101 A dvances in Environmental Biology, 3(1): 101-106, 2009 ISSN 1995-0756
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101 A dvances in Environmental Biology, 3(1): 101-106, 2009 ISSN 1995-0756
101 A dvances in Environmental Biology, 3(1): 101-106, 2009 ISSN 1995-0756 © 2009, A merican-Euras ian Network for Scientific Information ORIGINAL ARTICLE T his is a refereed journal and all articles are professionally screened and reviewed Genetic Relatedness among Romanian Olive Trees and Varieties Using Amplified Fragment Length Polymorphism (AFLP) Markers 1 Ibrahim Mohammad Rawashdeh, 1Na s a b Q. Rawashdeh, Amri, Saleh Shdaifat and 4Abdel Rahman Al-Tawaha. 2 Abdel Nabi Fardous ³Ahmed 1 Medicinal plants and biodiversity program, National C enter for Agricultural Research and Technology Transfer (NCARTT), P. O. Box 639. Baq’a, Jordan. 2 water management in dry lands and environmental biophysics, (NCARTT) ³Internati o n a l C enter for Agriculture Research in the Dry Areas (ICARDA), West Asia office, Amman. 4 Olive program, NCART, P. O. Box 639. Baq’a, Jordan. 4 Department of Biological Sciences, Al Hussein Bin Talal University, Maan, P.O. Box 20, Jordan. Ibrahim M ohammad Rawas hdeh,; Genetic Related n e s s among Romanian Olive Trees and Varieties Us ing A mplified Fragment Length Polymorphis m (A F LP) M arkers ,Am.-Eurasian J. Sustain. Agric., 3(1): 101-106, 2009 ABS TRACT A mplified fragment length polymorphis m (A FLP) a nalys is was us ed to s tudy the genetic variations among and within different individuals o f Ro ma n ian olive trees from two regions Tafilah and A jlun along with s ix varieties . Four primer combinations were us ed which pro d u ced about 538 amplified fragment. Dendrogram and matrix of s imilarity were obtained by the Unweighted Pair-Group M ethod analys is (U P GM A ). A jlun Romanian o liv e trees formed a s eparated group and mos t of Tafilah trees were formed with a s eparated grou p . H ig h s imilarity (39%) among all tes ted individuals was obs erved between two s amples of A jlun. A mong varieties Ras ee and Improved Nabali were s howed high s imilarit y (25%). A FLP confirmed that their is a genetic variations within Romania n o liv e tres s which lead to enlarge the s tudying thos e trees morphologically and biochemically to entering p ro mis e o n es within breeding programs in the future. Finally, A FLP has a powerful tool for detecting ge n e t ic v a riability among cultivars and s pecies help in known the pedigree of relatives and ances tors . Key words: A FLP, Olive, Jordan, Romanian trees and Polymorphis m. Introduction O live (Olea europaea L.) is an evergreen t re e grown at temperate regions with altitude ranged from (400m to 1500m) above s ea level (a . s . l.). The produ c tion is bas ed on the climatic conditions , tree cu ltivation as well the phys iological s tate of trees , thes e lead to phenomenon known "alternate bearing". In Jordan, olive culture is one o f the mos t important agriculture activities , the olive plantations accounted more than 10 million trees , where the Nabali Ba la d i is the mos t wides pread and the dominant cultivar. Oil production was exceeded the needs that allow for government to export the s urplus into neig h b o r countries and Europe markets . M oreover, Jordan oliv e oil cons idered the bes t among other countries bas ed on the p e rcentage of PH. However, mos t framers s aid that the old trees (Roma n ia n ) are bes t than t h e in t ro d u c e d v a rie t ie s t a kin g into cons iderations the fruit quality and oil perc e n tage. This s aying oriented the direction to s t u d y t he genetic relatednes s among thos e and introduced varieties us ing the molecular markers . Corres ponding Author Ibrahim M ohammad Rawashdeh, M edicinal plants and biodiversity program, National Center for Agricultural Research and Technology Transfer (NCARTT), P. O. Box 639. Baq’a, Jordan. E-mail: [email protected]. Adv. Environ. Biol., 3(1): 101-106, 2009 Changes in lifes tyles and cooking habits towards healthy eating, enviro n me ntal concerns , exotic cuis ine, and convenience food have opened n e w market opportunities for olive oil products [11]. Olive oil is the principal s ource