Comparative Genome Mapping Between Apple and Pear by Apple Mapped SSR Markers

Transcription

1 Amerin-Eursin J. Agri. & Environ. Si., 9 (3): , 2010 ISSN IDOSI Pulitions, 2010 Comprtive Genome Mpping Between Apple nd Per y Apple Mpped SSR Mrkers Min Lu, Horu Tng, Xioyng Chen, Ji Go, Qing Chen nd Ling Lin 1 College of Hortiulture, Sihun Agriulturl University, Y n , Sihun, Chin 2 College of Forestry, Sihun Agriulturl University, Y n , Sihun, Chin Astrt: Twenty nine pple-mpped SSRs were sreened out to onstrut per segment mp of Mishirzi (Pyrus pyrifoli P. ommunis) Jinhu (P. retshneideri). Synteny etween pple nd per ws dopted to onlude the linkge group numer. The Jinhu ws primry tken s representtive Chinese per to ompre geneti mp of pple nd Europen per (P. ommunis), Jpnese per (P. pyrifoli) nd Chinese per (P. retshneideri).the lignment of the speies mps sed on JoinMp nlysis mde it possile to verify the degree of synteny etween the pple nd per genomes. The pple SSR loi showed the sme order nd orresponding distnes in the per nd pple mps, strongly suggesting the presene of highly onserved regions etween the two genomes nd tht pple SSRs were more preferle to trnsfer nd onserve to Europen pers thn Asin pers. The most onserved segments of linkge group etween pple nd per were loted in LG 9, LG 11 nd LG 14 relying on 101 pple-mpped SSRs. The SSRs in LG 10 nd 12 wouldn t like to link eh other in the ultivr of P. retshneideri in Chin nd P. pyrifoli in Jpn, respetively. Key words: Comprtive genome mpping Apple Per Apple SSRs INTRODUCTION pers, P. ommunis is the mjor ultivted speies nd hs een widely produed throughout Europe, North nd SSRs (simple sequene repets, lso designted s South Amerin, Afri [10]. And of the Orientl pers, mirostellites) hve severl dvntges over other the ultivted speies re minly omposed of four moleulr mrkers, suh s o-dominnt inheritne nd groups: P. pyrifoli (minly in Jpn nd Chin) lrge numer of lleles per lous, undnt in genomes, nd nother three Chinese speies P. Ussuriensis, suitle for utomtion, only smll mount of DNA P. retshneideri nd P. sinkingensis [12]. In this pper required nd trnsferle mong speies in the sme we primry took Jinhu s representtive Chinese per genus, even mong gener in the sme fmily [1]. Apple of Sihun provine in Chin to ompre geneti mp nd per re oth lssified in fmily Rosee. And it of pple nd per (P. ommunis, P. pyrifoli nd is well-known tht pple SSRs n e suessfully P. retshneideri), to promote the further development trnsferred to per to study the ultivr identifition of omprtive genome mpping etween pple nd per. [2], prentge nlysis [3], geneti diversity [1, 4] nd mp onstrution [5, 6]. So omprtive genome mpping MATERIALS AND METHODS etween pple nd per hs developed muh more in the reent yers [7-9]. But ll the ojets for study were Plnt Mterils nd DNA Extrtion: An F 1 popultion Europen pers (Pyrus ommunis), exept Jpnese of Mishirzi (M) (P. pyrifoli P. ommunis) Jinhu ultivr Housui, still lking of Chinese pers. (JH) (P. retshneideri) (62 individuls) ws