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AFLP and MS-AFLP analysis of the variation within saffron crocus (Crocus sativus L.) germplasm.

Busconi M, Colli L, Sánchez RA, Santaella M, De-Los-Mozos Pascual M, Santana O, Roldán M, Fernández JA - PLoS ONE (2015)

Bottom Line: The presence and extent of genetic variation in saffron crocus are still debated, as testified by several contradictory articles providing contrasting results about the monomorphism or less of the species.While the genetic variability was low (4.23% polymorphic peaks and twelve (12) effective different genotypes), the methyl sensitive analysis showed the presence of high epigenetic variability (33.57% polymorphic peaks and twenty eight (28) different effective epigenotypes).Two clearly defined clusters grouping accessions from the West (Toledo and Ciudad Real) and accessions from the East (Cuenca and Teruel) were clearly recognised.

View Article: PubMed Central - PubMed

Affiliation: Faculty of Agricultural, Food and Environmental Sciences, Università Cattolica del Sacro Cuore, Piacenza, Italy; BioDNA, Centro di Ricerca sulla biodiversità e sul DNA antico, Università Cattolica del Sacro Cuore, Piacenza, Italy.

ABSTRACT
The presence and extent of genetic variation in saffron crocus are still debated, as testified by several contradictory articles providing contrasting results about the monomorphism or less of the species. Remarkably, phenotypic variations have been frequently observed in the field, such variations are usually unstable and can change from one growing season to another. Considering that gene expression can be influenced both by genetic and epigenetic changes, epigenetics could be a plausible cause of the alternative phenotypes. In order to obtain new insights into this issue, we carried out a molecular marker analysis of 112 accessions from the World Saffron and Crocus Collection. The accessions were grown for at least three years in the same open field conditions. The same samples were analysed using Amplified Fragment Length Polymorphism (AFLP) and Methyl Sensitive AFLP in order to search for variation at the genetic (DNA sequence) and epigenetic (cytosine methylation) level. While the genetic variability was low (4.23% polymorphic peaks and twelve (12) effective different genotypes), the methyl sensitive analysis showed the presence of high epigenetic variability (33.57% polymorphic peaks and twenty eight (28) different effective epigenotypes). The pattern obtained by Factorial Correspondence Analysis of AFLP and, in particular, of MS-AFLP data was consistent with the geographical provenance of the accessions. Very interestingly, by focusing on Spanish accessions, it was observed that the distribution of the accessions in the Factorial Correspondence Analysis is not random but tends to reflect the geographical origin. Two clearly defined clusters grouping accessions from the West (Toledo and Ciudad Real) and accessions from the East (Cuenca and Teruel) were clearly recognised.

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FCA analysis based on the MS-AFLP epigenotypes of Spanish accessions.Factorial Correspondence Analysis showing multivariate relationships among MS-AFLP epigenotypes of different saffron crocus accessions of Spanish provenance on the axes corresponding to first (x axis, 12.88% of inertia) vs. second (y axis, 10.15% of inertia) main factors. Only the points corresponding to accessions of Spanish origin have been plotted. Accessions from the WEST (Toledo and Ciudad Real) and from the EAST (Cuenca and Teruel) tended to cluster separately with just few exceptions. Climatic conditions between the two areas are very different and this may be reflected in the epigenetic composition.
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pone.0123434.g002: FCA analysis based on the MS-AFLP epigenotypes of Spanish accessions.Factorial Correspondence Analysis showing multivariate relationships among MS-AFLP epigenotypes of different saffron crocus accessions of Spanish provenance on the axes corresponding to first (x axis, 12.88% of inertia) vs. second (y axis, 10.15% of inertia) main factors. Only the points corresponding to accessions of Spanish origin have been plotted. Accessions from the WEST (Toledo and Ciudad Real) and from the EAST (Cuenca and Teruel) tended to cluster separately with just few exceptions. Climatic conditions between the two areas are very different and this may be reflected in the epigenetic composition.

Mentions: While no relationship between geographical region of origin and genotypes could be defined for S accessions with AFLPs, a different situation emerged with MS-AFLPs (Fig 2). Almost all of the S accessions (67 out of 73) were from the administrative regions of Castilla-La Mancha (provinces of Toledo, Ciudad Real, Albacete, and Cuenca) and Aragón (province of Teruel). By focusing on these samples, it was possible to observe that their distribution in the FCA scatterplot is somewhat influenced by the geographical origin. Accessions coming respectively from the EAST (Cuenca and Teruel) and from the WEST (Toledo and Ciudad Real, light grey) tended to cluster together in two separate groups with only a few exceptions, while accessions from Albacete (South-East part of Castilla–La Mancha), bordering the provinces of Ciudad Real and Cuenca, tended to be in the middle and partially superimposed to the two groups (S5 Fig).


