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Construction of the Reference Genetic Linkage Map of Amasya Apple by Microsatellite (SSR) Markers

Year 2016, Volume: 45 Issue: (Özel Sayı 1) 7. Ulusal Bahçe Bitkileri Kongresi, 200 - 206, 31.03.2016

Elmira Ziya Motalebipour Nergiz Çoban Mortaza Khodaeiaminjan Hayat Topçu , Murat Güney , Şerif Özongun , Ayşe Nilgün Atay , Salih Kafkas

Abstract

This study aimed to construct reference genetic map of ‘Amasya’ apple cultivar with SSR markers. With this aimed, the cross between selected ‘Kaşel-41’ from ‘Amasya’ apple cultivar and ‘Willams Pride’ cultivar establishes this study's materials. As a result of screening 699 SSR pairs of primer in 96 hybrid individuals showed 417 polymorphisms. A reference map was constructed by using 207 common SSR markers. The reference genetic map was 1351 cM long , average marker number 12.17 with a mean marker density of 6.52. Thereby producing the densest SSR-based reference map currently reported for apple. In the future genetic mapping and genomic studies, use of the new SSR markers and other marker methods will be useful to obtain high density map.

Keywords

Apple SSR reference map microsatellite

References

  • Aslan, N., 2012. Amasya elmasında SSR markörler ile genetik haritalama. Yüksek Lisans Tezi. Çukurova Üniversitesi, Ziraat Fakültesi, Bahçe Bitkileri Bölümü, Adana.
  • Cipriani, G., Lot, G., Huang, W.G., Marazzo, M. T., Peterlunger, E., Testolin, R., 1999. AC/GT and AG/CT microsatellite repeats in peach [Prunus persica (L.) Batsch]: isolation, characterization and cross-species amplification in Prunus. Theoretical and Applied Genetics, 99:65-72.
  • Cheng, F.S., Weeden, N.F., Brown, S.K., 1996. Identification of co-dominant RAPD markers tightly linked to fruit skin color in apple. Theoretical and Applied Genetics, 93:222–227.
  • Dirlewanger, E., Cosson, P., Tavaud, M., Aranzana, M., Poizat, C., Zanetto, A., Arús, P., Laigret, F., 2002. Development of microsatellite markers in peach [Prunus persica (L.) Batsch] and their use in genetic diversity analysis in peach and sweet cherry (Prunus avium L.). Theoretical and Applied Genetics, 105:127-138.
  • Doyle, J.J., Doyle, J.L., 1987. A Rapid isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin, 19:11-15.
  • Eltez, M., Kaşka, N., 1983. Niğde yöresinde her yıl meyve veren üstün özellikte Kaşel-Amasya elma türlerinin seleksiyonu. Doğa Bilim Dergisi Seri D., Cilt 9, Sayı 1.
  • FAOSTAT, 2015. Food and Agriculture Organization of The United Nations. http://faostat.fao.org/default.aspx.
  • Fernández-Fernández, F., Harvey N.G., James C.M., 2006. Isolation and characterization of polymorphic microsatellite markers from European pear (Pyrus communis L.). Molecular Ecology Notes, 6: 1039-1041.
  • Gasic, K., Han, Y., Kertbundit, S., Shulaev, V., Iezzoni, A.F., Bell, E.W., Wisniewski, M.E., Korban, S.S., 2009. Characteristics and transferability of new apple EST-derived SSRs to other Rosaceae species. Molecular Breeding, 23:397-411.
  • Gianfrancesco, F., Esposito, T., Montanini, L., Ciccodicola, A., Mumm, S., Mazzarella, R., Rao, E., Giglio, S., Rappold, G., Forabosco, A., 1998. A novel pseudo autosomal gene encoding a putative GTP-binding protein resides in the vicinity of the Xp/Yp telomere. Human Molecular Genetics, 7:407-414.
  • Guilford, P., Prakash, S., Zhu, J.M., Rikkerink, E., Gardiner, S., Bassett, H., Forster, R., 1997. Microsatellites in: Malus domestica (Apple): abundance, polymorphism and cultivar identification. Theoretical and Applied Genetics, 94: 249-254.
  • Han, Y., Chagne, D., Gasic, K., Rikkerink, E.H.A., Beever, J.E., Gardiner, S.E., Korban, S.S., 2009. BAC-end sequence-based SNPs and Bin mapping for rapid integration of physical and genetic maps in apple. Genomics, 93:282-288.
