Genetic redundancy among durum wheat accessions as assessed by SSRs and endosperm proteins
Abstract
Reducing duplication in ex-situ collections is complicated and requires good quality genetic markers. This study was conducted to assess the value of endosperm proteins and SSRs for validation of potential duplicates and monitoring intra-accession variability. Fifty durum wheat (Triticum turgidum ssp. durum) accessions grouped in 23 potential duplicates, and previously characterised for 30 agro-morphological traits, were analysed for gliadin and high molecular weight glutenin (HMWG) subunit alleles, total protein, and 24 SSRs, covering a wide genome area. Similarity and dissimilarity matrices were generated based on protein and SSRs alleles. For heterogeneous accessions at gliadins the percent pattern homology (PH) between gliadin patterns and the Nei’s coefficient of genetic identity (I) were computed. Eighteen duplicates identical for proteins showed none or less than 3 unshared SSRs alleles. For heterogeneous accessions PH and I values lower than 80 identified clearly off-types with more than 3 SSRs unshared. Only those biotypes differing in no more than one protein-coding locus were confirmed with SSRs. A good concordance among proteins, morphological traits, and SSR were detected. However, the discrepancy in similarity detected in some cases showed that it is advisable to evaluate redundancy through distinct approaches. The analysis in proteins together with SSRs data are very useful to identify duplicates, biotypes, close related genotypes, and contaminations.Downloads
References
Aguiriano E., Ruiz M., Fité R., Carrillo J.M., 2006. Analysis of genetic variability in a sample of the durum wheat Spanish collection based on gliadin markers. Genet Resour Crop Ev 53, 1543-1552. http://dx.doi.org/10.1007/s10722-005-7767-z
Aguiriano E., Ruiz M., Fité R., Carrillo J.M., 2009. Effects of N fertilisation, year and prolamin alleles on gluten quality in durum wheat (Triticum turgidum L. ssp. turgidum) landraces from Spain. Span J Agric Res 7, 342-348. http://dx.doi.org/10.5424/sjar/2009072-425
Crouch K, Crouch J.H., Madsen S, Vuylsteke D.R., Ortiz R., 2000. Comparative analysis of phennotypic and genotypic diversity among plantain landraces (Musa spp., AABB group).Theor Appl Genet 101, 1056-1065. http://dx.doi.org/10.1007/s001220051580
Doyle J.J., Doyle J.L., 1990. Isolation of plant DNA from fresh tissue. Focus 12, 13-15.
Fra-Mon P., Salcedo G., Aragoncillo C., García-Olmedo F., 1984. Chromosomal assignment of genes controlling salt-soluble proteins (albumins and globulins) in wheat and related species. Theor Appl Genet 69, 167-172.
Ghosh S., Karanjawala Z.E., Hauser E.R., Ally D., Knapp J.I., Rayman J.B., Musick A., Tannenbaum J., Te C., Shapiro S., 1997. Methods for precise sizing, automated binning of alleles, and reduction of error rates in large-scale genotyping using fluorescently labeled dinucleotide markers. Genome Res 7, 165-178. http://dx.doi.org/10.1101/gr.7.2.165
GOLDSTEIN D.B., POLLOCK D.D., 1997. Launching microsatellites: A review of mutation processes and method for phylogenetic inference. Genetics 139, 463-471. http://dx.doi.org/10.1093/oxfordjournals.jhered.a023114
Hardy O.J., Vekemans X., 2002. SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Molecular Ecology Notes 2, 618-620. http://dx.doi.org/10.1046/j.1471-8286.2002.00305.x
Hintum TH.J.L. Van, Knupffer H., 1995. Duplication within and between germplasm collections. I. Identifying duplication on the basis of passport data. Genet Resour Crop Evol 42, 127-133. http://dx.doi.org/10.1007/BF02539516
JACCARD P., 1908. Nouvelles recherches sur la distribution florale. Bull Soc Vaud Sci Nat 44, 223-270. [In French].
