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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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Factorial Correspondence Analysis evidencing the relationships among AFLP genotypes and MS-AFLP epigenotypes of different saffron crocus accessions.1A) Factorial Correspondence Analysis showing multivariate relationships among AFLP genotypes of different accessions on the axes corresponding to first (x axis, 9.72% inertia) vs. second (y axis, 6.75% of inertia) main factors (1A I). The two populations Pop A and Pop B correspond to the main clusters identified by STRUCTURE analysis at K = 2 (1A II). Population A included just the S accessions and three different genotypes, while population B included both S and NS accessions and 9 different genotypes. Inside population B, samples included in the dashed line refer to accessions from Iran, India, Afghanistan and Turkey. 1B) Factorial Correspondence Analysis showing multivariate relationships among MS-AFLP epigenotypes of different accessions on the axes corresponding to first (x axis, 12.88% of inertia) vs. second (y axis, 10.15% of inertia) main factors (1B I). The two populations Pop C and Pop D correspond to the main clusters identified by STRUCTURE analysis at K = 2 (1B II). Population C included just Spanish accessions and 6 effective epigenotypes, while population D included both S and NS accessions and 22 effective epigenotypes.
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pone.0123434.g001: Factorial Correspondence Analysis evidencing the relationships among AFLP genotypes and MS-AFLP epigenotypes of different saffron crocus accessions.1A) Factorial Correspondence Analysis showing multivariate relationships among AFLP genotypes of different accessions on the axes corresponding to first (x axis, 9.72% inertia) vs. second (y axis, 6.75% of inertia) main factors (1A I). The two populations Pop A and Pop B correspond to the main clusters identified by STRUCTURE analysis at K = 2 (1A II). Population A included just the S accessions and three different genotypes, while population B included both S and NS accessions and 9 different genotypes. Inside population B, samples included in the dashed line refer to accessions from Iran, India, Afghanistan and Turkey. 1B) Factorial Correspondence Analysis showing multivariate relationships among MS-AFLP epigenotypes of different accessions on the axes corresponding to first (x axis, 12.88% of inertia) vs. second (y axis, 10.15% of inertia) main factors (1B I). The two populations Pop C and Pop D correspond to the main clusters identified by STRUCTURE analysis at K = 2 (1B II). Population C included just Spanish accessions and 6 effective epigenotypes, while population D included both S and NS accessions and 22 effective epigenotypes.

Mentions: The first two factors of the Factorial Correspondence Analysis (FCA) explained 16.47% of total inertia (Table 2). In particular, despite the overall reduced variability at the genomic level, the distribution of the points representing single accessions along the first factor (x axis in Fig 1) seems to correspond to the geographical provenance: most of the Spanish accessions (S) cluster on the right, with only a few points overlapping with Non-Spanish (NS) samples in the central part of the graph (Fig 1A I). Iranian accessions, instead, are located on the left of the plot and do not overlap with any other group. These results were also supported by Crocus diversity indices (S3 Table). In fact, excluding French and Greek accessions that have the same dominant genotype as Spanish ones (A1), the samples from other areas (Iran, Turkey, Italy and so on) have slightly different genotypes. Among S accessions, no relationship between geographic origin (different areas of Spain) and genotype can be defined, because the genotype was almost always the same (A1). While in Fig 1 the evident distinction is between S and NS origin, the same representation based on the effective genotypes is also provided (S1 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)

Factorial Correspondence Analysis evidencing the relationships among AFLP genotypes and MS-AFLP epigenotypes of different saffron crocus accessions.1A) Factorial Correspondence Analysis showing multivariate relationships among AFLP genotypes of different accessions on the axes corresponding to first (x axis, 9.72% inertia) vs. second (y axis, 6.75% of inertia) main factors (1A I). The two populations Pop A and Pop B correspond to the main clusters identified by STRUCTURE analysis at K = 2 (1A II). Population A included just the S accessions and three different genotypes, while population B included both S and NS accessions and 9 different genotypes. Inside population B, samples included in the dashed line refer to accessions from Iran, India, Afghanistan and Turkey. 1B) Factorial Correspondence Analysis showing multivariate relationships among MS-AFLP epigenotypes of different accessions on the axes corresponding to first (x axis, 12.88% of inertia) vs. second (y axis, 10.15% of inertia) main factors (1B I). The two populations Pop C and Pop D correspond to the main clusters identified by STRUCTURE analysis at K = 2 (1B II). Population C included just Spanish accessions and 6 effective epigenotypes, while population D included both S and NS accessions and 22 effective epigenotypes.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4401542&req=5

pone.0123434.g001: Factorial Correspondence Analysis evidencing the relationships among AFLP genotypes and MS-AFLP epigenotypes of different saffron crocus accessions.1A) Factorial Correspondence Analysis showing multivariate relationships among AFLP genotypes of different accessions on the axes corresponding to first (x axis, 9.72% inertia) vs. second (y axis, 6.75% of inertia) main factors (1A I). The two populations Pop A and Pop B correspond to the main clusters identified by STRUCTURE analysis at K = 2 (1A II). Population A included just the S accessions and three different genotypes, while population B included both S and NS accessions and 9 different genotypes. Inside population B, samples included in the dashed line refer to accessions from Iran, India, Afghanistan and Turkey. 1B) Factorial Correspondence Analysis showing multivariate relationships among MS-AFLP epigenotypes of different accessions on the axes corresponding to first (x axis, 12.88% of inertia) vs. second (y axis, 10.15% of inertia) main factors (1B I). The two populations Pop C and Pop D correspond to the main clusters identified by STRUCTURE analysis at K = 2 (1B II). Population C included just Spanish accessions and 6 effective epigenotypes, while population D included both S and NS accessions and 22 effective epigenotypes.
Mentions: The first two factors of the Factorial Correspondence Analysis (FCA) explained 16.47% of total inertia (Table 2). In particular, despite the overall reduced variability at the genomic level, the distribution of the points representing single accessions along the first factor (x axis in Fig 1) seems to correspond to the geographical provenance: most of the Spanish accessions (S) cluster on the right, with only a few points overlapping with Non-Spanish (NS) samples in the central part of the graph (Fig 1A I). Iranian accessions, instead, are located on the left of the plot and do not overlap with any other group. These results were also supported by Crocus diversity indices (S3 Table). In fact, excluding French and Greek accessions that have the same dominant genotype as Spanish ones (A1), the samples from other areas (Iran, Turkey, Italy and so on) have slightly different genotypes. Among S accessions, no relationship between geographic origin (different areas of Spain) and genotype can be defined, because the genotype was almost always the same (A1). While in Fig 1 the evident distinction is between S and NS origin, the same representation based on the effective genotypes is also provided (S1 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