  • Han, Y., Zheng, D., Vimolmangkang, S., Khan, M.A., Beever, J.E., Korban, S.S, 2011. Integration of physical and genetic maps in apple confirms whole-genome and segmental duplications in the apple genome. J. Exp. Botany, 1-14. doi:10.1093/jxb/err215.
  • Hemmat., Weeden, N.F., Brown, S.K., 2003. Mapping and evaluation of ‘Malus’ x ‘domestica’ microsatellites in apple and pear. J. Amer. Soc. for Hort. Sci., 128(4):515-520.
  • Hokanson, S.C., Szewc-Mcfadden, A.K. Lamboy, W.F., Mcferson, J.R. 1998. Microsatellite (SSR) markers reveal genetic identities, genetic diversity, and relationships in a ‘Malus’ × ‘domestica’ Borkh. Theoretical and Applied Genetics, 97:671-683.
  • Inoue, E., Matsuki, Y., Anzai, H., Evans, K., 2007. Isolation and characterization of microsatellite markers in Japanese pear (Pyrus pyrifolia Nakai). Molecular Ecology Notes, 7:445-447.
  • Kafkas, S., 2006. Phylogenetic analysis of the genus Pistacia by AFLP markers. Plant Systematics and Evolution, 262: 113-124.
  • Kafkas, S., Özgen, M., Doğan, Y., Özcan, B., Ercişli, S., Serçe, S., 2008. Molecular characterization of mulberry accessions in Turkey by AFLP markers. J. Amer. Soc. for Hort. Sci., 133: 593597.
  • Khan, M.A., Durel, C.E., Duffy, B., Drouet, D., Kellerhals, M., Gessler, C., Patocchi, A., 2007. Development of molecular markers linked to the ‘Fiesta’ linkage group 7 major QTL for fire blight resistance and their application for marker-assisted selection. Genome, 50(6):568-577.
  • Kosambi, D.D., 1944. The estimation of map distance from recombination values. Annals of Eugenics, 12(3):172-175.
  • Liebhard, R., Gianfranceschi, L., Koller, B., Ryder, C.D., Tarchini, R., Weg, Van De E., Gessler, C., 2002. Development and characterisation of 140 new microsatellites in apple (‘Malus’ x ‘Domestica’ Borkh.). Molecular Breeding, 10:217–241.
  • Liebhard, R., Koller, B., Potacchi, A., Kellerhals, M., Pfammatter, W., Jermini, M., Gessler, C., 2003. Mapping quantitative field resistance against apple scap in a ‘Fiesta’ x ‘Discovery’ progeny. Phytopathology, 93:493-501.
  • Oddou-Muratorio S.R., Petit, J., Le Guerroue, B., Guesnet, D., Demesure, B., 2001. Pollen-versus seed-mediated gene flow in a scattered forest tree species. Evolution, 55:1123-1135.
  • O’Rourke, D., 2003. World Production, Trade, Consumption and Economic Outlook for Apples. (In Apples Books). CABI Publishing, Cambridge, pp:15-29.
  • Scheulke, M., 2000. An economic method for the fluorescent labeling of PCR fragments. Nature Biotechnology, 18: 233-234.
  • Silfverberg-Dilworth, E., Matasci, C.L., Van De Weg, W.E., Van Kaauwen, M.P.W., Walser, M., Kodde, L. P., Soglio, V., Gianfranceschi, L., Durel, C. E., Costa, F., Yamamoto, T., Koller, B., Gessler, C., Patocchi, A., 2006. Microsatellite markers spanning the apple (‘Malus’ x ‘domestica’ Borkh.) genome. Tree Genetics and Genomes, 2(4):202-224.
  • Tartarini, S., Gianfranceschi, L., Sansavini, S., Gessler, C., 1999. Development of reliable PCR markers for the selection of the Vf gene conferring scab resistance in apple. Plant Breeding, 118:183186.
  • Testolin, R., Marrazzo, T., Cipriani, G., Quarta, R., Verde, I., Dettori, M.T., Pancaldi, M., Sansavini, S., 2000. The use of microsatellite DNA for fingerprinting and testing the genetic origin of peach (Prunus persica (L) Batsch) cultivars. Genome, 43(3):512-520.
  • Van Ooijen, 2011. JoinMap ® 4, Software for the calculation of genetic linkage
  • Voorrips, R.E., 2002. MapChart: Software for the graphical presentation of linkage maps and QTLs. The Journal of Heredity, 93:77-78.
  • Yamamoto, T., Kimura, T., Shoda, M., Ban, Y., Hayashi, T., Matsuta, N., 2002-a. Development of microsatellite markers in the Japanese pear (Pyrus pyrifolia Nakai) . Molecular Ecology Notes, 2:14-16.
  • Yamamoto, T., Kimura T., Sawamura, Y., Manabe, T., Kotobuki, K., Hayashi, T., Ban, Y., Matsuta, N., 2006-b. Simple sequence repeats for genetic analysis in pear. Euphytica, 124:129-137.

