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用SSR标记研究柑橘属及其近缘属植物的亲缘关系_英文_

 遗传学报 Acta G enetica Sinica ,January 2003,30(1):81~87ISS N 0379-4172

收稿日期:2002-08-05;修回日期:2002-10-08

基金项目:国家自然科学基金资助(N o.39970081)[Supported by the National Natural Science F oundation of China (N o.39970081)]作者简介:庞晓明(1973-),湖南宁乡人,博士,专业方向:生物技术。E 2mail :xm pangcn @https://www.doczj.com/doc/0717499436.html, ① 通讯作者。E 2mail :dxxw wlj @https://www.doczj.com/doc/0717499436.html,

Phylogenetic R elationships Among Citrus and Its R elatives

as R evealed by SSR Markers

PANG X iao 2Ming ,H U Chun 2G en ,DE NG X iu 2X in ①

(National K ey Laboratory o f Crop G enetic Improvement ,Huazhong Agricultural Univer sity ,

National Center o f Crop Moleculor Breeding ,Wuhan 430070,China )

Abstract :Phylogenetic relationships am ong 29accessions belonging to Citrus ,Poncirus Fortunella ,Microcitrus ,Eremocitrus ,At 2lantia and Severinia were investigated using SSR markers.Seven SSR primers generated 114polym orphic alleles ,with an average of

1613alleles per primer.Cluster analysis via neighbour -joining method showed that Microcitrus was close to Citrus ;Poncirus was distant from Citrus ,which suggested that Poncirus could not be derived from Citrus.High frequency of the hom ozyg ous SSR locus supported the species status of Fumin trifoliate orange.Seperation of neither Papeda and Citrus nor Archicitrus and Metacitrus was well res olved.The present w ork con firmed citron ,pummelo and mandarin as basic species of cultivated citrus since they could be placed into three distinct clusters.

K ey w ords :citrus;fumin trifoliate orange ;microcitrus ;SSR ;phylogenetic relationship

用SSR 标记研究柑橘属及其近缘属植物的亲缘关系

庞晓明,胡春根,邓秀新①

(华中农业大学作物遗传改良国家重点实验室,国家农作物分子育种中心,武汉 430070)

摘 要:用SSR 标记分析了29份柑橘属及近缘属植物的亲缘关系。7对SSR 引物在29个样品中扩增得到114个等位基因,平均每个位点有1613个等位基因。计算匹配系数后用邻接法进行聚类,结果表明,澳洲指橘与柑橘属的亲缘关系很近;SSR 位点的高纯合频率支持富民枳种的地位;枳与柑橘属的关系较远,枳不大可能是从柑橘属衍生而来;S wingle 的亚属的划分以及田中的原生柑橘类和后生柑橘类的划分界线都不清晰;现代栽培柑橘的起源与大翼橙关系密切;柑橘属的枸橼、柚和宽皮橘都能很好地分离,支持其为现代栽培柑橘的3个基本种的观点。关键词:柑橘属;富民枳;澳洲指橘属;SSR ;亲缘关系

中图分类号:Q949 文献标识码:A 文章编号:0379-4172(2003)01-0081-07

Citrus is one of the major fruit crops in the w orld.H owever ,Citrus tax onomy and phylogeny are very com pli 2cated ,con flicting and confusing ,mainly due to apomixis ,widely sexual com patibility between Citrus and related genera ,the high frequency of bud mutations and the long history of cultivation and wide dispersion [1].Before mid 1970s ,Citrus tax onomy was mainly based on m orphologi 2cal and geographical data ,resulting in various tax onomic

system ,am ong which those of S wingle [2]and T anaka [3]are m ost widely accepted.In the mid 1970s ,a com prehensive numerical classification study based on 146m orphological and biochemical characteristics [4]and studies of Scora [5]proposed that cultivated Citrus com prises only three basic species ,i.e.,citron (C.medica ),mandarin (C.reticula 2

ta )and pummelo (C.grandis ;now C.maxima ),later C.halimii added as the fourth basic species

[1]

.The other

biotypes were derived from hybridization am ong these true species or between them and species of the subgenus Papeda or closely related genera.The other species names are retained as“convenient species”[1].