Kudryavtsev A.M., Boggini G., Benedettelli S., Illichevskii N.N., 1996. Gliadin polymorphism and genetic diversity of modern Italian durum wheat. J Genet Breed 50, 239-248.
Lafiandra D., Kasarda D.D., 1985. One- and two-dimensional (two pH) polyacrylamide gel electrophoresis in a single gel: separation of wheat proteins. Cereal Chem 62, 314–319.
Lund B., Ortiz R., Skovgaard I.M., Waugh R., Andersen S.B., 2003. Analysis of potential duplicates in barley gene bank collections using re-sampling of microsatellite data. Theor Appl Genet 106, 1129-1138.
Maccaferri M., Sanguineti M.C., Donini P., Tuberosa R., 2003. Microsatellite analysis reveals a progresive widening of the genetic basis in the elite durum wheat germplasm. Theor Appl Genet 107, 783-797. http://dx.doi.org/10.1007/s00122-003-1319-8
Metakovsky E.V., 1991. The value of gliadin biotypes in commercial cultivars of wheat. In: Gluten proteins 1990 (Bushuk W., Tkachuk R., eds). AACC, St Paul, Mi, USA, pp. 569-580.
Nei M., 1972. Genetic distance between populations. Am Nat 106, 283-292. http://dx.doi.org/10.1086/282771
Payne P.I., Law C.N., Mudd E.E., 1980. Control of homo-eologous group 1 chromosomes of the high molecular-weight subunit, a major protein of wheat endosperm. Theor Appl Genet 58, 113-120. http://dx.doi.org/10.1007/BF00263101
Payne P.I., Holt L.M., Lawrence C.J., Law C.N., 1982. The genetics of gliadin and glutenin the major storage proteins of the wheat endosperm. Qualtitas Plantarium-Plant Foods for Human Nutrition 31, 229-241. http://dx.doi.org/10.1007/BF01108632
Payne P.I., Lawrence C.J., 1983. Catalogue of alleles for the complex gene loci, Glu-A1, Glu-B1, Glu-D1 which code for high-molecular-weight subunits of glutenin in hexaploid wheat. Cereal Res Commun 11, 29-35.
Röder M.S., Korzun V., Wendehake K., Plaschke J., Tixier M.H., Leroy P., Ganal M.W., 1998. A microsatellite map of wheat. Genetics 149, 2007-2023.
Rogers J.S., 1972. Measures of genetic similarity and genetic distance. In: Studies in Genetics VII. University of Texas, Austin, Tx, USA, pp.145-153.
Rohlf F.J., 1992. NTSYS-pc Numerical taxonomy and multivariate analysis system. Exeter software, NewYork.
Ruiz M., Aguiriano E., 2004. Analysis of duplication in the Spanish durum wheat collection maintained in the CRF-INIA on the basis of agro-morphological traits and gliadin proteins. Genet Resour Crop Evol 51, 231-235. http://dx.doi.org/10.1023/B:GRES.0000024024.59141.e3
Sapirstein H.D., Bushuk W., 1985. Computer-aided analysis of gliadin electrophoregrams. II. Wheat cultivar identification and class comparisons. Cereal Chem 62, 377-392.
Singh J., Skerritt J.H., 2001. Chromosomal control of albumins and globulins in wheat grain assessed using different fractionation. J Cereal Sci 33, 163-181. http://dx.doi.org/10.1006/jcrs.2000.0351
Tranquilli G., Appendino M.L., Pflüger L.A., Bullrich L., Lewis S., Suarez E.Y., 2000. Morphoagronomic and biochemical variation in an Argentian landrace of wheat. Genet Resour Crop Evol 47, 281-284. http://dx.doi.org/10.1023/A:1008711903949
Virk P.S., Newbury H.J., Jackson M.T., Ford-Lloyd B.V., 1995. The identification of duplicate accessions within a rice germplasm collection using RAPD analysis. Theor Appl Genet 90, 1049–1055. http://dx.doi.org/10.1007/BF00222920
WRIGHT S., 1978. Evolution and the genetics of populations, vol 4. Variability within and among natural populations. University of Chicago Press, Chicago.
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