SSR Markörleri İle Amasya Elmasının İskelet Haritasının Oluşturulması

Year 2016, Volume: 45 Issue: (Özel Sayı 1) 7. Ulusal Bahçe Bitkileri Kongresi, 200 - 206, 31.03.2016

Elmira Ziya Motalebipour Nergiz Çoban Mortaza Khodaeiaminjan Hayat Topçu , Murat Güney , Şerif Özongun , Ayşe Nilgün Atay , Salih Kafkas

Abstract

Bu çalışmada ‘Amasya’ elmasının SSR markörleri ile iskelet haritasının oluşturulması amaçlanmıştır. Bu amaçla Amasya elması içerisinden seçilen ‘Kaşel-41’ çeşidi ile ‘Williams Pride’ çeşitlerinin melezlenmesinden oluşan F1 popülasyonu çalışmanın materyalini oluşturmuştur. SSR primer çiftlerinin taranması sonucunda 699 primer çiftinden 417 adedi açılım göstermiş ve bunlardan 207 adet ortak SSR markörü olarak 96 melez bireyde analiz edilerek iskelet harita oluşturulmuştur. Amasya elmasının iskelet haritasının oluşturulmasında açılım gösteren 207 markör, 17 bağlantı grubuna dağılım göstermiştir. Bu harita 1351 cM uzunluğunda olup, markör yoğunluğu 12.2 ve markörler arası ortalama uzaklık ise 6.5 cM olarak saptanmıştır. Böylece elmada şimdiye kadarki en iyi SSR markörleri ile iskelet harita bu çalışma ile oluşturulmuştur. Yeni SSR markörleri ve farklı markör yöntemlerinin kullanılması, ileriki zamanlarda yapılacak genetik haritalama çalışmalarında yüksek yoğunluklu harita elde edilmesinde fayda sağlayacaktır.

