Phylogeography of Medicinal and Edible Homologous Plant Allium macrostemon

doi:10.7525/j.issn.1673-5102.2022.04.007

Abstract

Abstract:

In order to reveal the distribution pattern of genetic variation and haplotype geographical distribution pattern of Allium macrostemon， and to infer the refugia in the quaternary glaciation， the chloroplast gene fragments（psbA-trnH， rps16 and trnL-F） and nuclear gene fragments（ITS） of A. macrostemon in 14 regions of China were analyzed respectively. The results showed that the genetic diversity of A. macrostemon chloroplast gene（cpDNA） was lower than that of nuclear gene（nrDNA）（cpDNA：H_T=0.868； nrDNA：H_T=0.890）. The AMOVA analysis of cpDNA and nrDNA showed that the genetic variations occurred mainly among populations （cpDNA：92.84%； nrDNA：98.40%）， there was significant genetic differentiation among populations（cpDNA：N_st=0.918，G_st=0.866，F_st=0.928；nrDNA：N_st=0.984，G_st=0.855，F_st=0.984）， and had an obvious phylogeographical structure in A. macrostemon populations（N_st>G_st）. A total of 11 chloroplast and 14 nuclear haplotypes were identified in the A. macrostemon populations. The haplotype network and geographical distribution map showed that the chloroplast haplotype H3 and nuclear DNA genotype H1 had the highest frequency and were located in the center of the network structure， which might be the ancient haplotype. In addition， the glacial refuge hypothesis suggested that the region with high genetic diversity， ancient haplotype and more endemic haplotype might be the glacial refugia of A. macrostemon. Therefore， it was speculated that in the quaternary glaciation， A. macrostemon might be multiple glacial refuges in Dapanshan， Tianshui and Tonghua. The analysis could provide references for the evolution of similar herbs and enrich our understanding of the molecular phylogeography of herbaceous plants in East Asia.

Key words: Allium macrostemon, population, phylogeography, genetic variation, glacial refugia

CLC Number:

Q948

Tian SHI, Zhongmei MO, Min WU, Cai ZHAO. Phylogeography of Medicinal and Edible Homologous Plant Allium macrostemon[J]. Bulletin of Botanical Research, 2022, 42(4): 574-583.