In recent several decades,plant m olecular systemat2 ics developed rapidly,which has been em ployed in the phylogenetic relationship studies of Citrus.The application of RF LP,ISSR,SC AR and PCR-RF LP of specific region of organelle genome in Citrus phylogenetic relationship have brought new prospect to it[6].H owever,the results are not always in agreement.C ombining analysis with sev2 eral approaches will probably better im prove the accuracy of phylogenetic in ference.O f the many m olecular tech2 niques available to researchers,sim ple sequence repeats (SSRs)or microsatellites is becoming increasingly widespread because it is codominant,highly polym orphic, frequently and evenly distributed throughout the genome. And it was regarded to be the m ost reliable marker.It has been used in the phylogeny studies of many plants such as G lycine[7],potato[8]and Vitaceae[9].But there is no re2 port about the application of SSR markers in phylogenetic relationships of Citrus and its relatives as yet.China is one of the m ost im portant origin places of Citrus with abundant germ plasms.Herein SSR markers were utilized to analyze 29accessions of Citrus and six related genera,aiming to provide new data for the study of phylogenetic relation2 ships of Citrus.

1 Materials and Methods

1.1 P lant m aterials

19accessions of Citrus and10accessions from six related genus were included(T able1).The plant materi2 als were collected from five places and DNA of three ac2 cessions were donated by Dr.DQ Fang(T able1).

1.2 DNA extraction

About3g of fresh y oung leaf tissue were collected from each plant,which were kept at-76℃until use for DNA preparation.The leaf was grounded to fine powder with the aid of frozen in liquid nitrogen.A m odified S DS method described by Chen et al.[10]was used for DNA extraction.DNA concentration was determined with the abs orbance in260nm using spectrophotometer UV1601 (Shimadzu Inc.,Japan).The DNA tem plates were diluted to25ng/μl.

T able1 P lant m aterial used in the study

C ode C omm on name S wingle system S ourcea a)

1Atlantia Atlantia monophylla DC.A

2Australia finger lime Microcitrus australasica A

3Australia dessert lime Eremocitrus glauca Swingle A

4Chinese box orange Severinia buxifolia Tenore A

5Z aoshi trifoliate orange P.trifoliata Raf.C

6Fum in P.polyandra Ding et al.D

7Flying drag on P.trifoliata Raf.B

8T anghe trifoliate orange P.trifoliata Raf.D

9M eiwa K umquat Fortunella crassifolia B

10K ahsi papeda https://www.doczj.com/doc/0717499436.html,tipes S wingle F

11M aritius papeda C.hystrix DC E

12H onghe papeda C.honghensis YL D L A

13Ichang papeda C.ichangensis S wingle A

14Lime C.aurantifolia S wingle B

15Valancia sweet orange C.sinensis Osbeck B

16S our orange C.aurantium Linn.B

17R ough lem on C.jambhiri Osbeck B

18Shatian pummelo C.maxima(Burm.)M erril A

19G rapefruit C.paradisi M acf.B

20Lime C.aurantifolia S wingle B

21Daoxian wild tangerin C.reticulata Blanco A

22Bendizao tangerin C.reticulata Blanco B

23Changsha tangerin C.reticulata Blanco F

24T achibana C.tachibana T an.B

25unnamed C.halimii S tone B

26Small citron C.medica Linn.A

27H ongkong kumquat F.hindsii B

28Lem on C.limon Burm.B

29Red lem on C.limonia Osbeck A

 a)A:Citrus Research Institute,Chinese Academy of Agricultural Science (Chongqing,China);B:Citrus Research Institute,Huazhong Agricultural Uni2 versity(Wuhan,China);C:Y ichang,Hubei,China;D:T anghe,Henan,Chi2 na;E:K unm ing,Y unnan,China;F:D onated by Dr.Fang from UCR,River2 side,US A