Keywords

Elma SSR iskelet harita mikrosatellit

References

  • Aslan, N., 2012. Amasya elmasında SSR markörler ile genetik haritalama. Yüksek Lisans Tezi. Çukurova Üniversitesi, Ziraat Fakültesi, Bahçe Bitkileri Bölümü, Adana.
  • Cipriani, G., Lot, G., Huang, W.G., Marazzo, M. T., Peterlunger, E., Testolin, R., 1999. AC/GT and AG/CT microsatellite repeats in peach [Prunus persica (L.) Batsch]: isolation, characterization and cross-species amplification in Prunus. Theoretical and Applied Genetics, 99:65-72.
  • Cheng, F.S., Weeden, N.F., Brown, S.K., 1996. Identification of co-dominant RAPD markers tightly linked to fruit skin color in apple. Theoretical and Applied Genetics, 93:222–227.
  • Dirlewanger, E., Cosson, P., Tavaud, M., Aranzana, M., Poizat, C., Zanetto, A., Arús, P., Laigret, F., 2002. Development of microsatellite markers in peach [Prunus persica (L.) Batsch] and their use in genetic diversity analysis in peach and sweet cherry (Prunus avium L.). Theoretical and Applied Genetics, 105:127-138.
  • Doyle, J.J., Doyle, J.L., 1987. A Rapid isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin, 19:11-15.
  • Eltez, M., Kaşka, N., 1983. Niğde yöresinde her yıl meyve veren üstün özellikte Kaşel-Amasya elma türlerinin seleksiyonu. Doğa Bilim Dergisi Seri D., Cilt 9, Sayı 1.
  • FAOSTAT, 2015. Food and Agriculture Organization of The United Nations. http://faostat.fao.org/default.aspx.
  • Fernández-Fernández, F., Harvey N.G., James C.M., 2006. Isolation and characterization of polymorphic microsatellite markers from European pear (Pyrus communis L.). Molecular Ecology Notes, 6: 1039-1041.
  • Gasic, K., Han, Y., Kertbundit, S., Shulaev, V., Iezzoni, A.F., Bell, E.W., Wisniewski, M.E., Korban, S.S., 2009. Characteristics and transferability of new apple EST-derived SSRs to other Rosaceae species. Molecular Breeding, 23:397-411.
  • Gianfrancesco, F., Esposito, T., Montanini, L., Ciccodicola, A., Mumm, S., Mazzarella, R., Rao, E., Giglio, S., Rappold, G., Forabosco, A., 1998. A novel pseudo autosomal gene encoding a putative GTP-binding protein resides in the vicinity of the Xp/Yp telomere. Human Molecular Genetics, 7:407-414.
  • Guilford, P., Prakash, S., Zhu, J.M., Rikkerink, E., Gardiner, S., Bassett, H., Forster, R., 1997. Microsatellites in: Malus domestica (Apple): abundance, polymorphism and cultivar identification. Theoretical and Applied Genetics, 94: 249-254.
  • Han, Y., Chagne, D., Gasic, K., Rikkerink, E.H.A., Beever, J.E., Gardiner, S.E., Korban, S.S., 2009. BAC-end sequence-based SNPs and Bin mapping for rapid integration of physical and genetic maps in apple. Genomics, 93:282-288.
  • Han, Y., Zheng, D., Vimolmangkang, S., Khan, M.A., Beever, J.E., Korban, S.S, 2011. Integration of physical and genetic maps in apple confirms whole-genome and segmental duplications in the apple genome. J. Exp. Botany, 1-14. doi:10.1093/jxb/err215.
  • Hemmat., Weeden, N.F., Brown, S.K., 2003. Mapping and evaluation of ‘Malus’ x ‘domestica’ microsatellites in apple and pear. J. Amer. Soc. for Hort. Sci., 128(4):515-520.
  • Hokanson, S.C., Szewc-Mcfadden, A.K. Lamboy, W.F., Mcferson, J.R. 1998. Microsatellite (SSR) markers reveal genetic identities, genetic diversity, and relationships in a ‘Malus’ × ‘domestica’ Borkh. Theoretical and Applied Genetics, 97:671-683.
