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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.


Divergence between populations.Pairwise FST values between the OL and the RL, NI, FMM and DMM (red squares) populations, and between the RL and the OL, NI, FMM and DMM (grey triangles) populations for the SSR (a) and AFLP (b) molecular markers.
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pone.0121381.g001: Divergence between populations.Pairwise FST values between the OL and the RL, NI, FMM and DMM (red squares) populations, and between the RL and the OL, NI, FMM and DMM (grey triangles) populations for the SSR (a) and AFLP (b) molecular markers.

Mentions: Estimates of differentiation (FST) between the pairs of populations computed with the SSR and AFLP datasets are reported in S3 Table. The Mantel test showed that the matrices obtained with the two molecular markers were almost identical (r2 = 0.87; P = 0.01; S1 Fig.). The lowest differentiation was between the OL and RL populations (FST = 0.03 and 0.04, for SSR and AFLP, respectively; Fig. 1 and S3 Table). While consistent with the data of Bitocchi et al. [24] that were obtained only with SSRs, also for the AFLP dataset, the genetic differentiation between OL and the other populations increased from NI (FST = 0.12) to FMM (FST = 0.15), to a maximum FST of 0.22 for DMM. This trend was similar considering the differentiation between RL and the other populations, although all of the FST values were lower compared to those obtained for OL, with the estimates between the OL and the NI, FMM and DMM populations being, on average, 1.6-fold higher that those between the RL and the NI, FMM and DMM populations (Fig. 1 and S3 Table).


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)

Divergence between populations.Pairwise FST values between the OL and the RL, NI, FMM and DMM (red squares) populations, and between the RL and the OL, NI, FMM and DMM (grey triangles) populations for the SSR (a) and AFLP (b) molecular markers.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0121381.g001: Divergence between populations.Pairwise FST values between the OL and the RL, NI, FMM and DMM (red squares) populations, and between the RL and the OL, NI, FMM and DMM (grey triangles) populations for the SSR (a) and AFLP (b) molecular markers.
Mentions: Estimates of differentiation (FST) between the pairs of populations computed with the SSR and AFLP datasets are reported in S3 Table. The Mantel test showed that the matrices obtained with the two molecular markers were almost identical (r2 = 0.87; P = 0.01; S1 Fig.). The lowest differentiation was between the OL and RL populations (FST = 0.03 and 0.04, for SSR and AFLP, respectively; Fig. 1 and S3 Table). While consistent with the data of Bitocchi et al. [24] that were obtained only with SSRs, also for the AFLP dataset, the genetic differentiation between OL and the other populations increased from NI (FST = 0.12) to FMM (FST = 0.15), to a maximum FST of 0.22 for DMM. This trend was similar considering the differentiation between RL and the other populations, although all of the FST values were lower compared to those obtained for OL, with the estimates between the OL and the NI, FMM and DMM populations being, on average, 1.6-fold higher that those between the RL and the NI, FMM and DMM populations (Fig. 1 and S3 Table).

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.