used for Per (Pyrus spp.) is one of the most importnt fruit this study. The ross ws rried out t the Sihun rops, hving een ultivted in Europe nd Asi for t Agriulturl University (Sihun, Chin), for reeding lest 2-3 thousnd yers [10]. Aording to the originl purposes. For eh F 1 genotype, 4 g of fresh young distriution, Pyrus is divided into two ntive groups: leves were ground in liquid nitrogen. DNA extrtion Oidentl nd Orientl pers [11]. Of the Oidentl ws performed following modified CTAB protool [13]. Corresponding Author: Horu Tng, College of Hortiulture, Sihun Agriulturl University, Y n , Sihun, Chin. Tel: , E-mil: htng@siu.edu.n. 303

2 Am-Eurs. J. Agri. & Environ. Si., 9 (3): , 2010 DNA qulity nd quntity were tested in 1% grose nd Mp Constrution: JoinMp 3.0 [16] ws used for the mesured y BioPhotometer for nulei id nd protein onstrution of prentl linkge mps M nd JH; (Eppendorf, Germn). Kosmi s funtion mde it possile to onvert reomintion perentges into entimorgn distnes. SSR Mrkers: A totl of 101 SSR pple mrkers [14, 15] For mpping, LOD sore of 5.0 ws onsidered were tested for segregtion in the F 1 popultion eptle. A single lous nlysis ws performed to desried ove. PCR mplifitions were performed in identify mrkers showing distortion from the expeted PTC-200 Therml Cyler (BioRd, USA) under the segregtion rtio. Skewed mrkers were disrded only if following onditions: 50 ng genomi DNA, 1 µm eh they introdued ovious disrepnies during the mp primer, 100 µm dntps, 1.5 mm MgCl 2, 50 mm KCl, 10 mm onstrution. The segments numer of linkge groups Tris-HCl ph 9.0, 1U Tq polymerse. The first yle of were onluded depend on the synteny theory in pple denturtion t 94 C for 2 min nd 30 s ws followed y 24 nd per [7, 8]. yles of nneling (60 C for 45s), extension (72 C for 1 min) nd denturtion (94 C for 30s); finl yle of RESULTS AND DISCUSSION extension (72 C for 10 min) ws dded. In some ses, the mplifition onditions were optimized for per y The SSR segregtion dt ws reported in Tle (1), djusting the nneling temperture. Amplifition together with the llele size s ompred to pple [15] nd produts were seprted on 6% denturing Europen per [8]. Twenty-four mrkers produed no or polyrylmide gels stined with the silver method nd fint mplifition. Some of them were greed with their weights determined y Gelpro32 softwre with 100 the results of Pierntoni et l. [8], suh s CH01f09, p DNA ldder (Tingen, Chin) s the stndrd. CH02g09, CH03g04, CH04d07, CH05d02 nd CH05e04. Tle 1: The trnsferility nd segregtion of pple mpped SSRs in per nd onlusion of per LGs sed on pple LGs Linkge Group on Mps Moleulr weight(p) segregtion type Apple Per SSR loi Apple Europen per M JH ode (M JH) Segregtion 2 d x vlue F D M JH CH03g lm ll lm:ll=33: /3 CH05g CS 1 CH02f NA 2 CH CS 2 CH lm ll lm:ll=32: CH CS 2/7 CH03d hk hk h-:kk=46: CH05e NA 2 CH03d NS 2 CH03e NS 3 CH03g ef eg ee:ef:eg:fg=19:16:9: MS14h lm ll lm:ll=33: NZ05g NA 4 CH04e NS 4 CH02h lm ll lm:ll=30: CH05d NA 4 CH01d lm ll lm:ll=36: /12 4 CH lm ll lm:ll=30: CH CS 4/12/13 CH lm ll lm:ll=36: CH05e lm ll lm:ll=26: CH04g lm ll lm:ll=28: /10 5 CH05f NA 5 CH CS 5/10 CH NA 5 CH nn np nn:np=31: CH04e lm ll lm:ll=33:

3 Am-Eurs. J. Agri. & Environ. Si., 9 (3): , 2010 Continued Tle 1: The trnsferility nd segregtion of pple mpped SSRs in per nd onlusion of per LGs sed on pple LGs Linkge Group on Mps Moleulr weight(p) Segregtion type Apple Per 2 d SSR loi Apple Europen per M JH ode (M JH) Segregtion x vlue F D M JH CH03d NA 6 NZ23g04 88 NA 6 CH03d d :d::d=17:22:8: CH lm ll lm:ll=24: CH04e lm ll lm:ll=31: CH hk hk h-:kk=46: CH01f NA 8 CH02g NA 8 CH hk hk hh:k-=19: *** 8/15 CH01h ef eg ee:ef:eg:fg=23:16:10: CH01f ef eg ee:ef:eg:fg=19:18:17: CH ef eg ee:ef:eg:fg=10:21:12: CH01h nn np nn:np=34: CH05d lm ll lm:ll=37: CH NA 10 CH lm ll lm:ll=33: CH01f NS 10 CH NS 10 CH03d CS 10 Col NS 10 CH NA 10 CH01f nn np nn:np=38:24 3.2* 10 MS hk hk hh:hk:kk=17:29: MS06g lm ll lm:ll=33: MS NA 10 CH04h ef eg ee:ef:eg:fg=20:15:10: CH02d NS 11 CH03d hk hk kk:h-=15: CH02d NA 11 CH d :d::d=13:15:15: CH04g lm ll lm:ll=34: CH04d NS 11 CH04d CS 11 MS NA 12 CH05d lm ll lm:ll=34: hk hk h-:kk=43: NZ28f lm ll lm:ll=32: CH04g NS 12 CH05d CS CH05g hk hk h-:kk=45: /14 14 hk hk h-:kk=39:23 4.8** 12 CH01g NS 12 CH01d NS 12 CH04d ef eg ee:ef:eg:fg=14:10:20: CH01f nn np nn:np=29: lm ll lm:ll=34: CH NA 12 CH03h NA 13 CH CS 13 CH NS 13 CH05f lm ll lm:ll=36: CH01g NS 14 CH03d hk hk hk:hh=42: ***

4 Am-Eurs. J. Agri. & Environ. Si., 9 (3): , 2010 Continued Tle 1: The trnsferility nd segregtion of pple mpped SSRs in per nd onlusion of per LGs sed on pple LGs Linkge Group on Mps Moleulr weight (p) Segregtion type Apple Per SSR loi Apple Europen per M JH ode (M JH) Segregtion 2 d x vlue F D M JH CH04f ef eg ee:ef:eg:fg=13:19:13: CH01e NA 14 MS nn np nn:np=40:22 5.2** CH05e NA 14 CH03g NA 14 CH05g ef eg ee:ef:eg:fg=13:10:16: CH nn np nn:np=31: CH NA 14 CH05d lm ll lm:ll=29: NZ CS 15 CH01d NS 15 CH02d lm ll lm:ll=32: CH lm ll lm:ll=30: CH NS 15 CH02d NS 16 CH CS 16 CH lm ll lm:ll=25: CH05e NA 16 CH NS 16 CH04f NA 16 CH nn np nn:np=24:38 3.2* CH05g hk hk h-:kk=45: nn np nn:np=31: CH02g NA 17 CH01h lm ll lm:ll=34: Dt from Grilford et l. (1997), Liehrd et l. (2002); Dt from Pierntoni et l. (2004); Segregtion type ode: NA no mplifition, NS no segregtion, CS omplex segregtion, d lous heterozygous in oth prnts, four lleles, ef eg lous heterozygous in oth prents, three lleles, hk hk lous heterozygous in oth prents, two lleles, lm ll lous heterozygous in femle prent, nn np d lous heterozygous in pollen prent; *, **, *** indite distortions t the 5%, 1%, 0.1% levels. Tle 2: Comprtive geneti mpping of pple nd per Per Europen per Asin per Apple P. ommunis P. Pyrifoli P. retshneideri SSR loi F D B L PC HS d AF MRB e Hosui Jinhu CH03g12 1/3 1/3 1/3 CH05g CH02f CH CH CH0204 2/7 2 CH03d CH03g MS14h NZ05g CH04e CH02h CH01d03 4/ CH CH CH05e CH04g09 5/10 5/10 CH05f CH0208 5/10 5/10 CH CH03d