AFLP and MS-AFLP analysis of the variation within saffron crocus (Crocus sativus L.) germplasm.

Busconi M, Colli L, Sánchez RA, Santaella M, De-Los-Mozos Pascual M, Santana O, Roldán M, Fernández JA - PLoS ONE (2015)

FCA analysis based on the MS-AFLP epigenotypes of Spanish accessions.Factorial Correspondence Analysis showing multivariate relationships among MS-AFLP epigenotypes of different saffron crocus accessions of Spanish provenance on the axes corresponding to first (x axis, 12.88% of inertia) vs. second (y axis, 10.15% of inertia) main factors. Only the points corresponding to accessions of Spanish origin have been plotted. Accessions from the WEST (Toledo and Ciudad Real) and from the EAST (Cuenca and Teruel) tended to cluster separately with just few exceptions. Climatic conditions between the two areas are very different and this may be reflected in the epigenetic composition.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4401542&req=5

pone.0123434.g002: FCA analysis based on the MS-AFLP epigenotypes of Spanish accessions.Factorial Correspondence Analysis showing multivariate relationships among MS-AFLP epigenotypes of different saffron crocus accessions of Spanish provenance on the axes corresponding to first (x axis, 12.88% of inertia) vs. second (y axis, 10.15% of inertia) main factors. Only the points corresponding to accessions of Spanish origin have been plotted. Accessions from the WEST (Toledo and Ciudad Real) and from the EAST (Cuenca and Teruel) tended to cluster separately with just few exceptions. Climatic conditions between the two areas are very different and this may be reflected in the epigenetic composition.
Mentions: While no relationship between geographical region of origin and genotypes could be defined for S accessions with AFLPs, a different situation emerged with MS-AFLPs (Fig 2). Almost all of the S accessions (67 out of 73) were from the administrative regions of Castilla-La Mancha (provinces of Toledo, Ciudad Real, Albacete, and Cuenca) and Aragón (province of Teruel). By focusing on these samples, it was possible to observe that their distribution in the FCA scatterplot is somewhat influenced by the geographical origin. Accessions coming respectively from the EAST (Cuenca and Teruel) and from the WEST (Toledo and Ciudad Real, light grey) tended to cluster together in two separate groups with only a few exceptions, while accessions from Albacete (South-East part of Castilla–La Mancha), bordering the provinces of Ciudad Real and Cuenca, tended to be in the middle and partially superimposed to the two groups (S5 Fig).

Bottom Line: The presence and extent of genetic variation in saffron crocus are still debated, as testified by several contradictory articles providing contrasting results about the monomorphism or less of the species.While the genetic variability was low (4.23% polymorphic peaks and twelve (12) effective different genotypes), the methyl sensitive analysis showed the presence of high epigenetic variability (33.57% polymorphic peaks and twenty eight (28) different effective epigenotypes).Two clearly defined clusters grouping accessions from the West (Toledo and Ciudad Real) and accessions from the East (Cuenca and Teruel) were clearly recognised.

View Article: PubMed Central - PubMed

Affiliation: Faculty of Agricultural, Food and Environmental Sciences, Università Cattolica del Sacro Cuore, Piacenza, Italy; BioDNA, Centro di Ricerca sulla biodiversità e sul DNA antico, Università Cattolica del Sacro Cuore, Piacenza, Italy.

ABSTRACT
The presence and extent of genetic variation in saffron crocus are still debated, as testified by several contradictory articles providing contrasting results about the monomorphism or less of the species. Remarkably, phenotypic variations have been frequently observed in the field, such variations are usually unstable and can change from one growing season to another. Considering that gene expression can be influenced both by genetic and epigenetic changes, epigenetics could be a plausible cause of the alternative phenotypes. In order to obtain new insights into this issue, we carried out a molecular marker analysis of 112 accessions from the World Saffron and Crocus Collection. The accessions were grown for at least three years in the same open field conditions. The same samples were analysed using Amplified Fragment Length Polymorphism (AFLP) and Methyl Sensitive AFLP in order to search for variation at the genetic (DNA sequence) and epigenetic (cytosine methylation) level. While the genetic variability was low (4.23% polymorphic peaks and twelve (12) effective different genotypes), the methyl sensitive analysis showed the presence of high epigenetic variability (33.57% polymorphic peaks and twenty eight (28) different effective epigenotypes). The pattern obtained by Factorial Correspondence Analysis of AFLP and, in particular, of MS-AFLP data was consistent with the geographical provenance of the accessions. Very interestingly, by focusing on Spanish accessions, it was observed that the distribution of the accessions in the Factorial Correspondence Analysis is not random but tends to reflect the geographical origin. Two clearly defined clusters grouping accessions from the West (Toledo and Ciudad Real) and accessions from the East (Cuenca and Teruel) were clearly recognised.

Show MeSH
Related in: MedlinePlus