Identifying profiles of SSR and SNP markers in cultivars of tetraploid wheat: physical and chemical analysis

Yousefi Javan, Iman; Augusto Pagnotta, Mario; D΄Ovidio, Renato

doi:10.33945/SAMI/ECC.2020.4.9

Document Type : Original Research Article

Authors

¹ Assistant Professor, Department of Plant Production, Faculty of Agriculture, University of Torbat Heydarieh, Torbat Heydarieh, Iran

² Department of Agricultural and Forest sciences (DAFNE), Tuscia University, Via S. C. de Lellis, snc, 01100 Viterbo, Italy

10.33945/SAMI/ECC.2020.4.9

Abstract

In this work, we studied the distribution of molecular markers in the chromosomes of tetraploid wheat. This distribution was drawn through the 192 line came from based on a cross between two durum wheat genotypes. The first parental line was a Triticum turgidum ssp. durum (Desf.). The second parental line was a durum wheat genotype derived from a cross between the Triticum turgidum ssp. Durum, (Omrabi 5). One hundred ninety-two F8 recombinant inbred lines (RILs) derived from the above mentioned cross by single-seed descent. A total of 254 markers were analyzed, including 216 microsatellites and 38 SNPs markers. Linkage analysis defined 14 linkage groups. Most markers (57.2%) were found to be located to the A genome, with an average of 12 markers per chromosome. The remaining (42.7%) were located to the B genome. To construct a stabilized (skeleton) map, markers interfering with map stability were removed. Efficient user-friendly methods for mapping plant genomes were highly desirable for the studies marker-assisted selection. SSR (microsatellite) markers are user-friendly and efficient in detecting polymorphism, but they detect few loci. The skeleton map consisted of 100 markers with a total length of 3170.29 cM and an average distance of 31.7 cM between adjacent markers. Majority of the markers showed a statistical significantly Mendelian segregation with 1:1 ratio (α=0.01). The highest percentage of markers was similar with the first parental. This SSR and SNP markers revealed a high proportion of clustering, which may be indicative of gene-rich regions. Some of the SSR, SNP markers were distributed for the first time on the current work. This project provided a useful groundwork for further genetic map, genetic analysis of important quantitative traits, positional cloning, and marker-assisted selection, as well as for genome comparative genomics and genome organization studies in wheat and other cereals.

Graphical Abstract

Keywords

References

[1] A.B. Damania, M. Tahir, B.H. Somaroo, ICARDA., 1992.

[2] M. Nesbitt, D. Samuel, IPGRI, Rome, 1995.

[3] G. Laghetti, A.R. Piergiovanni, N. Volpe, D. Semeraro, M. Falivene, M. Basile, Info Agrario., 1997. 40, 105–108.

[4] P. Perrino, S. Infantino, P. Basso, A. Di Marzo, N. Volpe, G. Laghetti, Inform Agrario., 1993, 41–45.

[5]G. Laghetti, A.R. Piergiovanni, N. Volpe, P. Perrino, Agr Med., 1999, 129, 199–211.

[6] R. Cubadda, E. Marconi, IPGRI, Rome, 1995, 203–221.

[7] G. Galletti, P. Bocchini, L.F. D’Antuono, J Agric food chem., 1996, 44, 31–33.

[8] G. Galterio, M. Cappelloni, E. Desiderio, N.E. Pogna, J Genet Breed., 1994, 48, 391–398.

[9] L. Corazza, M. Pasquini, P. Perrino, Genet Agrar., 1986, 40, 243–254.

[10] M.C. Luo Z.L. Yang, J. Dvorak, Theor Appl Genet., 2000, 100, 602– 606.

[11] J. MacKey, Hereditas., 1954, 40, 65–180.

[12] J. Bai, K. Liu, X. Jia, D. Wang, Plant Sci., 2004, 166, 341-347.

[13] A. Blanco, M.P. Bellomo, A. Cenci, C. De Giovanni, R. D’Ovidio, E. Iacono, B. Laddomada, M.A.

[14] D.J. Somers, P. Isaac, K. Edwards, Theor Appl Genet., 2004, 109, 1105-1114.

[15] G.J. Bryan, A.J. Collins, P. Stephenson, A. Orry, J.B. Smith, M.D. Gale. Theoret App Gen., 1997, 94, 557-563.

[16] Pagnotta, E. Porceddu, A. Sciancalepore, R. Simeone, O.A. Tanzarella, TAG., 1998, 97, 721-728.

[17] J. Plaschke, M.W. Ganal, M.S. Röder, Theor Appl Genet., 1995, 92, 1078–1084.