1.3 SSR

1.3.1 PCR am plification

A total of seven primer pairs were used(T able2). The primer pairs were synthesized by Sang on Inc.(Shang2 hai,China)according to published sequences of K ijas et al[11].The PCR am plifications were performed in20μl reaction v olume containing10mm ol/L T ris2HCl(pH

28遗 传 学 报30卷 

813),50mm ol/L K Cl ,115mm ol/L MgCl 2,110unit Taq polymerase (Sang on Inc.),012mm ol/L of each dNTP ,011μm ol/L of each forward and reverse primer ,50ng of tem plate DNA and sterilized double stilled water.PCR am plifications were performed in a PT C 200therm ocycler (M J Research Inc.,US A )with the following cycling pa 2rameters :an initial denaturation step at 94℃for 5min ,followed by 30cycles at 94℃for 1min ,an annealing

tem perature at 55℃(T AA3345℃

)for 1min and an ex 2tension at 72℃for 1min ,with a final extension step at 72℃for 5min prior to being holded at 4℃.

T able 2 Polymorphism of the SSR primers

Primer Alleles number

PIC

T AA1100.521T AA15240.750T AA52170.864AGG 170.613T AA3390.473T AA27110.458T AA45260.858

total 114 NA

mean

16.3

0.648

1.3.2 Detection of the SSR products

The PCR products were first run on a 115%agarose gel and visualized with ethidium bromide in order to de 2tect am plification success.I f am plification was success ful ,the PCR product was run on a 0104mm thick 6%poly 2acrylamide denaturing gel.G els were pre -run at 60W for 30min.The sam ples were loaded and run under the

same conditions for about 115h.Fragments were visual 2ized by the silver -staining method according to the man 2

ual of Silver Staining K it Q4132(Promega ,US A ).1.3.3 Statistical analysis

SSR was scored as A for presance and T for absence manually.Diversity level of locus were evaluated with the

polym orphic in formation content (PIC =1-

∑n

j =1

P 2i

)[12].

The genetic distance was calculated as p -distance of nu 2cleotide acid by MEG A2[13],equivalent to that estimated with a sim ple matching coefficient ,the proportion of shared A ’s and T ’s subtracted from 1.Thus a matrix was constructed ,which are available upon request.Neighbor -joining method was used to cluster and bootstrap [14]esti 2mates were calculated for 500re -sam plings.

2 Results

2.1 Polymorphism of the SSR m arkers

Seven pairs of SSR primers generated 114alleles ,all

of them were polym orphic.The SSR profile generated by primer T AA1was shown in Fig.1.

Primer T AA33am pli 2fied nine alleles ,whereas primer T AA45am plified as many as 26alleles.An average of w 1613alleles were am 2plified per primer.Primer T AA52had the highest PIC (01864),while T AA27had the lowest (01458),with a mean PIC of 01648(T able 2).

Fig.1 SSR profile of 29Citrus accessions using primer p air TAA1

Number refers to the sam ples listed in T able 1;M:100bp DNA ladder (promega )

3

8 1期庞晓明等:用SSR 标记研究柑橘属及其近缘属植物的亲缘关系

2.2 Phylogenetic relationships revealed by SSR

m arkers clustering

The highest genetic distance (01219)was observed between C.ichangensis and Flyingdrag on trifoliate or 2ange ,while the lowest (0)was observed between Z aoshi trifoliate orange and T anghe trifoliate orange.Based on pairwise diatances ,a dendrogram was constructed using neighbour -joining method ,which is presented and only bootstrap values higher than 40%were added on the nodes (Fig.2).Neither the separation of subgenus Pape 2

da and Citrus nor that of subgenus Archicitrus and Metac 2itrus by T anaka were clearly res olved in the dendrogram.C.reticulata ,C.maxima and C.medica were separated

into three distinct clusters ,supporting the three basic

species concept [4].It could be seen from Fig.2that all

the accessions could be grouped into ten clusters :(1)At 2

lantia and Severinia which do not belong to the T rue Cit 2

rus Fruit T rees were distant from other accessions ;(2)