References

1	熊朝勇，陈霞.药食同源野生蔬菜小根蒜研究进展［J］.现代食品，2019，10（20）：103-105.
1	XIONG C Y， CHEN X.Research on the homology of medicine and food of wild vegetables of Allium macrostemon Bunge［J］.Modern Food，2019，10（20）：103-105.
2	朱小梅，洪立洲，王茂文，等.小根蒜的研究进展与利用前景［J］.安徽农学通报，2010，16（9）：114-115.
2	ZHU X M， HONG L Z， WANG M W，et al.Research progress and application prospects of Allium macrostemon Bunge［J］.Anhui Agricultural Science Bulletin，2010，16（9）：114-115.
3	乔凤仙，蔡皓，裴科，等.中药薤白的研究进展［J］.世界中医药，2016，11（6）：1137-1140.
3	QIAO F X， CAI H， PEI K，et al.Research progress of Allii macrostemonis Bulbus［J］.World Chinese Medicine，2016，11（6）：1137-1140.
4	张占军，王富花.药食两用植物薤白研究进展［J］.食品研究与开发，2012，33（11）：234-237.
4	ZHANG Z J， WANG F H.Advances in the study of Allium macrstemon Bunge used both as medicine and food［J］.Food Research and Development，2012，33（11）：234-237.
5	黄德青，李琴琴，周颂东，等.基于nrDNA ITS和cpDNA trnL-F序列探讨薤白的系统地位［J］.植物分类与资源学报，2015，37（5）：537-545.
5	HUANG D Q， LI Q Q， ZHOU S D，et al.Systematic position of Allium macrostemon based on nrDNA ITS and cpDNA trnL-F sequence data［J］.Plant Diversity and Resources，2015，37（5）：537-545.
6	杨鹏，舒建锋，蔡莎莎，等.贵州不同产地薤白nrDNA ITS序列分析及亲缘关系研究［J］.植物科学学报，2017，35（2）：171-176.
6	YANG P， SHU J F， CAI S S，et al.nrDNA ITS sequence analysis and genetic relationship of Allium macrostemon from different geographical regions in Guizhou［J］.Plant Science Journal，2017，35（2）：171-176.
7	莫忠妹，成宇，石甜，等.基于ITS序列西南地区不同居群薤白亲缘关系及其地理分布格局研究［J］.西北植物学报，2019，39（9）：1573-1580.
7	MO Z M， CHENG Y， SHI T，et al.Genetic relationship and geographical distribution pattern of different Allium macrostemon populations in southwest China based on ITS sequences［J］.Acta Botanica Boreali-Occidentalia Sinica，2019，39（9）：1573-1580.
8	YOUNG A， BOYLE T， BROWN T.The population genetic consequences of habitat fragmentation for plants［J］.Trends in Ecology & Evolution，1996，11（10）：413-418.
9	HEWITT G.The genetic legacy of the Quaternary ice ages［J］.Nature，2000，405（6789）：907-913.
10	BENNETT K D， PROVAN J.What do we mean by ‘refugia’？［J］.Quaternary Science Reviews，2008，27（27/28）：2449-2455.
11	龚奕青.叉叶类苏铁的遗传分化和谱系地理研究［D］.昆明：云南大学，2015.
11	GONG Y Q.Genetic differentiation and phylogeographic of four bipinnata Cycas species［D］.Kunming：Yunnan University，2015.
12	WANG Y H， JIANG W M， COMES H P，et al.Molecular phylogeography and ecological niche modelling of a widespread herbaceous climber，Tetrastigma hemsleyanum（Vitaceae）：insights into Plio-Pleistocene range dynamics of evergreen forest in subtropical China［J］.New Phytologist，2015，206（2）：852-867.
13	金建华，廖文波，王伯荪，等.新生代全球变化与中国古植物区系的演变［J］.广西植物，2003，23（3）：217-225.
13	JIN J H， LIAO W B， WANG B S，et al.Global change in Cenozoic and evolution of flora in China［J］.Guihaia，2003，23（3）：217-225.
14	SPICER R A， HARRIS N B W， WIDDOWSON M，et al.Constant elevation of southern Tibet over the past 15 million years［J］.Nature，2003，421（6923） 622-624.
15	ZHANG Q， CHIANG T Y， GEORGE M，et al.Phylogeography of the Qinghai-Tibetan Plateau endemic Juniperus przewalskii（Cupressaceae） inferred from chloroplast DNA sequence variation［J］.Molecular Ecology，2005，14（11）：3513-3524.
16	ZHOU T H， LI S， QIAN Z Q，et al.Strong phylogeographic pattern of cpDNA variation reveals multiple glacial refugia for Saruma henryi Oliv.（Aristolochiaceae），an endangered herb endemic to China［J］.Molecular Phylogenetics and Evolution，2010，57（1）：176-188.
