Advertisement

Cereal Research Communications

, Volume 46, Issue 3, pp 377–387 | Cite as

Exploring SNP Diversity in Wheat Landraces Germplasm and Setting of a Molecular Barcode for Fingerprinting

  • G. ManginiEmail author
  • D. Nigro
  • B. Margiotta
  • P. De Vita
  • A. Gadaleta
  • R. Simeone
  • A. Blanco
Article

Abstract

During the last century wheat landraces were replaced by modern wheat cultivars leading to a gradual process of genetic erosion. Landraces genotyping and phenotyping are strategically useful, as they could broaden the genetic base of modern cultivars. In this research, we explored Single Nucleotide Polymorphism (SNP) markers diversity in a collection of common and durum wheats, including both landraces and Italian elite cultivars. A panel of 6,872 SNP markers was used to analyze the genetic variability among the accessions, using both the Principal Components Analysis (PCA) and the Neighbour Joining clustering method. PCA analysis separated common wheat accessions from durum ones, and allowed to group separately durum landraces from durum elite cultivars. The Neighbour joining clustering validated PCA results, and moreover, separated common wheat landraces from common elite cultivars. The clustering results demonstrated that Italian durum landraces were poorly exploited in modern breeding programs. Combining cluster results with heterozygosity levels observed, it was possible to clarify synonymy and homonymy cases identified for Bianchetta, Risciola, Saragolla, Timilia and Dauno III accessions. The SNP panel was also used to detect the minimum number of markers to discriminate the studied accessions. A set of 33 SNPs were found to be highly informative and used for a molecular barcode, which could be useful for cultivar identification and for the traceability of wheat end-products.

Keywords

wheat landraces SNP markers cultivar identification molecular barcode 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Supplementary material

42976_2018_4603377_MOESM1_ESM.pdf (175 kb)
Exploring SNP Diversity in Wheat Landraces Germplasm and Setting of a Molecular Barcode for Fingerprinting

