Screening of DNA Barcodes for Medicago archiducis-nicolai and Its Relative Medicago ruthenica

doi:10.11733/j.issn.1007-0435.2023.08.008

Acta Agrestia Sinica ›› 2023, Vol. 31 ›› Issue (8): 2323-2333.DOI: 10.11733/j.issn.1007-0435.2023.08.008

Previous Articles Next Articles

Screening of DNA Barcodes for Medicago archiducis-nicolai and Its Relative Medicago ruthenica

WANG Xia, LIU Yan, JIA Xiu-xiu, LI Yong-qiang, FANG Qiang-en

College of Pratacultural Sciences, Gansu Agricultural University, Key Laboratory of Pratacultural Ecosystem, Ministry of Education, Sino-US Research Center for Sustainable Development of Grassland Animal Husbandry, Lanzhou, Gansu Province 730070, China

Received:2023-02-20 Revised:2023-04-07 Online:2023-08-15 Published:2023-09-01

矩镰荚苜蓿与近缘种花苜蓿的DNA条形码筛选

王霞, 刘艳, 贾秀秀, 李永强, 方强恩

甘肃农业大学草业学院, 草业生态系统教育部重点实验室, 中-美草地畜牧业可持续发展研究中心, 甘肃兰州 730070

通讯作者: 方强恩,E-mail:fangqen@163.com
作者简介:王霞(1999-),女,汉族,甘肃会宁人,硕士研究生,主要从事草地生物多样性研究,E-mail:18394151945@163.com
基金资助:
国家自然科学基金项目“花苜蓿越冬芽适应青藏高原寒冷胁迫的分子机制”(31760703)，甘肃省高校教师创新基金项目“野生特异种质矩镰荚苜蓿根茎芽抗寒基因筛选与功能分析”(2023A-49)、草业生态系统教育部重点实验室开放课题“青藏高原特有种矩镰荚苜蓿的遗传多样性与分子谱系地理研究”(KLGE202212)资助

Abstract

Abstract: In order to screen DNA barcodes suitable for identification of closely related speciesMedicago archiducis-nicolai and M. ruthenica,in this study,PCR amplification,sequencing and sequence alignment were performed out for six candidate barcode sequences (commonly used sequences rbcL,psbA-trnH,trnL-trnF,trnK-matK,ITS2 and a novel sequence GA3ox1) in 113 samples of both species. The identification ability of different sequences was evaluated by barcoding gap analysis,wilcoxn test and NJ phylogenetic tree. The results showed that the amplification rate of six candidate sequences and the success rate of sequencing were more than 85%. There was no variation site in rbcL sequence between the two related species,but the other five candidate sequences had different intraspecific variation and interspecific variation. The minimum interspecific genetic distance of the five candidate sequences was greater than the maximum interspecific genetic distance for both species. There was a significant “Barcoding Gap” between the intraspecific and interspecific for GA3ox1,ITS2and psbA-trnH sequences. In the NJ phylogenetic tree constructed with candidate sequences,both M. archiducis-nicolai and M. ruthenica could form individual monophyletic groups respectively by using GA3ox1 and psbA-trnH,but trnL-trnF,trnK-matK and ITS2 could not distinguish the two related species from each other. In this analysis,we recommend the nuclear coding gene GA3ox1 as a preferred sequence for identification between M. archiducis-nicolai and M. ruthenica,and the chloroplast gene psbA-trnH as the auxiliary barcode.

Key words: Medicago archiducis-nicolai, Species identification, psbA-trnH, GA3ox1, DNA barcoding