[18] P.K. Gupta, H.S. Balyan, K.J. Edwards, P. Isaac, V. Korzun, M. Röder, M.F. Gautier, P. Joudrier, A.R. Schlatter, J. Dubcovsky, R.C. De la Pena, M. Khairallah, G. Penner, M.J. Hayden, P. Sharp, B. Keller, R.C.C. Wang, J.P. Hardouin, P. Jack, P. Leroy, Theor Appl Genet., 2002, 105, 413-422.

[19] W. Karl, T. Broman, Johns Hopkins University, Baltimore, Maryland 21205, the Genetics Society of America., 2005.

[20] M.W. Ganal, M.S. Röder, Genom applic in crops. Springer, Berlin. 2007.

[21] H. Guyomarc’h, P. Sourdille, K.J. Edwards, M. Bernard, Theor Appl Genet., 2002, 105, 736-744.

[22] P. Sourdille, S. Singh, T. Cadalen, G. Brown-Guedira, G. Gay, L. Qi, B. Gill, P. Dufour, A. Murigneux, M. Bernard, Funct Integr Genom., 2004, 4, 12-25.

[23] Q.J. Song, J.R. Shi, S. Singh, E.W. Fickus, J.M. Costa, J. Lewis, B.S. Gill, R. Ward, P.B. Cregan, Theor Appl Genet., 2005, 110, 550-560.

[24] M.S. Röder, V. Korzun, K. Wendehake, B.S. Gill, M.W. Ganal, Genome., 1998a, 41, 278-283.

[25] N.D. Young, Phillips R.L, Vasil J.K. (eds.)., 2000, 32, 3445-3457.

[26] D.I. Mester, Y.I. Ronin, Y. Hu, J. Peng, E. Nevo, A.B. Korol, Theor Appl Genet., 2003a, 107, 1002-1112.

[27] D.I. Mester, Y.I. Ronin, D. Minkov, E. Nevo, A.B. Korol, Genet., 2003b, 165, 2269-2282.

[28] D.I. Mester, Y.I. Ronin, E. Nevo, A.B. Korol, Comput Biol Chem., 2004, 28, 281-290.

[29] Z.Q. Ma, M. Röder, M.E. Sorrells, Genome., 1996, 39, 123-130.

[30] M.S. Röder, J. Plaschke, S.U. Konig, A. Borner, M.E. Sorrells, Mol. Gen. Genet., 1995, 246, 327-333.

[31] V. Korzun, M.S. Röder, K. Wendekake, A. Pasqualone, C. Lotti, M.W. Ganal, P.Y. Kwok, C. Carlson, T.D. Yager, W. Ankener, D.A. Nickerson, Genom., 1999. 23, 138-144.

[32] M.S. Röder, V. Korzun, K. Wendehake, J. Plaschke, M.H. Tixier, P. Leroy, M.W. Ganal, Genetics., 1998b, 149, 2007-2023.

[33] I. Elouafi, M.M. Nachit, Theor Appl Genet., 2004, 108, 401-413.

[34] M. Heun, A.E. Kennedy, J.A. Anderson, N.L.V. Lapitan, M.E. Sorrells, S.D Tanksley, Genome., 1991, 34, 437-447.

[35] Y.G. Liu, K. Tsunewaki, Jap J Genet., 1991, 66, 617-633.

[36] A. Blanco, TAG., 1999, 98, 1202- 1207.

[37] M.M. Nachit, I. El ouafi, M.A. Pagnotta, A. El saleh, E. lacono, M. Labhilili, A.P. Asbati, M. Azrak, H. Hazzam, D. Benscher, M. Khairallah, J.M. Ribaut, O.A. Tanzarella, E. Porceddu, M.E. Sorrels, TAG., 2001, 102, 177-186.

[38] S.D. Tanksley, Chrom., 1984, 89, 352-360.

[39] M.R. Foolad, S. Arulsekar, V. Becerra, F.A. Bliss, TAG., 1995, 91, 262-269.

[40] J. Dvorak, P.E. Mc Guire, B. Cassidy, Genome., 1988, 30, 680-689.

[41] J.D. Faris, K.M. Haen, B.S. Gill, Genetics., 2000, 154, 823-835.

[42] K.S. Gill, B.S. Gill, T.R. Endo, E.V. Boyko, Gen., 1996a, 143, 1001-1012.

[43] K.S. Gill, B.S. Gill, T.R. Endo, T. Taylor, Gen., 1996b, 144, 1883-1891.

[44] A.B Korol, I.A. Preygel, S.I. Preygel, Chapman and Hall, London, UK, 1994.