of fat in the M editerranean die t , which has been as s ociated with a lower incidence of coronary heart dis eas e and cert ain cancers [15]. A dulteration is , the adding cheaper materials from other oil products , the bigges t problem faced the cons umers and the directions now toward to have organic farming to ge t h igh quality and guarantee production. Traditionally, morphological and phys iological traits were us ed to identify olive cultivars , more recently, molecular markers have been fo u nd to be a us eful tool for cultiv ar identification and determining patterns of relatednes s amo ng cultivars . Recently, DNA –bas ed techniqu e s have been developed to detect genetic variations wit hin and among varieties , p o p u la t ions and s pecies . Ran d o m a mp lifie d polymorphic DNA (RA PD) us ed for detecting genetic variation in mutants of Nabali olive cultivar [13]. In a d d it io n , RA P D t e c h n iq u e w a s u s e d t o c h a ra cterization olive varie t ie s [16], g e n e t ic relations hips [6,2], cultivars analys is [10,3], genetic divers ity and A lbania n o live germplas m [4,5] and identification cultivars [8]. A mplified Fragment Length Polymo rp h is m (A FLP) markers have been developed by Vos et al., [14] and widely s pread due to its reliability and robus tnes s . The us e of A FLP has s ome advantages in terms of us e in the identification of d ia g nos tic or s pecific markers , it has s everal advantages , it does n’t require previous knowledge of the DNA s equence, gen erate reproducible fingerprinting profiles , allows the amplification of a h ig h number of DNA fragments per reaction and enabling the detectio n of s pecific amplified fragments [14,9]. A FLP markers w ere us ed to s tudy the relation between olive cultiv a rs from W es tern M editerranean [1] and dis criminated among olive varieties [5]. The purpos e of this s tudy was to detect the genetic relatednes s among the olive Romanian trees a n d olive cultivars were grown in Jordan by us in g A FLP markers . Materials and methods -Plant material Leaves s elected ra n d o mly from around the trees o f e ighteen olive Romanian trees and s ix varietie s were collected from private farms North (A jlu n - A lHas himiah) and s outh (Tafilah) regions of Jordan, while leaf s amples of olive varieties were collected from A l-Hus s ein nurs ery -M inis try of A griculture during A ugus t 2006. Olive s amples from Tafilah region were s tored at refrigerator until proces s ing for DNA is olation, but samples of varieties and thos e from North were us ed fres hly. 102 DNA isolation DNA was obtained after ground the s tored leaves in liquid n it rogen (-196ºC), the quality and quantity of genomic DNA were detected on agaros e gel. Total cellular DNA was extracte d us ing anew-modified CTA B is olation protocol. A pproximately (20 to 30 mg) fres h and s tored leaves were ground and mixed with 750 µl of fres hly and preheated of (2x CT A B s olution with 0.8g PVPP) in 2ml tubes then pla c ed a t 65º C for 30 min. the mixture was mixed with 750 µl of chlorop h o rm/ is oamyl alcohol (24:1) vortex a fe w s econds , thos e centrifuged at 14000g for 20 min. Upper ph a s e (s upernatant) was placed in 2ml tubes with 600ml is opropanol, tubes were s haked until the thread o f DNA appeared, then centrifuged for 20 min at 14000g. The s olution poured and tubes left to dry, the n 600 µl of cooled 70% ethanol added and placed at refrigerator (–20ºC) overnight. Next day ethanol w a s p o ured, tubes dried and 100µl of TE added an d p la c ed at 65ºC for 30min. Four micolitter of RN A s e (10mg/ml) were added per tube and left for 45min at 37ºC. DNA quantitation was meas ured us ing machine of S2100 UV/VIS DIODE-A rray-Spect rophotometer, Vers ion 1.7. AFLP procedure Th e A FLP procedure was performed as previous ly des cribed (Vos e e t al., 1995). Olive DNA (500ng) was double diges ted with EcoRI and Tru91 (an is ochizomer o f MseI) and double s tranded adaptors were ligated to the ends of DNA fragments , generat in g template DNA for s ubs equent PCR a mp lification (p re -a mp lific a t io n fo llo w e d b y s elective). Res t riction and ligation reactions were carried ou t s imultaneous