摘要： 为了筛选适于鉴定易混淆种矩镰荚苜蓿(Medicago archiducis-nicolai)和花苜蓿(M. ruthenica)的DNA条形码，本研究采集了两近缘种的113个样本，对6个候选条形码序列(通用序列rbcL，psbA-trnH，trnL-trnF，trnK-matK，ITS₂和新序列GA3ox1)进行PCR扩增、测序和序列比对，经过barcoding gap分析、wilcoxn检验以及构建NJ系统发育树评价各序列的鉴定能力。结果显示：6条候选序列的扩增和测序成功率在85%以上；rbcL序列在两近缘种间不存在变异位点，其余5条候选序列各有不同的种内变异和种间变异；5条候选序列的种间最小遗传距离均大于种内最大遗传距离，GA3ox1,ITS2和psbA-trnH序列在种内种间存在明显的“Barcoding Gap”区域；在候选序列构建的NJ系统进化树中，利用GA3ox1和psbA-trnH，矩镰荚苜蓿和花苜蓿均能各自形成单系，但trnL-trnF，trnK-matK和ITS2不能将两个近缘种区分开。通过分析，我们推荐使用核编码基因GA3ox1作为鉴定矩镰荚苜蓿和花苜蓿的首选序列，叶绿体基因psbA-trnH作为辅助条形码。

关键词: 矩镰荚苜蓿, 物种界定, psbA-trnH, GA3ox1, DNA条形码

CLC Number:

S326

WANG Xia, LIU Yan, JIA Xiu-xiu, LI Yong-qiang, FANG Qiang-en. Screening of DNA Barcodes for Medicago archiducis-nicolai and Its Relative Medicago ruthenica[J]. Acta Agrestia Sinica, 2023, 31(8): 2323-2333.

王霞, 刘艳, 贾秀秀, 李永强, 方强恩. 矩镰荚苜蓿与近缘种花苜蓿的DNA条形码筛选[J]. 草地学报, 2023, 31(8): 2323-2333.

0
/ / Recommend

Add to citation manager EndNote|Ris|BibTeX

URL: https://manu40.magtech.com.cn/Jweb_cdxb/EN/10.11733/j.issn.1007-0435.2023.08.008