Microcitrus and

Eremocitrus clustered together ,which

were close to Citrus ;(3)Three trifoliate orange acces 2sions;(4)Fumin trifoliate orange and C.halimii ;(5)

C.aurantium ,C.sinensis C.maxima and C.paradisi ;(6) C.honghensis ;(7) C.ichangensis and https://www.doczj.com/doc/0717499436.html,tipes ;

(8)T w o Fortunella accessions ;(9)three mandarin ac 2cessions and C.tachibana ;(10)the cluster consists of tw o subclusters ,one subcluster com prises of C.lemonia ,

C.jambhiri and C.medica ,C.limon while the other

com prises of C.aurantifolia var.mexican lime ,C.au 2

rantifolia and C.

hytrix.

Fig.2 A neighbour -joining tree for 29accessions of Citrus and its related genera derived from bootstrap analysis (500relications)of SSR d ata with percentage of confidence levels higher th an 40%on arms

48遗 传 学 报30卷 

3 Discussion

In the present study,based on the results of SSR analysis,Microcitrus was nested in Citrus,which im plied the close relationship between Microcitrus and Citrus.The results was in agreement with the m orphlogical studies of S wingle and Reece[2]and is ozyme results[15].Likewise com plete pairing of chrom os omes in meiosis in the inter2 generic hybrid between Microcitrus and Citrus dem onstrat2 ed that they originated from a comm on ancestor[16].These data indicates that it is acceptable as proposed by Mab2 berley[17]to reclassify Microcitrus into Citrus.

Huang[18]that Poncirus was probably the offspring of certain Citrus species,which ev olved into Poncirus when it was spread from the s outh to the north of China.H owever,Poncirus was believed to be phylogenet2 icly distant from Citrus in m ost studies[15,16,19,20],which was similar in the SSR results herein.Therefore it is hard to consider Poncirus was derived from Citrus.

Fumin trifoliate orange was found by Ding et al.[21] in1977in Y unan province.Based on the m orphological data,Ding et al recognized it as a new species Poncirus polyandra S.Q.Ding et al..,which was subsequently supported by is ozyme data[22]and pollen m orphology[23].

H owever G uo et al.[24]asserted it was the intergenric hy2 brid between Citrus and Poncirus.Based on the is ozyme data,Fang postulated that the taxa with the higher ho2 m ozyg osity was of m ore primitive origin[25].The distinct position of Fumin trifoliate orange was reflected by the fact that it was hom ozyg ous in six of seven SSR loci,whereas the three P.trifoliate accessions had only three hom ozy2 g ous loci.Thus,our results gave further evidence to the species status of Fumin trifoliate orange.

S wingle and Reece[2]reported that there were signif2 icantly differences between Fortunella and Citrus in m or2 phology.O f the six genus of the T rue Citrus Fruit T rees, Fortunella was the m ost sim ple and primitive genera while Citrus represented the highest stage of ev olution.H owev2 er,recent m olecular approaches found there has not the same level of divergence at the m olecular level[26].It was not unexpected since m orphological change and m olecular divergence are quite independent,responding to different ev olutionary pressures and following different rules[27]. Fortunella was nested within Citrus based on is ozyme[28], RF LP[26]and protein analysis[29].But it was found to be distant from Citrus by cpDNA data[20,30],which is in ac2 cordance with the present research.This incongruence may result from different m olecular marker sam pling different regions in the genome[31],which manifests that it is nec2 essary to analyze with different methods dealing with Cit2 rus phylogeny.