17	ZHANG T C， COMES H P， SUN H.Chloroplast phylogeography of Terminalia franchetii（Combretaceae） from the eastern Sino-Himalayan region and its correlation with historical river capture events［J］.Molecular Phylogenetics and Evolution，2011，60（1）：1-12.
18	DOYLE J.DNA protocols for plants［M］.Berlin：Springer-Verlag，1991.
19	HAMILTON M B.Four primer pairs for the amplification of chloroplast intergenic regions with intraspecific variation［J］.Molecular Ecology，1999，8（3）：521-523.
20	OXELMAN B， MAGNUS L， BERGLUND D.Chloroplast rps16 intron phylogeny of the tribe Sileneae（Caryophyllaceae）［J］.Plant Systematics and Evolution，1997，206（1/2/3/4）：393-410.
21	TABERLET P， GIELLY L， PAUTOU G，et al.Universal primers for amplification of three non-coding regions of chloroplast DNA［J］.Plant Molecular Biology，1991，17（5）：1105-1109.
22	WENDEL J F， SCHNABEL A， SEELANAN T.Bidirectional interlocus concerted evolution following allopolyploid speciation in cotton（Gossypium）［J］.Proceedings of the National Academy of Sciences of the United States of America，1995，92（1）：280-284.
23	BURLAND T G.DNASTAR’s lasergene sequence analysis software［M］//MISENER S，KRAWETZ S A.Methods in Molecular Biology.Totowa：Humana Press，2000：71-91.
24	KUMAR S， STECHER G，TAMURA.MEGA7：Molecular evolutionary genetics analysis version 7.0 for bigger datasets［J］.Molecular Biology and Evolution，2016，33（7）：1870-1874.
25	LIBRADO P， ROZAS J.DnaSP v5：a software for comprehensive analysis of DNA polymorphism data［J］.Bioinformatics，2009，25（11）：1451-1452.
26	TAJIMA F.Statistical method for testing the neutral mutation hypothesis by DNA polymorphism［J］.Genetics，1989，123（3）：585-595.
27	FU Y X.Statistical tests of neutrality of mutations against population growth，hitchhiking and background selection［J］.Genetics，1997，147（2）：915-925.
28	PONS O， PETIT R J.Measwring and testing genetic differentiation with ordered versus unordered alleles［J］.Genetics，1996，144（3）：1237-1245.
29	BANDELT H J， FORSTER P， R?HL A.Median-joining networks for inferring intraspecific phylogenies［J］.Molecular Biology and Evolution，1999，16（1）：37-48.
30	路雪林.金花茶的谱系地理学研究［D］.桂林：广西师范大学，2018.
30	LU X L.Phylogeography of Camellia nitidissima ［D］.Guilin：Guangxi Normal University，2018.
31	EXCOFFIER L， LISCHER H E L.Arlequin suite ver 3.5：a new series of programs to perform population genetics analyses under Linux and Windows［J］.Molecular Ecology Resources，2010，10（3）：564-567.
32	PETIT R J， DUMINIL J， FINESCHI S，et al.Comparative organization of chloroplast，mitochondrial and nuclear diversity in plant populations［J］.Molecular Ecology，2005，14（3）：689-701.
33	任梦云，杜乐山，陈彦君，等.锁阳ITS序列遗传多样性分析［J］.植物学报，2018，53（3），313-321.
33	REN M Y， DU L S， CHEN Y J，et al.Analysis on genetic diversity of Cynomorium songaricum by ITS sequence［J］.Bulletin of Botany，2018，53（3），313-321.
34	丁振杰，于丹，徐新伟.青藏高原东北部及其邻近地区无苞香蒲的谱系地理学［J］.生物多样性，2015，23（6）：759-766.
34	DING Z J， YU D， XU X W.Phylogeography of Typha laxmannii in the northeast Qinghai-Tibet Plateau and adjacent areas［J］.Biodiversity Science，2015，23（6）：759-766.
35	ZHANG X H， TAPIA M， WEBB J B，et al.Molecular signatures of two cattail species，Typha domingensis and Typha latifolia（Typhaceae），in South Florida［J］.Molecular Phylogenetics and Evolution，2008，49（1）：368-376.
36	KRATTINGER K.Genetic mobility in Typha ［J］.Aquatic Botany，1975，1：57-70.