ly in a s ingle reaction tube [14]. To c a rry out the reaction, an enzyme mas ter mix for 16 reactions was prepared containing 2µl Ec o R I buffer, 2µl Tru91 buffer, 0.25µl EcoRI enzyme (12u/µl), 0.25µl Tru91 enzyme (12u/µl), 0.625µl 1mg/ml BSA , 9.875µl d d H 2O and 5µl genomic DNA (500ng ), t he mix was centrifuged for a few s econds then s tored at 37ºC for 3 hr. The res triction-ligation reactions cons is t e d of 0.5 µl 10x T4 buffer, 0.2µl T4 DNA ligas e (3u/µl), 0.5µl Tru 9 1 a daptor forward, 0.5µl Tru91 adaptor backward, 0.5µl EcoRI adaptor forward, 0.5µl EcoRI adaptor backward and 2.3µl ddH2O. Thos e dis tributed 5µl for the res triction tubes , then s tored at 37ºC for 3hr.T he res trictionligatio n reactions were diluted 1: 4, then us ed in preamplification s tep . The Tru91complementary primer had a 3'-C and the EcoRI compleme n t a ry primer had a 3'-A . The pre-amplification (pres elective) mix was prepared by adding 2µl of 5-fo ld diluted DNA from the res triction-lig a t ion reaction, 2.5µl 10xbuffer (PCR), 2.5µl dNTPs (5mM ), 1µl A FLP pres elective Adv. Environ. Biol., 3(1): 101-106, 2009 primer (EcoRI+ A -3'), 1µl A FLP pres e lective primer (Tru91+ C-3'), 0.2µl Taq polymeras e (5u/µl) and 15.8µl ddH2O. The pre-amplification (pres elective) amplification was carried out in a th e rmal cycler prog rammed at 72ºC for 2min followed by 20 cycles of 94ºC for 30 s , 56ºC for 40s and 72ºC for 50s and finally incubated at 4º C. The pre-amplification DNA w a s diluted 5-fold with ddH2O and s elective amplifica t io ns were carried out by us ing different EcoRI and Tru91 primer combination (A lpha DNA ). Primers s elected fo r the s election amplification were from available A FLP s elective primers that purchas ed before and s tore d at –20ºC at NCA RTT lab. The EcoRI primers contained thre e s elective nucleotides with s equence (Table 1) while the Tru91 primers had the s elective nucleotides s tarting with G (Table 1). For the s elective amplification, the reactions were s et up as follows : 2µl of 5-fold diluted pre-s elective amplification reaction product, 1.0µl Tru91 p rimers , 1.0µl EcoRI primers , 2µl of 10 x buffer, 2µl dNTPs (0.25mM ), 0.2µlT a q polymeras e (5u/µl), 0.25µl of M gCl2 (15mM ) and 11.55ddH2O. Se le c t ive amplification was carried out in a thermal cycler programmed at 94ºC for 2min, follo w ed by 13 cycles of 94ºC for 20s , 68ºC (0.7ºC /cycle) fo r 30s and 72ºC for 1min, and 23 cycles of 94ºC for 30s , 59º C for 30s and 72ºC for 1min and fin al incubation at 4ºC.The s amples were loaded on 6% polyacrylamide gel o n A pelex gel s equencing apparatus (vertical). The s elective amplifica tion reaction product (6µl) w a s mixed with 4ul of loading buffer (98% deionized fo ramide, 10mM EDTA (pH: 8), 0.05% b romofenol, 0.05% xylene cyanol), from which 6µl was finally loaded on the gel. Four primer pair combinations (EcoRI- / Tru91-) were us ed in analys is (Table 2), s ix olive varie ties and eighteen s amples o f Romanian trees from each A jlun and Tafilah regions were s ubjected to the s e le c t iv e a mp lific a t io n w it h t h e s e p rime r combinations , and treated under the s ame conditions by the s ame res earc h e r. To determine the s ize of the A FLP fragments , we us ed an A F LP DNA marker (50bp s tep ladder) (Promega), ranging in length fro m 50 - 800bp. Data analysis A FLP polymorphic bands were s cored as pres ent (1) o r abs ent (0) an es timates of s imilarity among all varieties w e e calculated according to Nei and Li, [12] definition o f s imilarity Sij= 2a/ 2a+b+c, where S ij is the s imilarity between t w o v a rie t ie s (in d ividuals ) i and j, a is the number of bands pres ent in both individuals , b is the number of bands pres ent in j and abs ent in i. The matrix of s imilarity was analyzed by the Unweighted Pair-Group M ethod (UPGM A ) and the d e n d rogram was obtained us ing s ps s . Vers ion 10. Program. 