References

  1. Akhunov, E., Nicolet, C., Dvorak, J. 2009. Single nucleotide polymorphism genotyping in polyploid wheat with the Illumina Golden Gate assay. Theor. Appl. Genet. 119:507–517.CrossRefGoogle Scholar
  2. Anderson, J.A., Churchill, G.A., Sutrique, J.E., Tanksley, S.D., Sorrells, M.E. 1993. Optimizing parental selection for genetic linkage maps. Genome 36:181–186.CrossRefGoogle Scholar
  3. Bányai, J., Szűcs, P., Karsai, I., Mészáros, K., Kuti, C., Láng, L., Bedő Z. 2006. Cultivar identification by molecular markers. Cereal Res. Commun. 34:865–870.CrossRefGoogle Scholar
  4. Bonneuil, C., Thomas, F. 2009. Gènes, Pouvoirs et Profits. Ed. Quae-FPH, Paris.Google Scholar
  5. Bonnin, I., Bonneuil, C., Goffaux, R., Montalent, P., Goldringer, I. 2014. Explaining the decrease in the genetic diversity of wheat in France over the 20th century. Agr. Ecosyst. and Environ. 195:183–192.CrossRefGoogle Scholar
  6. Bradbury, P.J., Zhang, Z., Kroon, D.E., Casstevens, T.M., Ramdoss, Y., Buckler, E.S. 2007. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633–2635.CrossRefGoogle Scholar
  7. Cavanagh, C.R., Chao, S., Wang, S. 2013. Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars. P. Natl. Acad. Sci. USA 110:8057–8062.CrossRefGoogle Scholar
  8. De Cillis, E. 1927. I grani d’Italia. Tipografia della Camera dei Deputati (ed.), Roma, Italy.Google Scholar
  9. Fujita, Y., Fukuoka, H., Yano, H 2009. Identification of wheat cultivars using EST–SSR markers. Breeding Sci. 59:159–167.CrossRefGoogle Scholar
  10. Ganal, M.W., Altmann, T., Röder, M.S. 2009. SNP identification in crop plants. Curr. Opin. Plant Biol. 12:211–217.CrossRefGoogle Scholar
  11. Gao, L., Jia, J., Kong, X. 2016. A SNP-Based molecular barcode for characterization of common wheat. PLoS ONE 11(3):e0150947.CrossRefGoogle Scholar
  12. Grifoni, E. 1955. Nuovi grani per l’Italia meridionale. Genetica agraria, pp. 366–377.Google Scholar
  13. Harlan, J.R. 1975. Crops and Man. American Society of Agronomy. Madison, Wisconsin. pp. 150–189.Google Scholar
  14. Lopes, S.M., El-Basyoni, I., Baenziger, P.S., Singh, S., Royo, C., Ozbek, K., Aktas, K., Ozer, E., Ozdemir, F., Manickavelu, A., Ban, T., Vikram, P. 2015. Exploiting genetic diversity from landraces in wheat breeding for adaptation to climate change. J. Exp. Bot. 66:3477–3486.CrossRefGoogle Scholar
  15. Maccaferri, M., Sanguineti, M.C., Donini, P., Tuberosa, R. 2003. Microsatellite analysis reveals a progressive widening of the genetic basis in the elite durum wheat germplasm. Theor. Appl. Genet. 107:783–797.CrossRefGoogle Scholar
  16. Maccaferri, M., Sanguineti, M.C., Xie, C., Smith, J.S.C., Tuberosa, R., 2007. Relationships among durum wheat accessions. II. A comparison of molecular and pedigree information. Genome 50:385–399.Google Scholar
  17. Mangini, G., Margiotta, B., Marcotuli, I., Signorile, M.A., Gadaleta, A., Blanco, A. 2017. Genetic diversity and phenetic analysis in wheat (Triticum turgidum subsp. durum and Triticum aestivum subsp. aestivum) landraces based on SNP markers. Genet. Resour. Crop Ev. 64:1269–1280.CrossRefGoogle Scholar
  18. Mangini, G., Taranto, F., Giove, S.L., Gadaleta, A., Blanco, A. 2010. Identification of durum wheat cultivars by a minimum number of microsatellite markers. Cereal Res. Commun. 38:155–162.CrossRefGoogle Scholar
  19. Moore, G. 2015. Strategic pre-breeding for wheat improvement. Nature Plants 1:15018CrossRefGoogle Scholar
  20. Oliveira, H.R., Hagenbland, J., Leino, M.W., Leigh, F., Lister, D.L., Penã-Chocarro, L., Jones, M.K. 2014. Wheat in the Mediterranean revisited-tetraploid wheat landraces assessed with elite bread wheat Single Nucleotide Polymorphism markers. BMC Genet. 15:54CrossRefGoogle Scholar
  21. Price, A.L., Patterson, N.J., Plenge, R.M., Weinblatt, M.E., Shadick, N.A., Reich, D. 2006. Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet. 38:904–909.CrossRefGoogle Scholar
  22. Saitou, N., Nei, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406–425.PubMedGoogle Scholar
  23. Stapley, J., Reger, J., Feulner, P.G., Smadja, C., Galindo, J., Ekblom, R., Bennison, C., Ball, A.D., Beckerman, A.P., Slate, J. 2010. Adaptation genomics: the next generation. Trends Ecol. Evol. 25:705–712.CrossRefGoogle Scholar
  24. van de Wouw, M., van Hintum, T., Kik, C., van Treuren, R., Visser, B. 2010. Genetic erosion in crops: concept, research results and challenges. Plant Genetic Resources 8:1–15.CrossRefGoogle Scholar
  25. Wang, S., Wong, D., Forrest, K. 2014. Characterization of polyploid wheat genomic diversity using a high-density 90000 single nucleotide polymorphism array. Plant Biotechnol. J. 12:787–796.CrossRefGoogle Scholar
  26. Wingen, L.U., Orford, S., Goram, R., Leverington-Waite, M., Bilham, L., Patsiou, L.S., Ambrose, M. Dicks J., Griffiths S. 2014. Establishing the A. E. Watkins landrace cultivar collection as a resource for systematic gene discovery in bread wheat. Theor. Appl. Genet. 127:1831–1842.Google Scholar
  27. Wingen, L.U., West, C., Leverington-Waite, M., Collier, S., Orford, S., Goram, R., Yang, C.Y., King, J., Allen, A.M., Burridge, A., Edwards, K.J., Griffiths, S. 2017. Wheat landrace genome diversity. Genetics. 205:1657–1676.CrossRefGoogle Scholar
  28. Zeven, A.C. 1998. Landraces: A review of definitions and classifications. Euphytica 104:127–139.CrossRefGoogle Scholar

Copyright information

© Akadémiai Kiadó, Budapest 2018

Authors and Affiliations

  • G. Mangini
    • 1
    Email author
  • D. Nigro
    • 1
  • B. Margiotta
    • 2
  • P. De Vita
    • 3
  • A. Gadaleta
    • 4
  • R. Simeone
    • 1
  • A. Blanco
    • 1
  1. 1.Department of Soil, Plant and Food Sciences (DiSSPA), Sect. Genetics and Plant BreedingUniversity Aldo MoroBariItaly
  2. 2.Institute of Biosciences and Bioresources of the National Research Council (IBBR-CNR)BariItaly
  3. 3.Council for Agricultural Research and Economics — Research Centre for Cereal and Industrial Crops (CREA-CI)FoggiaItaly
  4. 4.Department of Agricultural and Environmental Sciences (DiSAAT), Research Unit of Genetics and Plant BiotechnologyUniversity Aldo MoroBariItaly

Personalised recommendations