  • Inoue, E., Matsuki, Y., Anzai, H., Evans, K., 2007. Isolation and characterization of microsatellite markers in Japanese pear (Pyrus pyrifolia Nakai). Molecular Ecology Notes, 7:445-447.
  • Kafkas, S., 2006. Phylogenetic analysis of the genus Pistacia by AFLP markers. Plant Systematics and Evolution, 262: 113-124.
  • Kafkas, S., Özgen, M., Doğan, Y., Özcan, B., Ercişli, S., Serçe, S., 2008. Molecular characterization of mulberry accessions in Turkey by AFLP markers. J. Amer. Soc. for Hort. Sci., 133: 593597.
  • Khan, M.A., Durel, C.E., Duffy, B., Drouet, D., Kellerhals, M., Gessler, C., Patocchi, A., 2007. Development of molecular markers linked to the ‘Fiesta’ linkage group 7 major QTL for fire blight resistance and their application for marker-assisted selection. Genome, 50(6):568-577.
  • Kosambi, D.D., 1944. The estimation of map distance from recombination values. Annals of Eugenics, 12(3):172-175.
  • Liebhard, R., Gianfranceschi, L., Koller, B., Ryder, C.D., Tarchini, R., Weg, Van De E., Gessler, C., 2002. Development and characterisation of 140 new microsatellites in apple (‘Malus’ x ‘Domestica’ Borkh.). Molecular Breeding, 10:217–241.
  • Liebhard, R., Koller, B., Potacchi, A., Kellerhals, M., Pfammatter, W., Jermini, M., Gessler, C., 2003. Mapping quantitative field resistance against apple scap in a ‘Fiesta’ x ‘Discovery’ progeny. Phytopathology, 93:493-501.
  • Oddou-Muratorio S.R., Petit, J., Le Guerroue, B., Guesnet, D., Demesure, B., 2001. Pollen-versus seed-mediated gene flow in a scattered forest tree species. Evolution, 55:1123-1135.
  • O’Rourke, D., 2003. World Production, Trade, Consumption and Economic Outlook for Apples. (In Apples Books). CABI Publishing, Cambridge, pp:15-29.
  • Scheulke, M., 2000. An economic method for the fluorescent labeling of PCR fragments. Nature Biotechnology, 18: 233-234.
  • Silfverberg-Dilworth, E., Matasci, C.L., Van De Weg, W.E., Van Kaauwen, M.P.W., Walser, M., Kodde, L. P., Soglio, V., Gianfranceschi, L., Durel, C. E., Costa, F., Yamamoto, T., Koller, B., Gessler, C., Patocchi, A., 2006. Microsatellite markers spanning the apple (‘Malus’ x ‘domestica’ Borkh.) genome. Tree Genetics and Genomes, 2(4):202-224.
  • Tartarini, S., Gianfranceschi, L., Sansavini, S., Gessler, C., 1999. Development of reliable PCR markers for the selection of the Vf gene conferring scab resistance in apple. Plant Breeding, 118:183186.
  • Testolin, R., Marrazzo, T., Cipriani, G., Quarta, R., Verde, I., Dettori, M.T., Pancaldi, M., Sansavini, S., 2000. The use of microsatellite DNA for fingerprinting and testing the genetic origin of peach (Prunus persica (L) Batsch) cultivars. Genome, 43(3):512-520.
  • Van Ooijen, 2011. JoinMap ® 4, Software for the calculation of genetic linkage
  • Voorrips, R.E., 2002. MapChart: Software for the graphical presentation of linkage maps and QTLs. The Journal of Heredity, 93:77-78.
  • Yamamoto, T., Kimura, T., Shoda, M., Ban, Y., Hayashi, T., Matsuta, N., 2002-a. Development of microsatellite markers in the Japanese pear (Pyrus pyrifolia Nakai) . Molecular Ecology Notes, 2:14-16.
  • Yamamoto, T., Kimura T., Sawamura, Y., Manabe, T., Kotobuki, K., Hayashi, T., Ban, Y., Matsuta, N., 2006-b. Simple sequence repeats for genetic analysis in pear. Euphytica, 124:129-137.
There are 32 citations in total.