103 Res ults and Dis cus s ion Only one primer combinatio n s o ut of five, A GCCA T, w a s failed to produce at leas t one amplified fragment. T h e A FLP fingerprinting of the s ix olive v a rieties and eighteen s amples of Romanian trees were collected from each A jlun and Tafia lh regions (Table 1), tes ted us ing four random primer pair combinations (Table 2 and 3), revealed a total number of 1119 amplified D N A fragments , 538 out of t h em turned to be polymorphic and were dis tributed acros s the entire lanes . The av erage percentage of polymorphis m ranged from 25% for EA A C-M CCT (Tafialh Romania n t rees ) to 71% for EA GC-M CA C for (Tafialh Romanian trees ) (Table 3) for olive v a rieties high percentage of polymorphis m s howed by EA CT-M CA A and t he lowes t percentage of polymorphis m is 45% for EA A C-M CCT (Table 3). S o me bands wee s pecific to one or more of A jlun and Tafialh als o the s ame to olive varieties . V a r iations among olive varieties, Ajlun and Tafila h Romanian olive trees Dendrogram cons tructed by UPGM A derived from s imilarity matrix des cribed above, s howed five main dis tinct clus ters (Figure 1). The firs t clus ter was formed twelve olive s amples of A jlun. The s e c ond clus ter formed two individuals from A jlu n . The third group formed four s a mples of A jlun, four s amples of Tafilah and two s amples of Tafilah with one A jlun s ample . The four clus ter formed two s amples of Tafilah Romanian trees with one s ample of A jlun. The fifth clus ter can be divided into tw o groups , the firs t included two s ub–s ub clus ters ; one formed olive variety K18 with one individual tree from Tafila, the s econd formed two indiv id uals of Tafilah and Nabali Baladi s howed s eparated grou p (Figure 1). The s econd s ub-s ub clus ter is included two groups ; the first has two Tafilah individuals w h ich are more clos ely and one s ample has s eparated group. The s ec ond group of the fifth clus ters were formed three groups the firs t formed Nas ohee variety an d o ne individual Tafilah s ample als o it was wholly s eparated fro m this group (Figure 1). The s econd group s howed that Ras ee and imp roved Nabali more c los ely but s howed s haring with one A jlun s a mp le and all of them collected in one gro u p . W ithin this group one s ample of Tafilah individuals was s howed s eparated from other. O n e s ample of Tafilah was s howed a s eparated one among all s a mp les within this group. Jaccard´s genetic s imilarity (Table 4) e s timated w ithin and among all tes ted individuals s howed the highes t s imila rity values in Ras ee variety and A jlun s ample (0.182) and the lowes t value (0.000) between improved Nabali a nd A jlun. High s imilarity was regis tered between K18 and onTafila h s ample (0.205) and the lowes t value (0.017). Adv. Environ. Biol., 3(1): 101-106, 2009 104 Table 1: Olive varieties were collected from Al-Hussein nursery / Ministry of Agriculture in Jordan. Variety name Source of collection 1-K18 AL-Hussein nursery 2-Nabali baladi AL-Hussein nursery 3- Rasee AL-Hussein nursery 4- Grosadee AL-Hussein nursery 5- Nasohee AL-Hussein nursery 6-Improved Nabali AL-Hussein nursery Table 2: Oligonucleotides adaptors and primer combinations used for AFLP analysis. Name EcoRI adaptor Tru91 adaptor Primers used in pre-amplification EcoRI+1-A Tru91+1-C Primers used in selective amplification EcoRI+3-AGC EcoRI+3-ACT EcoRI+3-AAC MseI (an isochizomer of Tru91) MseI+3-CAC MseI+3-CAA MseI+3-CCT Primer pair combinations (EcoRI/ MseI). 1-AGC-CAC 2-ACT -CAC 3-AAC-CCT 4-ACT -CAA / / / / / / Ministry Ministry Ministry Ministry Ministry Ministry of of of of of of Agriculture Agriculture Agriculture Agriculture Agriculture Agriculture Sequence 5'- CT CGT AGACT GCGT ACC-3' 3'- AAT T GGT ACGCAGT C-5' 5'-GACGAT AGT CCT GAG-3' 3'-T ACT CAGGACT CAT -5' 5'-GACTGCGTACCAATTCA-3' 5'-GAT GAGT CCT GAGT AAC-3' 5'-GACT GCGT ACCAAT T C+AGC-3' 5'-GACT GCGT ACCAAT T C+ACT -3' 5'-GACT GCGT ACCAAT T C+AAC-3' 5'-GAT GAGT CCT GAGT AAC+CAC-3' 5'-GAT GAGT CCT GAGT AAC+CAA-3' 5'-GAT GAGT CCT GAGT AAC+CCT -3' Table 3: Polymorphism rates related t o t h e fo u r A F LP primer combinations among eighteen Romanian olive trees from each T afilah and Ajlun governorate and six varieties. Primer combination Source of genome T otal number of fragments Polymorphic fragments Polymorphism (%) AGC-CAC -T afilah-Romanian olive trees 70 50 71 -Ajlun-Romanian olive trees. 