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European flint landraces grown in situ reveal adaptive introgression from modern maize.

Bitocchi E, Bellucci E, Rau D, Albertini E, Rodriguez M, Veronesi F, Attene G, Nanni L - PLoS ONE (2015)

Bottom Line: In particular, the locus showing the strongest signals of selection is a Misfit transposable element.Finally, molecular characterisation of the same samples with two different molecular markers has allowed us to compare their performances.Although the genetic-diversity and population-structure analyses provide the same global qualitative pattern, which thus provides the same inferences, there are differences related to their natures and characteristics.

View Article: PubMed Central - PubMed

Affiliation: Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy.

ABSTRACT
We have investigated the role of selection in the determination of the detected levels of introgression from modern maize hybrid varieties into maize landraces still cultivated in situ in Italy. We exploited the availability of a historical collection of landraces undertaken before the introduction and widespread use of modern maize, to analyse genomic changes that have occurred in these maize landraces over 50 years of co-existence with hybrid varieties. We have combined a previously published SSR dataset (n=21) with an AFLP loci dataset (n=168) to provide higher resolution power and to obtain a more detailed picture. We show that selection pressures for adaptation have favoured new alleles introduced by migration from hybrids. This shows the potential for analysis of historical introgression even over this short period of 50 years, for an understanding of the evolution of the genome and for the identification of its functionally important regions. Moreover, this demonstrates that landraces grown in situ represent almost unique populations for use for such studies when the focus is on the domesticated plant. This is due to their adaptation, which has arisen from their dynamic evolution under a continuously changing agro-ecological environment, and their capture of new alleles from hybridisation. We have also identified loci for which selection has inhibited introgression from modern germplasm and has enhanced the distinction between landraces and modern maize. These loci indicate that selection acted in the past, during the formation of the flint and dent gene pools. In particular, the locus showing the strongest signals of selection is a Misfit transposable element. Finally, molecular characterisation of the same samples with two different molecular markers has allowed us to compare their performances. Although the genetic-diversity and population-structure analyses provide the same global qualitative pattern, which thus provides the same inferences, there are differences related to their natures and characteristics.

No MeSH data available.


Pairwise comparisons performed with DFDIST using the AFLP markers.Plot of FST values against heterozygosity estimates for the OL–RL (a), RL–DMM (b) and OL–DMM (c) populations pairs. Each dot indicates an AFLP locus (black dot, neutral locus; red dot, outlier locus).
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pone.0121381.g004: Pairwise comparisons performed with DFDIST using the AFLP markers.Plot of FST values against heterozygosity estimates for the OL–RL (a), RL–DMM (b) and OL–DMM (c) populations pairs. Each dot indicates an AFLP locus (black dot, neutral locus; red dot, outlier locus).

Mentions: A total of nine AFLP loci were detected as outliers by the DFDIST analysis (significance level, 0.01) (Table 4 and Fig. 4). Eight loci (11c, 15d, 25d, 8f, 33f, 39f, 40f, 45f) were detected as under selection in the OL–RL comparison, and two (26d, 33f) in the OL–DMM comparison, with 26d being detected also in the RL–DMM comparison. Bayescan analysis identified locus 26d as an outlier, with very strong evidence of selection in the OL–DMM comparison, and only slight evidence in the RL–DMM comparison. Thus, both of these different methods provided strong evidence of selection for the AFLP locus of 26d; moreover, this locus showed very high differentiation between the landraces and the modern maize (FST(OL-DMM) = 0.93; FST(OL-DMM) = 0.72) (Fig. 4).


European flint landraces grown in situ reveal adaptive introgression from modern maize.

Bitocchi E, Bellucci E, Rau D, Albertini E, Rodriguez M, Veronesi F, Attene G, Nanni L - PLoS ONE (2015)

Pairwise comparisons performed with DFDIST using the AFLP markers.Plot of FST values against heterozygosity estimates for the OL–RL (a), RL–DMM (b) and OL–DMM (c) populations pairs. Each dot indicates an AFLP locus (black dot, neutral locus; red dot, outlier locus).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4390310&req=5

pone.0121381.g004: Pairwise comparisons performed with DFDIST using the AFLP markers.Plot of FST values against heterozygosity estimates for the OL–RL (a), RL–DMM (b) and OL–DMM (c) populations pairs. Each dot indicates an AFLP locus (black dot, neutral locus; red dot, outlier locus).
Mentions: A total of nine AFLP loci were detected as outliers by the DFDIST analysis (significance level, 0.01) (Table 4 and Fig. 4). Eight loci (11c, 15d, 25d, 8f, 33f, 39f, 40f, 45f) were detected as under selection in the OL–RL comparison, and two (26d, 33f) in the OL–DMM comparison, with 26d being detected also in the RL–DMM comparison. Bayescan analysis identified locus 26d as an outlier, with very strong evidence of selection in the OL–DMM comparison, and only slight evidence in the RL–DMM comparison. Thus, both of these different methods provided strong evidence of selection for the AFLP locus of 26d; moreover, this locus showed very high differentiation between the landraces and the modern maize (FST(OL-DMM) = 0.93; FST(OL-DMM) = 0.72) (Fig. 4).

Bottom Line: In particular, the locus showing the strongest signals of selection is a Misfit transposable element.Finally, molecular characterisation of the same samples with two different molecular markers has allowed us to compare their performances.Although the genetic-diversity and population-structure analyses provide the same global qualitative pattern, which thus provides the same inferences, there are differences related to their natures and characteristics.

View Article: PubMed Central - PubMed

Affiliation: Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy.

ABSTRACT
We have investigated the role of selection in the determination of the detected levels of introgression from modern maize hybrid varieties into maize landraces still cultivated in situ in Italy. We exploited the availability of a historical collection of landraces undertaken before the introduction and widespread use of modern maize, to analyse genomic changes that have occurred in these maize landraces over 50 years of co-existence with hybrid varieties. We have combined a previously published SSR dataset (n=21) with an AFLP loci dataset (n=168) to provide higher resolution power and to obtain a more detailed picture. We show that selection pressures for adaptation have favoured new alleles introduced by migration from hybrids. This shows the potential for analysis of historical introgression even over this short period of 50 years, for an understanding of the evolution of the genome and for the identification of its functionally important regions. Moreover, this demonstrates that landraces grown in situ represent almost unique populations for use for such studies when the focus is on the domesticated plant. This is due to their adaptation, which has arisen from their dynamic evolution under a continuously changing agro-ecological environment, and their capture of new alleles from hybridisation. We have also identified loci for which selection has inhibited introgression from modern germplasm and has enhanced the distinction between landraces and modern maize. These loci indicate that selection acted in the past, during the formation of the flint and dent gene pools. In particular, the locus showing the strongest signals of selection is a Misfit transposable element. Finally, molecular characterisation of the same samples with two different molecular markers has allowed us to compare their performances. Although the genetic-diversity and population-structure analyses provide the same global qualitative pattern, which thus provides the same inferences, there are differences related to their natures and characteristics.

No MeSH data available.