https://manu40.magtech.com.cn/Jweb_cdxb/EN/Y2023/V31/I8/2323

References

[1] 吴小培,沈迎芳,王海庆. 基于trnL-trnF序列的扁蓿豆和青藏扁蓿豆遗传多样性及其群体遗传结构分析[J]. 草业科学,2016,33(6):1136-1146
[2] 田春育,武自念,李贤松,等. 扁蓿豆叶绿体基因组密码子偏好性分析[J]. 草地学报,2021,29(12):2678-2684
[3] 青海省生物研究所,同仁县隆务诊疗所.青藏高原药物图鉴[M]. 西宁:青海人民出版社,1972:84
[4] 姜颖倩,王霞,贾秀秀,等. 气候变化下矩镰荚苜蓿的地理分布格局及潜在适生区预测[J]. 西北植物学报,2022,42(9):1611-1620
[5] 贾笃敬,张映生,张自和,等. 高寒地区优良豆科牧草阴山扁蓿豆一些性状的研究[J]. 甘肃农大学报,1984(1):63-69
[6] 胡一凡,张雪梅,石乃星,等. 云南草果种质资源DNA条形码序列分析[J]. 中草药,2019,50(24):6091-6097
[7] 陈芙蓉,郭巧生,杨锋,等. ITS2二级结构系统发育信息在野菊及其近缘种植物DNA条形码鉴定中的应用价值[J]. 中国中药杂志,2019,44(22):4813-4819
[8] SENAPATI A,BASAK S,RANGAN L. A Review on application of DNA barcoding technology for rapid molecular diagnostics of adulterants in herbal medicine[J]. Drug Safety:An International Journal of Medical Toxicology and Drug Experience,2022,45(3):193-213
[9] 陈士林,宋经元,姚辉,等. 药用植物DNA条形码鉴定策略及关键技术分析[J]. 中国天然药物,2009,7(5):322-327
[10] 陈士林,庞晓慧,姚辉,等. 中药DNA条形码鉴定体系及研究方向[J]. 世界科学技术(中医药现代化),2011,13(5):747-754
[11] 陈士林,姚辉,韩建萍,等. 中药材DNA条形码分子鉴定指导原则[J]. 中国中药杂志,2013,38(2):141-148
[12] HOLLINGSWORTH P, FORREST L L,SPOUGE J, et al. A DNA barcode for land plants[J]. Proceedings of the National Academy of Sciences,2009,106(31):12794-12797
[13] HOLLINGSWORT P M,LI D Z,BANK M,et al. Telling plant species apart with DNA:From barcodes to genomes[J]. Philosophical Transactions of the Royal Society B:Biological Sciences,2016,371(1702):20150338
[14] KRESS W J,ERICKSON D L. A two-locus global DNA barcode for land plants:the coding rbcL gene complements the non-coding psbA-trnH spacer region[J]. PLoS One,2007,2(6):e508
[15] FAZEKES A J,BUEGESS K S,KESANAKURTI P R,et al. Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well.[J]. PLoS One,2008,3(7),e2802
[16] STEELE K P,ICKERT-BOND S M,ZARRES,et al. Phylogeny and character evolution in Medicago (Leguminosae):Evidence from analyses of plastid trnK/matK and nuclear GA3ox1 sequences[J]. American Journal of Botany,2010,97(7):1142-1155
[17] HU D,LI F,LIU J,et al. Systematic positions of Medicago edgeworthii and M. archiducis-nicolai (Leguminosae) inferred from plastid trnK/matK,nuclear GA30X1 and its sequences[J]. Pakistan Journal of Botany,2014,46(3):775-778
[18] CHEN J Y,WU G L,SHESTHA N,et al. Phylogeny and species delimitation of Chinese Medicago (Leguminosae) and its relatives based on molecular and morphological evidence[J]. Frontiersin Plant Science,2021(11):619-799
[19] 刘亚田. 优良野生豆科牧草——藏青胡卢巴[J]. 中国草原,1987(3):71-73
[20] 王天佐,张文浩. 发根农杆菌介导的花苜蓿毛状根转化体系的建立[J]. 草地学报,2020,28(1):268-272
[21] 王英芳,张业猛,刘德梅,等. 基于转录组测序的青藏扁蓿豆EST-SSR标记开发与验证[J]. 草业科学,2020,37(4):718-727
[22] HALL T A.BIOEDIT:A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT[J]. Nuclc Acids Symposium Series,1999,41(41):95-98
[23] 高连明,刘杰,蔡杰,等. 关于植物DNA条形码研究技术规范[J]. 植物分类与资源学报,2012,34(6):592-606
[24] KELLER A,SCHLEICHER T,SHULTZ J,et al. 5.8S-28S rRNA interaction and HMM-based ITS2 annotation[J]. Gene,2009,430(1/2):50-57
[25] 赵日杂,张英秀,王君军,等. 基于DNA条形码鉴别缘毛紫菀及狭苞紫菀[J]. 中草药,2022,53(19):6167-6173
[26] 高效梅,伍宝朵,胡丽松,等. 面包果DNA条形码筛选与遗传多样性分析[J/OL]. http://kns.cnki.net/kcms/detail/46.1068.S.20221008.1811.010.html,2023-05-30
[27] SUN Z Y,GAO T,YAO H,et.al. Identification of Lonicera japonica and its related species using the DNA barcoding method.[J]. Planta Medica,2011,77(3);301-306
[28] 陈静仪,张靖,张丹纯,等. 21种广东省珍稀保护药用植物的DNA条形码分析[J]. 中药新药与临床药理,2019,30(8):979-984
[29] SONG J Y,YAO H,LI Y,et al. Authentication of the family Polygonaceae in Chinese pharmacopoeia by DNA barcoding technique[J]. Journal of Ethnopharmacology,2009,124(3);434-439
[30] LIU J Q. DNA barcodes,speciation and taxonomy in plants[J]. Biodiversity Science,2015,23(3):283-285
[31] LESTER D R,ROSS J J,DAVIES P J,et al. Mendel's stem length gene (le) encodes a gibberellin 3β-hydroxylase[J]. The Plant Cell,1997,9(8):1435-1443
[32] ANDERSSON L,PURUGGANAN M. Molecular genetic variation of animals and plants under domestication.[J]. Proceedings of the National Academy of Sciences of the United States of America,2022,119(30):e2122150119
[33] MARTINS L B,BALINNKURTI P,REBERGHOTON S C. Genome-wide association study for morphological traits and resistance to Peryonella pinodes in the USDA pea single plant plus collection[J]. G3 (Bethesda,Md.),2022,12(9):jkac168