86 49 57 -Six olive varieties 67 37 55 ACT -CAA -T afilah-Romanian olive trees 49 24 49 -Ajlun-Romanian olive trees. 129 44 34 -Six olive varieties 62 45 72 AAC-CCT -T afilah-Romanian olive trees 154 38 25 -Ajlun-Romanian olive trees. 104 46 44 -Six olive varieties 60 27 45 ACT -CAA -T afilah-Romanian olive trees 113 59 52 -Ajlun-Romanian olive trees. 172 85 49 -Six olive varieties 53 34 64 T otal: 1119 T otal: 538 Mean: 51 Variations among olive varieties Dendrogram (Figure 1) was s h owed that the two following varieties Ras ee and Improved Nabali w ere more clos ely but formed with A jlun s ample. Nabali baladi and K18 w e re s hared with Tafilah Romanian oliv e trees . High s imilarity was s howed between improved Nabali and Ras ee (0.254) and the lowe s t was s howed between Nabali Ba ladi and improved Nabali (0.074). Variations within Ajlun Romanian olive trees Out of 18 individuals of Romanian oliv e trees , twelve individuals were formed a s eparate gro up and is olated from the whole dendrogram. W ithin this group, the dend rogram can be divided and formed two s ub-groups , the firs t includes s ix s amples , but the s econd formed five s amples , further the firs t group have two s ub groups , while the s econd formed two s ub groups , als o four individual trees were s hare d with four s amples from Tafilah. High s imilarity (0.39) was s howed between individuals n umbers (5 and 6) while the lowes t (0.000) w a s recorded for individuals numbers (10 and 14). Variations within Tafilah Romanian olive trees Out of 18 individuals of Roma nian olive trees , s ix trees were s howed s eparated gro u p , while two individuals formed alone, two individuals formed alone and s h ared with K18. Four individuals formed alone but s hared with s ame s amples of A jlun. Olive variety "Nabali Bala di" was formed with the group of Tafila h , in addition Nas hoe variety s hared with one Tafilah s ample. Not only Tafilah but als o one Adv. Environ. Biol., 3(1): 101-106, 2009 105 Fig. 1: Dendrogram generated among Romanian olive Trees and s ix varietie s b y us ing four primer pair combinations bas ed on A FLP markers . A j.: A jlun s ouree for Romanian trees , T a .: T a fa ilah s ource for Romanian tree. Impro. Nabal: improved nabali. s ample fro m A jlun s hared with the s ame group of Ras ee, Gros adee and improved Nabali. Tafilah. High s imilarity was s howed between (0.20) betwe e n number of individuals (22 and 25) but the lowes t value is (0.000) between individual numbers (25 and 35). Discussion The minimum us ing of primer combinations and s amples are better to have highly polymorphic amplified fragments and eas ily to dis criminate among t es ted genotypes . A mong tes ted primers , A CT-CA A and A GC-CA A were very important primers th a t can b e u s ed for either s creening wild, landraces acces s ions and remaining olive varietie s were unknown or untes ted. A FLP analys is demons trated that Romanian olive trees either fromTafilah or A jlu n had high genetic varia b ility within and among tes ted individuals this was s howed through dendrogram. M oreover, there is s ome individuals from A jlun or Tafilah als o s howed broad genetic variability when th e y are formed a s eparated group. This variability is related to the g enetic changes over all pas t years were expos ed t o through s pontaneous mutations of naturally s election or s ometimes human capacities . Lo c a l farmers and s ome res earchers s aid that their is a relatio n s h ip between Ras ee and improved nabali, this s tudy was confirmed this s a y ing through a dendrogram that s howed both were grouped together. M ore over, Nas ohee v a rie t y which c ommonly known its origin from Tafilah s o, in our res ults this va rie t y was grouped with s ome individuals o f this region. M oreover, in addition to genetic make up there is als o geographical features , is olation an d c limatic conditions als o play a great role for creating variability within o r a mong individuals . A FLP has a p o werful for detecting genetic variability among cultivars and s pecies als o help in known the pedigree relatives and ances tors . References 1. A ngiolillo, A ., M .O. M e n c u c cini and L. Baldoni, 1999. 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