37	TATE J A， SIMPSON B B.Paraphyly of Tarasa（Malvaceae） and diverse origins of the polyploidy species［J］.Systematic Botany，2003，28（4）：723-737.
38	HU X S， LI B.Seed and pollen flow and cline discordance among genes with different modes of inheritance［J］.Heredity，2002，88（3）：212-217.
39	刘丽.濒危植物脱皮榆的谱系地理学研究［D］.临汾：山西师范大学，2017.
39	LIU L.Phylogeography of the endangered species Ulmus lamellosa（Ulmaceae）［D］.Linfen：Shanxi Normal University，2017.
40	HEWITT G M.Genetic consequences of climatic oscillations in the Quaternary［J］.Philosophical Transactions of the Royal Society of London.Series B，Biological Sciences，2004，359（1442）：183-195.
41	郭凤平.迎红杜鹃亚属植物的群体遗传学研究［D］.长春：东北师范大学，2019.
41	GUO F P.Population genetics study of Rhododendron subg.Rhodorastrum［D］.Changchun：Northeast Normal University，2019.
42	许佳瑶，陈俏丽，张瑞芝，等.松材线虫Bx-ubc-3基因克隆及泛素通路鉴定［J］.森林工程，2019，35（5）：9-15.
42	XU J Y， CHEN Q L， ZHANG R Z，et al.Genetic cloning of bx-ubc-3 and identification of ubiquitin pathway from Bursaphelenchus xylophilus（Aphelenchida：Aphelenchoididae）full text replacement［J］.Forest Engineering，2019，35（5）：9-15.
43	朱仁斌.中国特有植物文冠果（Xanthoceras sorbifolium Bunge）的谱系地理研究与应用［D］.杨凌：西北农林科技大学，2016.
43	ZHU R B.Phylogeography of Xanthoceras sorbifolium Bunge，an endemic plant to China［D］.Yangling：Northwest A&F University，2016.
44	CARNAVAL A C， MORITZ C.Historical climate modelling predicts patterns of current biodiversity in the Brazilian Atlantic forest［J］.Journal of Biogeography，2008，35（7）：1187-1201.
45	FAVRE A， YUAN Y M， KüPFER P，et al.Phylogeny of subtribe Gentianinae（Gentianaceae）：biogeographic inferences despite limitations in temporal calibration points［J］.Taxon，2010，59（6）：1701-1711.
46	TZEDAKIS P C， LAWSON I T， FROGLEY M R，et al.Buffered tree population changes in a quaternary refugium：evolutionary implications［J］.Science，2002，297（5589）：2044-2047.
47	刘济明，管睿婷，王敏，等.不同喀斯特小生境中小蓬竹的遗传多样性［J］.植物研究，2019，39（1）：69-77.
47	LIU J M， GUAN R T， WANG M，et al.Genetic diversity of Ampelocalamus luodianensis in different microhabitats［J］.Bulletin of Botanical Research，2019，39（1）：69-77.
48	GONG W， CHEN C， DOBES C，et al.Phylogeography of a living fossil：pleistocene glaciations forced Ginkgo biloba L.（Ginkgoaceae） into two refuge areas in China with limited subsequent postglacial expansion［J］.Molecular Phylogenetics and Evolution，2008； 48（3）：1094-1105.
49	周天华.中国特有属植物——马蹄香（Saruma henryi Oliv.）的分子谱系地理学与遗传多样性研究［D］.西安：西北大学，2010.
49	ZHOU T H.Molecular phylogeographic and genetic diversity study on an endangered herb，Saruma henryi Oliv.（Aristolochiaceae） endemic to China［D］.Xi’an：Northwest University，2010.
50	CHEN D M， KANG H Z， LIU C J.An overview on the potential quaternary glacial refugia of plants in China mainland［J］.Bulletin of Botanical Research，2011，31（5）：623-632.
51	李慧敏.基于叶绿体DNA片段和核微卫星标记的槲树群体历史和遗传多样性研究［D］.西安：西北大学，2018.
51	LI H M.Phylogeography and genetic diversity of Quercus dentata Thunb. revealed by cpDNA and nuclear SSR markers［D］.Xi’an：Northwest University，2018.
52	张华杰.中国山莓草属植物物种界定及广义山莓草谱系地理学研究［D］.武汉：中国科学院大学，中国科学院武汉植物园，2019.
52	ZHANG H J.The circumscription of genus Sibbaldia in China and the phylogeographical study of Sibbaldia procumbens s.l.［D］.Wuhan：University of Chinese Academy of Sciences：Wuhan Botanical Garden，Chinese Academy of Sciences，2019.
53	WANG Y， LIU K， BI D，et al.Molecular phylogeography of East Asian Boea clarkeana（Gesneriaceae） in relation to habitat restriction［J］.PLoS One，2018，13（7）：e0199780.