Screening of DNA Barcodes for Medicago archiducis-nicolai and Its Relative Medicago ruthenica

矩镰荚苜蓿与近缘种花苜蓿的DNA条形码筛选

PDF

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 12

Recommended Articles

Metrics

Comments

[1]	ZHANG Peng, BAO Gen-sheng, JIA Zhi-feng, LIU Wen-hui. Genetic Diversity Analysis of Agronomic Traits of 150 Pisum sativum Germplasm Resources in Alpine Region [J]. Acta Agrestia Sinica, 2023, 31(7): 2116-2127.
[2]	LIU Man, QIN Yan, LIU Wen-hui, ZHANG Yong-chao, WU Yu-han, QI Hui-fang. Evaluation on and Screening of Production Performance of Bromus inermis Resources in Alpine Regions of Qinghai-Tibet Plateau [J]. Acta Agrestia Sinica, 2023, 31(5): 1469-1480.
[3]	ZENG Han-guo, YUE Jia-ming, ZHANG Shu-heng, YI Kun, WEI Kai, YANG Shuang-feng, LIU Gui-xia, LI Man-li, YANG Chun-hua. Comprehensive Evaluation of Agronomic Traits of 76 Germplasm Resources of Elymus sibiricus [J]. Acta Agrestia Sinica, 2022, 30(11): 3046-3055.
[4]	DING Ming-lei, WANG Jing-hong, WANG Wei-wei, LI Song, WANG Zhi-cheng, ZHANG Chao, SUN Feng-li, LIU Shu-dong, XI Ya-jun. Screening and Evaluation of Dual-purpose Wheat Germplasm Resources [J]. Acta Agrestia Sinica, 2022, 30(8): 2027-2036.
[5]	ZHANG Dian-ye, ZHANG Li-jing, HUANG De-jun, FU Hua. Comprehensive Evaluation of Germplasm Resource of Elymus nutans in Alpine Region [J]. Acta Agrestia Sinica, 2015, 23(6): 1239-1246.
[6]	HU Hua-guang, ZHANG Zhen-ming, JI Fang-fang, LIU Jian-xiu. Variation Analysis of Drought Resistance of Germplasm Resources of Zoysia Willd. in Chinese Main Region [J]. , 2014, 22(2): 224-228.
[7]	LIU Da-lin, WANG Xiu-ping, HU Kai-qi, LIU Wei-guo, ZHANG Hua, CAO Xi-chun. Adaptability Evaluation of Cool-season Turf Grasses in Yangzhou [J]. , 2012, 20(5): 967-971.
[8]	HAO Feng, XU Zhu, YAN Wei-hong, LI Ping, LIU Ying, HU Yan-cheng. Morphological Variations Analysis of Bromus catharticus Germplasm [J]. , 2011, 19(4): 668-673.
[9]	SHI Kun, ZHOU Da-sen, GUO Yong-wang, SHI Da-zhao, WANG Deng. Acute Toxicity Analyses of Stellera chamaejasme Root in Mongolian Gerbils(Meriones unguiculatus) [J]. , 2010, 18(5): 731-734.
[10]	YANG Zhan-hua, WEI Zhen-wu, LEI Yan-fang, ZHANG Li-fang. Identification of the Genetic Diversity and Relationship of Medicago Germplasms by Two Kinds of SSR Markers [J]. , 2008, 16(6): 559-565.
[11]	LIU Jian-xiu, ZHU Xue-hua, GUO Ai-gui, GUO Hai-lin. Morphological Variations of Eremochloa Ophiuroides and its Morphological Types [J]. , 2004, 12(3): 183-188.
[12]	YANG Hang, QI Juan, LIU Wen-hui, LIU Yan-jun, SU Jing-long, LI Ming. Fatty Acid Substance Detection and Self-toxic Effect in Rhizosphere Soil of Elymus sibiricus L. with Different Planting Years [J]. Acta Agrestia Sinica, 2021, 29(1): 52-59.