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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.


Introgression from modern maize into landraces.Level of introgression from modern maize into the RL population (q2 values) computed using only the neutral loci. For the comparison, the q2 values were standardised based on the upper q2 value (q2 of the DMM population) and the lower q2 value (q2 of the OL population). *, P <0.05.
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pone.0121381.g005: Introgression from modern maize into landraces.Level of introgression from modern maize into the RL population (q2 values) computed using only the neutral loci. For the comparison, the q2 values were standardised based on the upper q2 value (q2 of the DMM population) and the lower q2 value (q2 of the OL population). *, P <0.05.

Mentions: A neutral dataset was built for both the SSRs and AFLPs by excluding the loci that showed even a minimal effect of selection (all of the loci that also showed minimal signs of selection are reported in Table 4). The level of introgression of this neutral dataset (q2 estimate for RL) was then computed. This analysis was carried out to estimate the level of introgression from modern maize into landraces that was not inflated by selection, and thus to determine whether selection had a relevant role in determining the introgression detected. The SSRs and AFLPs gave different results here. In particular, the level of introgression in the RL population computed with the SSRs indicated a similar q2 value for the neutral loci (q2 = 0.39) and all of the loci (q2 = 0.37) (Wilcoxon–Kruskal–Wallis non-parametric test, P = 0.36; Fig. 5). The AFLP results indicated a significantly lower level of introgression with the neutral loci (q2 = 0.16) than with all of the loci (q2 = 0.21) (Wilcoxon–Kruskal–Wallis non-parametric test, P = 0.04; Fig. 5).


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)

Introgression from modern maize into landraces.Level of introgression from modern maize into the RL population (q2 values) computed using only the neutral loci. For the comparison, the q2 values were standardised based on the upper q2 value (q2 of the DMM population) and the lower q2 value (q2 of the OL population). *, P <0.05.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0121381.g005: Introgression from modern maize into landraces.Level of introgression from modern maize into the RL population (q2 values) computed using only the neutral loci. For the comparison, the q2 values were standardised based on the upper q2 value (q2 of the DMM population) and the lower q2 value (q2 of the OL population). *, P <0.05.
Mentions: A neutral dataset was built for both the SSRs and AFLPs by excluding the loci that showed even a minimal effect of selection (all of the loci that also showed minimal signs of selection are reported in Table 4). The level of introgression of this neutral dataset (q2 estimate for RL) was then computed. This analysis was carried out to estimate the level of introgression from modern maize into landraces that was not inflated by selection, and thus to determine whether selection had a relevant role in determining the introgression detected. The SSRs and AFLPs gave different results here. In particular, the level of introgression in the RL population computed with the SSRs indicated a similar q2 value for the neutral loci (q2 = 0.39) and all of the loci (q2 = 0.37) (Wilcoxon–Kruskal–Wallis non-parametric test, P = 0.36; Fig. 5). The AFLP results indicated a significantly lower level of introgression with the neutral loci (q2 = 0.16) than with all of the loci (q2 = 0.21) (Wilcoxon–Kruskal–Wallis non-parametric test, P = 0.04; Fig. 5).

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.