[1]	Huiying GUI, Fazhi FANG, Zhaojia LI, Youzhuan MAI, Xiaofeng ZHANG. Population Structure and Dynamic Characteristics of the Endangered Plant Chunia bucklandioides in Diaoluo Mountain of Hainan [J]. Bulletin of Botanical Research, 2024, 44(1): 75-85.
[2]	Huaizhi MU, Qingyu WANG, Yue ZHANG, Songtong LÜ, Xuhong JIN, Xiao ZHANG, Fucai XIA. Phenotypic Variation and Diversity Analysis of Tilia mandshurica Natural Populations Based on Leaf and Fruit Traits [J]. Bulletin of Botanical Research, 2023, 43(6): 826-834.
[3]	Mengwen ZHANG, Cairong ZHONG, Xiaobo LÜ, Zanshan FANG, Cheng CHENG. Population Structure and Dynamic Characteristics of Three Endangered Mangrove Species from Genus Sonneratia [J]. Bulletin of Botanical Research, 2023, 43(2): 231-241.
[4]	Lei YANG, Qiumei CAO, Ying FENG, Wenjun LI. Genetic Diversity and Genetic Structure of the Rare and Endangered Plant Ferula fukanensis [J]. Bulletin of Botanical Research, 2023, 43(1): 51-58.
[5]	Siru TANG, Tiejuan WANG, Fang XIU, Mengyao LIU, Hui ZHANG. Genetic Structure and Phylogeography Analysis of Artemisia intramongolica Based on Single Copy Nuclear Genes [J]. Bulletin of Botanical Research, 2022, 42(6): 956-963.
[6]	Ermei CHANG, Jianfeng LIU, Yuening HUANG, Hongli LI, Bingyan SHAN, Zeping JIANG, Xiulian ZHAO. Comparison of Genetic Diversity Between Wild and ex-situ Conservation Populations of Cupressus chengiana [J]. Bulletin of Botanical Research, 2022, 42(5): 772-779.
[7]	Yujie ZHANG, Pengxia SHI, Fan ZHAO, Xiaodan CHEN, Kun SUN, Hui ZHANG. Genetic Diversity Analysis from Different Geographic Populations of Linaria vulgaris var. sinensis by rpl32-trnL Fragment [J]. Bulletin of Botanical Research, 2022, 42(5): 780-789.
[8]	Xueyan ZHOU, Biying WANG, Xuefeng HAO, Xinguo HU, Jiangtao WU, Kai LANG, Qinbo HU, Xiyang ZHAO. Genetic Variation and Joint Selection of Growth and Wood Traits in Half-sib Families of Larix olgensis [J]. Bulletin of Botanical Research, 2022, 42(3): 383-393.
[9]	Yibo Yin, Jixiang Li, Yingjie Guo, Ziting Lu, Ying Xiao, Hualing Liu, Yaguang Zhan, Fansuo Zeng. Variation of Lignin Content and Association Analysis of FmPAL Nucleotide Polymorphism in Progenies of Interspecific Hybrids of Fraxinus [J]. Bulletin of Botanical Research, 2022, 42(2): 191-199.
[10]	Yi-Zhong DUAN, Hai-Tao WANG, Ge-Ge ZHANG, Wei-Na YAN. Genetic Diversity of Plant Tetraenamongolica by ISSR Markers [J]. Bulletin of Botanical Research, 2021, 41(3): 466-473.
[11]	Guo-Lin FU, Ting-Ting LI, Ye-Hua ZHANG, Xiang-Ying WEN, Xue-Chu MA, Chu-Ping WU. Phenological Observation of the Extremely Small Population Plant Styrax zhejiangensis [J]. Bulletin of Botanical Research, 2021, 41(2): 168-173.
[12]	Ping-Sheng ZHANG, Xi-Bing JIANG, Bang-Chu GONG, Yang XU, Jun-sheng LAI, Cong-Lian WU. Leaf Phenotype Variation and Heterosis in F₁ Progeny of Cross Between Castanea mollissima and C.henryi [J]. Bulletin of Botanical Research, 2021, 41(2): 281-294.
[13]	LIU Bing-Yu, HUANG Gui-Hua, LIANG Kun-Nan, WANG Xi-Yang, CHEN Tian-Yu, ZHOU Zai-Zhi, YANG Guang. Evaluation of Photosynthetic Characteristics and Growth Traits in Teak(Tectona grandis L.f) Clones [J]. Bulletin of Botanical Research, 2020, 40(2): 209-216.
[14]	ZHANG Shan-Shan, KANG Hong-Mei, YANG Wen-Zhong. Population Genetic Analysis of Nyssa yunnanensis by Reduced-representation Sequencing Technique [J]. Bulletin of Botanical Research, 2019, 39(6): 899-907.
[15]	WANG Fei, HUO Huai-Cheng, ZHAO Yang, CAO Xiu-Wen, LIU Jin-Qian, YANG Yong-Hong, ZHANG Tao, QI Hao, WANG Ruo-Jian. Population Structure and Dynamics of Original Abies faxoniana Rehd—Rhododendron simsii Planch in High-mountain Timberline of Southern Gansu Province [J]. Bulletin of Botanical Research, 2019, 39(5): 664-672.