[45] S.D. Tanksley, M.W. Ganal, J.P. Prince, M.C. De Vicente, M.W. Bonierbale, P. Broun, T.M. Fulton, J.J. Giovannoni, S. Grandillo, G.B. Martin, R. Messeguer, J.C. Miller, L. Miller, A.H. Paterson, O. Pineda, M.S. Röder, R.A. Wing, W. Wu, N.D. Young, Genet Soc Americ., 1992, 132, 1141-1160.

[46] J.H. Peng, T. Fahima, M.S. Röder, Y.C. Li, A. Grama, Y.I. Ronin, A.B. Korol, E. Nevo, Genome Res., 2000, 10, 1059-1031.

[47] Y. Weng, M.D. Lazar, Theor Appl Genet., 2002, 104, 1078-1085.

[48] L.L Qi, B. Echalier, S. Chao, G.R. Lazo, G.E. Butler, O. Anderson, O.D. Akhunov, E.D. Dvolák, J. Linkiewicz, A.M. Ratnasiri, A. Dubcovsky, J. Bermudez-Kandianis, C.E. Greene, R.A. Kantety, R. La Rota, M. Munkvold, J.D. Sorrells, S.F. Sorrells, M.E. Dilbirligi, M. Sidhu, D. Erayman, M. Randhawa, H.S. Sandhu, D. Bondareva, S. Gill, K.S. Mahmoud, A.A. Ma, X.F. Miftahudin, J.P. Conley, E.J. Nduati, V. Gonzalez-Hernandez, J.L. Anderson, J.A. Peng, J.H. Lapitan, N.L.V. Hossain, K.G. Kalavacharla, V. Kianian, S.F. Pathan, M.S. Zhang, D. Nguyen, H.T. Choi, D.W. Close, T.J. McGuire, P.E. Qualset, B.S. Gill, Genet., 2004. 168, 701-712.

[49] G. Wricke, W.E. Weber, Walter de Gruyter, 1986, Berlin. New York.

[50] Q.S. Zhang, L. Manche, R.M. Xu, A.R. Krainer, RNA., 2006, 12, 1116-1128.

[51] P. Taillon-Miller, Z.J. Gu, Q. Li, L. Hillier, P.Y. Kwok, Genome Res., 1998, 8, 748-754.

[52] L. Picoult-Newberg, T.E. Ideker, M.G. Pohl, S.L. Taylor, M.A. Donaldson, D.A. Nickerson, M. Boyce-Jacino, Genome Res., 1999, 9,167- 174.

[53] Z. Gu, L. Hillier, P.Y. Kwok, Hum Mutat., 1998, 12, 221–225.

[54] K.H. Buetow, M.N. Edmonson, A.B. Cassidy, Nat Genet., 1999, 21, 323-325.

[55] P.Y. Kwok, C. Carlson, T.D. Yager, W. Ankener, D.A. Nickerson, Genom., 1994, 23, 138-144.

[56] K. Garg, P. Green, D.A. Nickerson, Gen Res., 1999, 9, 1087- 1092.

[57] G.T. Marth, I. Korf, M.D. Yandell, R.T. Yeh, Z.J. Gu, H. Zakeri, N.O. Stitziel, L. Hillier, P.Y. Kwok, W.R. Gish, Nat Genet., 1999. 23, 452-456.

[58] L.F. Gao, R.L. Jing, N.X. Huo, Y. Li, X.P. Li, H.R. Zhou, X.P. Chang, J.F. Tang, Z.Y. Ma, J.Z. Jia, Theor App Gen., 2004, 108, 1392-1400.

[59] C.M. Stack, S.G. Easwaramoorthy, U.K. Metha, M.J. Downes, C.T. Griffin, A.M. Burnell, Nemat., 2000, 2, 477-487.

[60] B.L. Johnson, H.S. Dhaliwal, Am J Bot., 1976, 63, 1088-1094.

[61] P. Sourdille, M. Tavaud, G. Charmet, M. Bernard, Theor Appl Genet., 2001, 103, 346-352.

[62] P.P. Jauhar, O. Riera-Lizarazu, W.G. Dewey, B.S. Gill, C.E. Crane, J.H. Bennett, Theor Appl Genet., 1991, 82, 441-449.

Eurasian Chemical Communications

Identifying profiles of SSR and SNP markers in cultivars of tetraploid wheat: physical and chemical analysis

References

References

Volume 2, Issue 4
April 2020
Pages 516-535

Identifying profiles of SSR and SNP markers in cultivars of tetraploid wheat: physical and chemical analysis

References

References

Volume 2, Issue 4April 2020Pages 516-535

Volume 2, Issue 4
April 2020
Pages 516-535