-1840. 师玉华, 马定乾, 张景景, 等. 凉茶药材凉粉草与混伪品的ITS2条形码鉴定[J]. 中国药学杂志, 2015, 50(15): 1282-1285. 夏微. 基于SLAF-seq技术的凉粉草居群遗传多样性分析[D]. 广州: 华南农业大学, 2018. 兰秀, 阮丽霞, 马仙花, 等. 基于主要农艺性状的25份凉粉草种质资源遗传多样性分析与综合评价[J]. 山东农业科学, 2023, 55(11): 57-64. Huang S H, Wei X M, Quan C Q, et al. Genetic diversity evaluation and germplasm identification of Mesona chinensis Benth from plant morphology, cytology, and EST-SSR molecular markers[J]. Acta Physiol Plant, 2024, 46(11): 98. Parthiban S, Govindaraj P, Senthilkumar S. Comparison of relative efficiency of genomic SSR and EST-SSR markers in estimating genetic diversity in sugarcane[J]. 3 Biotech, 2018, 8(3): 144. 吴仕蔓, 娄兵海, 陈传武, 等. 应用SSR荧光标记法构建22个柚类品种的分子身份证[J]. 果树学报, 2023, 40(4): 605-614. Luo L T. Correlation analysis of microsatellite DNA markers with some substantial economic traits in high quality fine wool strain of Gansu alpine fine-wool sheep[D]. Lanzhou: Gansu Agricultural University. 2009. Qin Y, Sun D Q, Xu T J, et al. Genetic diversity and population genetic structure of the miiuy croaker, Miichthys miiuy, in the East China Sea by microsatellite markers[J]. Genet Mol Res, 2014, 13(4): 10600-10606. Botstein D, White R L, Skolnick M, et al. Construction of a genetic linkage map in man using restriction fragment length polymorphisms[J]. Am J Hum Genet, 1980, 32(3): 314-331. 申屠圆玥, 吴昀, 周泓, 等. SSR分子标记在百合中的研究现状与展望[J]. 分子植物育种, 1-8[2025-05-23].http://kns.cnki.net/kcms/detail/46.1068.S.20241101.1338.004.html. 李春花, 陈蕤坤, 王艳青, 等. 利用SSR标记构建云南苦荞种质资源分子身份证[J]. 分子植物育种, 2019, 17(5): 1575-1582. 刘更森. 苹果SSR和SNP标记开发及在遗传图谱构建和品种鉴定中的应用[D]. 长沙: 湖南农业大学, 2018. Kalia R K, Rai M K, Kalia S, et al. Microsatellite markers: An overview of the recent progress in plants[J]. Euphytica, 2011, 177(3): 309-334. 郑长远. 黄缨菊SSR分子标记开发及遗传多样性研究[D]. 西宁: 青海师范大学, 2023. Kalia R K, Rai M K, Kalia S, et al. Microsatellite markers: An overview of the recent progress in plants[J]. Euphytica, 2011, 177(3): 309-334. 杨路存, 周国英, 聂学敏. 濒危植物宽叶羌活天然居群cpDNA非编码区多态性分析[J]. 西北植物学报, 2013, 33(8): 1535-1543.
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