5 Am-Eurs. J. Agri. & Environ. Si., 9 (3): , 2010 Continued Tle 2: Comprtive geneti mpping of pple nd per Per Europen per Asin per Apple P. ommunis P. pyrifoli P. retshneideri SSR loi F D B L PC HS d AF MRB e Hosui Jinhu CH CH04e CH CH0502 8/15 8/15 8 CH01h CH01f CH CH01h CH05d08 9 CH CH CH01f CH CH03d CH CH01f MS MS06g CH04h CH02d08 11 CH03d CH CH04g CH05d NZ28f CH04g CH05d CH05g07 12/14 12/ CH01d CH04d CH01f CH CH CH05f CH01g CH03d CH04f MS CH05g CH CH CH05d NZ CH01d CH02d CH CH CH CH CH CH CH05g CH01h Dt from Liehrd et l. (2002), Dt from Ymmoto et l. (2007), Dt from Dondini et l. (2004), d e Dt from Pierntoni et l. (2004), Dt from Ymmoto et l. (2004). 307

6 Am-Eurs. J. Agri. & Environ. Si., 9 (3): , 2010 But the others hd the opposite results, for exmple, pple mps (Fig. 1), strongly suggesting the presene CH0203, CH0207, CH02f06, CH03h03, CH05f06 whih of highly onserved regions etween the two were mpped on Europen pers nd CH01e01, CH02d12, genomes. The onservtion regions etween pple CH02g04, CH03d07, CH04f10, CH05e03, CH05e05 whih nd Europen per mps were t LG 10, LG 12 nd produed segregtion in Europen pers [8], hd no LG 14 [8]. But ompring to Chinese nd Jpnese mplifition in Mishirzi Jinhu. Seventeen mkers pers, the onserved segments of linkge group ws hd no segregtion nd eleven were omplex segregtion. loted in LG 9 (Fig. 1), LG 11 (Fig. 2) nd LG 14 (Fig. 3). The non-trnsferle SSR numer ws up to 52, whih The LG 14 eqully hd the densest SSRs, inluding ws doule more thn in Europen per [8], suggesting CH03d08, CH04f06, CH05g07 nd CH05g11, whih ws tht pple SSRs were more preferle to trnsfer to onsistent with Pierntoni et l. [8]. The oservtion Europen pers thn Asin pers. of synteny etween LG 9 nd LG 11 were lso the The lignment of the speies mps sed on sme s PC HS (6, 8, Tle 2). But the SSRs in LG 10 JoinMp nlysis mde it possile to verify the degree of nd 12 wouldn t like to link eh other in the ultivr of synteny etween the pple nd per genomes (Tle 2). P. retshneideri in Chin nd P. Pyrifoli in Jpn Brtlett L Frne mp hd the most numerous pple [7], respetively. All of these demonstrted tht SSRs in the five respetive per mps nd on the ontrry Europen nd Asin pers oriented to different ws Jinhu mp. The pple mpped SSRs oviously diretion during evolution, proly vried in LG 10 preferred Europen per to Asin per, espeilly nd LG 12. CH03d10 on LG 2, CH01d03 on LG 4, CH05e06 on LG 5, This pper studied the similrity etween two pple CH04e05 on LG 7, CH01f02, CH04g04 nd CH05d04 on LG nd per linkge mps, whih supported the study of the 12, CH05f04 on LG 13 nd CH01d08 on LG 15. reltionships etween these relted speies [8] nd The pple SSR loi showed the sme order proposed some new points of view. It represented nd orresponding distnes in the per nd in the further study in ompring pple nd per mps. Fig. 1: Alignment of the segment in LG 9 in pple vriety Fiest (F) [15] nd Europen per vriety L Frne (L) [9], Chinese per vrietiy Jinhu (JH) nd Jpnese per vrieties Housui (Ho) [5]. Fig. 2: Alignment of the segment in LG 11 in pple vriety Fiest (F) [15] nd Europen per vriety L Frne (L) [9], Chinese per vrietiy Jinhu (JH) nd Jpnese per vrieties Housui (Ho) [5]. 308