Details

Primary Language Turkish
Subjects Agricultural Engineering (Other)
Journal Section Makaleler
Authors

Elmira Ziya Motalebipour This is me

Nergiz Çoban This is me

Mortaza Khodaeiaminjan This is me

Hayat Topçu

Murat Güney

Şerif Özongun

Ayşe Nilgün Atay

Salih Kafkas

Publication Date March 31, 2016
Submission Date January 1, 2016
Acceptance Date January 31, 2016
Published in Issue Year 2016 Volume: 45 Issue: (Özel Sayı 1) 7. Ulusal Bahçe Bitkileri Kongresi

Cite

APA Motalebipour, E. Z., Çoban, N., Khodaeiaminjan, M., … Topçu, H. (2016). SSR Markörleri İle Amasya Elmasının İskelet Haritasının Oluşturulması. Bahçe, 45((Özel Sayı 1) 7. Ulusal Bahçe Bitkileri Kongresi), 200-206.
AMA Motalebipour EZ, Çoban N, Khodaeiaminjan M, et al. SSR Markörleri İle Amasya Elmasının İskelet Haritasının Oluşturulması. Bahçe. March 2016;45((Özel Sayı 1) 7. Ulusal Bahçe Bitkileri Kongresi):200-206.
Chicago Motalebipour, Elmira Ziya, Nergiz Çoban, Mortaza Khodaeiaminjan, Hayat Topçu, Murat Güney, Şerif Özongun, Ayşe Nilgün Atay, and Salih Kafkas. “SSR Markörleri İle Amasya Elmasının İskelet Haritasının Oluşturulması”. Bahçe 45, no. (Özel Sayı 1) 7. Ulusal Bahçe Bitkileri Kongresi (March 2016): 200-206.
EndNote Motalebipour EZ, Çoban N, Khodaeiaminjan M, Topçu H, Güney M, Özongun Ş, Atay AN, Kafkas S (March 1, 2016) SSR Markörleri İle Amasya Elmasının İskelet Haritasının Oluşturulması. Bahçe 45 (Özel Sayı 1) 7. Ulusal Bahçe Bitkileri Kongresi 200–206.
IEEE E. Z. Motalebipour, N. Çoban, M. Khodaeiaminjan, H. Topçu, M. Güney, Ş. Özongun, A. N. Atay, and S. Kafkas, “SSR Markörleri İle Amasya Elmasının İskelet Haritasının Oluşturulması”, Bahçe, vol. 45, no. (Özel Sayı 1) 7. Ulusal Bahçe Bitkileri Kongresi, pp. 200–206, 2016.
ISNAD Motalebipour, Elmira Ziya et al. “SSR Markörleri İle Amasya Elmasının İskelet Haritasının Oluşturulması”. Bahçe 45/(Özel Sayı 1) 7. Ulusal Bahçe Bitkileri Kongresi (March2016), 200-206.
JAMA Motalebipour EZ, Çoban N, Khodaeiaminjan M, Topçu H, Güney M, Özongun Ş, Atay AN, Kafkas S. SSR Markörleri İle Amasya Elmasının İskelet Haritasının Oluşturulması. Bahçe. 2016;45:200–206.
MLA Motalebipour, Elmira Ziya et al. “SSR Markörleri İle Amasya Elmasının İskelet Haritasının Oluşturulması”. Bahçe, vol. 45, no. (Özel Sayı 1) 7. Ulusal Bahçe Bitkileri Kongresi, 2016, pp. 200-6.
Vancouver Motalebipour EZ, Çoban N, Khodaeiaminjan M, Topçu H, Güney M, Özongun Ş, et al. SSR Markörleri İle Amasya Elmasının İskelet Haritasının Oluşturulması. Bahçe. 2016;45((Özel Sayı 1) 7. Ulusal Bahçe Bitkileri Kongresi):200-6.
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