The research dem onstrated that C.honghensis was related to pummelo,which was reported by RF LP and RAPD data elsewhere[26].The numerical tax onomic study by Zhong and Y e[32]als o showed pummelo had s ome rela2 tionships with C.honghensis. C.hystrix is a con fusing type.S wingle and Reece[2]believed it was a g ood species.It was clustered together with C.medica by RAPD data[33],s o did by our SSR data,im plying possible relationship between C.hystrix and C.medica.Zhou[34] als o deduced that it might be of hybrid origin based on the cladistic analysis of m orphological characters.H owever,its heterozgy osity index based on RF LP was very low[26], which argued against the view of hybrid origin.

The Papeda did not form a single cluster,in agree2 ment with RF LP data[26],cpDNA data[20],numerical tax o2 nomic study of m orphological characters[32].H owever,the RF LP plus RAPD[26]RAPD data[20]clustered Papeda to2 gether.The close relationships between Citrus and Papeda might lend the evidence to T anaka’s hypotheses that Cit2 rus originated in Asia about30million years ag o from Papeda species[35],which is consistent with cpDNA re2 sults[20].

Recently,with the application of is ozyme,RAPD, RF LP and ISSR,the focus of research on Citrus classifica2 tion has shifted from the speices number to the phyloge2 netic relationships.The origin of several biotypes has been clarified[6].M ore and m ore studies supported the view2 point of three basic species,however the three basic species do not inv olve Papeda while several studies found the strong relationship between Papeda and Cit2 rus[15,20,26,28,36].The present data did not support the subgenus separation as put forward by S wingle and Reece[2]or T anaka[3]and Papeda should have played an im portant role in the origin of Citrus.C onsequently,it

58

 1期庞晓明等:用SSR标记研究柑橘属及其近缘属植物的亲缘关系

should be interesting to study m ore sam ples from Papeda accessions,such as C.ichangensis,C.hystrix and C. macrosperma[37],in order to further decipher the Citrus o2 rigin and phylogenetic relationships.

Acknow ledgements:The authors wish to thank Prof.ZS Chen,Mr.D Jiang,Mr.X Q Li of Citrus Research Institute of Chinese Academy of Agricultural Science for their help in collecting the materials.Further m ore,we w ould like to extend our appreciation to Dr.DQ Fang for donating the DNA of three accessions and Dr.J H Liu and Dr.XP Wen for their critical reviewing the manuscript.

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(责任编辑:周 素)

“纪念DNA模型发表50周年暨《遗传学报》创刊30周年

学术研讨会”报名通知

1953年4月25日,英国《自然》杂志发表了沃森和克里克的文章“核酸的分子结构———脱氧核糖核酸的一个结构模型”。DNA双螺旋结构模型的建立,标志着人类在揭示生命的遗传奥秘方面迈出了具有里程碑意义的一步。

《遗传学报》是中国遗传学会和中国科学院遗传与发育生物学研究所主办、科学出版社出版的高级学术刊物,中国自然科学核心期刊,国家重点期刊,全国期刊方阵“双百期刊”,已被美国化学文摘(C A)、生物学文摘(BA)、医学索引(ME D)等30余种国内外重要检索系统和数据库收录。

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1.主办单位:中国遗传学会,中国科学院遗传与发育生

物学研究所,东南大学

承办单位:《遗传学报》、

《遗传》杂志编辑室,东南大学

医学院遗传学研究中心

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《遗传学报》、

《遗传》杂志主编 朱立煌

东南大学校长 顾冠群

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副所长薛勇彪、东南大学副校长浦跃朴大会秘书长:李绍武、谢 维

3.会议日期:2003年4月20~24日

2003年3月20日前报名并交费者,注册费400元,会上交款者,注册费600元。国内公司展费2000元,外商3000元。

4.地 点:南京丁家桥:东南大学医学院

5.会议内容:(1)纪念DNA双螺旋结构模型发表50周年学术报告,优秀征文颁奖

(2)《遗传学报》30年回顾与展望;表彰优秀编委;推荐下届编委人选

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2003年1月10日

78

 1期庞晓明等:用SSR标记研究柑橘属及其近缘属植物的亲缘关系

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