7 Am-Eurs. J. Agri. & Environ. Si., 9 (3): , 2010 Fig. 3: Alignment of the segment in LG 14 in pple vriety Fiest (F) [15] nd Europen per vriety L Frne (L) [9], Chinese per vriety Jinhu (JH) nd Jpnese per vrieties Housui (Ho) [5]. REFERENCES Chrteristion nd trnsferility of pple SSRs to two Europen per F 1 popultions. Theor. 1. Ymmoto, T., T. Kimur, Y. Swmur, K. Kotouki, Appl. Genet., 109: Y. Bn, T. Hyshi nd N. Mtsut, Ymmoto, T., T. Kimur, S. Terkmi, C. Nishitni, SSRs isolted from pple n identify polymorphism Y. Swmur, T. Sito, K. Kotouki nd T. Hyshi, nd geneti diversity in per. Theor. Appl. Genet., Integrted Referene Geneti Linkge Mps of 102: Per Bsed on SSR nd AFLP Mrkers. Bre. Si., 2. Ghosh, A.K., L.N. Lukens, D.M. Hunter nd 57: J.N. Strommer, Europen nd Asin Pers: 10. Bell, R.L., Pers (Pyrus). In: Moore JN, Simple Sequene Repet-Polyrylmide Gel Bllington JR (ed) Geneti resoures of temperte Eletrophoresis-sed Anlysis of Commerilly fruit nd nut rops. At Horti., 290: Importnt North Amerin Cutivrs. Hort. Si., 11. Biley, L.H., Pyrus. In: Stndrd ylopedi of 41(2): hortiulture. Vlo V. Mmilln, New York, 3. Swmur, Y., T. Sito, N. Tkd, T. Ymmoto nd pp: T. Kimur, Identifition of Prentge of 12. Bo, L., K.S. Chen, D. Zhng, Y.F. Co, T. Jpnese Per Housui. J. Jpn So. Hort. Si., Ymmoto nd Y.W. Teng, Geneti diversity 73(6): nd similrity of per (Pyrus L.) ultivrs ntive t Est 4. Brini, W., M. Mrs nd J.I. Hormz, Asi reveled y SSR (simple sequene repet) Geneti diversity in lol Tunisin pers mrekers. Genet. Resour. Crop. Evol., 54(5): (Pyrus ommunis L.) studied with SSR mrkers. 13. Mguire, T.L., G.G. Collins nd M. Sedgley, Si. Hort., 115: A modified CTAB DNA extrtion proedure for 5. Ymmoto, T., T. Kimur, M. Shod, T. Imi, T. Sito, plnts elonging to the fmily Proteee. Plnt Y. Swmur, K. Kotouki, T. Hyshi nd Mol. Biol. Rep., 12: N. Mtsut, Geneti linkge mps onstruted 14. Guiford, P., S. Prksh, J.M. Zhu, E. Rikkerink, y using n interspeifi ross etween Jpnese S. Grdiner, H. Bssett nd R. Forster, nd Europen pers. Theor. Appl. Genet., 106: Mirostellites in Mlus X domesti (pple): 6. Dondini, L., L. Pierntoni, F. Giotti, R. Chiodini, undne, polymorphism nd ultivr identifition. S. Trtrini, C. Bzzi nd Snsvini, Theor. Appl. Genet., 94: Identifying QTLs for fire-light resistne vi 15. Liehrd, R., L. Ginfrneshi, B. Koller, C.D. Europen per (Pyrus ommunis L.) geneti linkge Ryder, R. Trhini, E. Vn De Weg nd C. Gessler, mp. Mol. Bre., 14: Development nd hrteriztion of 140 new 7. Ymmoto, T, T. Kimur, T. Sito, K. Kotouki, mirostellites in pple (Mlus X domesti Borkh.). N. Mtsut, R. Liehrd, C. Gessler, W.E. vn de Mol. Breed, 10: Weg nd T. Hyshi, Geneti Linkge Mps 16. Vn Ooijen, J.W. nd R.E. Voorrips, of Jpnese nd Europen Pers Aligned to the Joinmp 3.0, softwre for the lultion of Apple Consensus Mp. At Hort (ISHS), 663: geneti linkge mps. Plnt Reserh Interntionl, 8. Pierntoni, L., K.H. Cho, I.S. Shin, R. Chiodini, Wgeningen, the Netherlnds. S. Trtrini, L. Dondini, S.J. Dng nd S. Snsvini, 309