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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.


Population structure at accession level.Average percentages of membership to cluster 1 (q1, red) and cluster 2 (q2, blue) for each of the 104 accessions for the SSR (a) and AFLP (b) molecular markers. Each accession is represented by a vertical bar divided into two coloured segments, the lengths of which indicate the proportions of the genome attributed to cluster 1 and cluster 2. The arrow indicates the control accession ANGRMC13.
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pone.0121381.g003: Population structure at accession level.Average percentages of membership to cluster 1 (q1, red) and cluster 2 (q2, blue) for each of the 104 accessions for the SSR (a) and AFLP (b) molecular markers. Each accession is represented by a vertical bar divided into two coloured segments, the lengths of which indicate the proportions of the genome attributed to cluster 1 and cluster 2. The arrow indicates the control accession ANGRMC13.

Mentions: The average percentages of membership at the accession level are reported in Fig. 3; the OL accessions were assigned to cluster 1 with high percentages of membership, which ranged from a minimum q1(SSR) of 0.62 and q1(AFLP) of 0.87, to a maximum q1(SSR-AFLP) of 0.99 (Fig. 3). Moreover, the average q1 values of the OL accessions were uniform (Wilcoxon–Kruskal–Wallis non-parametric test; PSSR = 0.08 and PAFLP = 0.09). Similarly, the DMM accessions were assigned to cluster 2 with high values of q2 (q2(SSR) from 0.90 to 0.99; q2(AFLP) from 0.73 to 0.99) (Fig. 3). As suggested by Bitocchi et al. [24] from their consideration of only the SSR dataset, the AFLP dataset confirmed that the applied population structure analysis can clearly discriminate between the landraces cultivated before the introduction of maize hybrids (OL) and the modern maize germplasm (DMM). This thus provides a powerful approach for the study of introgression from modern maize varieties into RL landraces, which should be proportional to the q2 values. The level of introgression of the RL accessions was highly variable, with the means of their q1 values being significantly different (Wilcoxon–Kruskal–Wallis non-parametric test; P <0.0001 for both the SSR and AFLP datasets; control accession ANGRMC13 excluded). To evaluate the different levels of introgression for the RL accessions (no/ low introgression, or admixture/ high introgression), a threshold value of q1 was defined for both of the molecular markers, as the lowest average values of q1 among the OL accessions (0.62 for SSR, and 0.87 for AFLP). Twelve of the RL accessions (63%) showed no or low introgression from modern maize (RL_A), while the remaining seven RL accessions were admixed or showed high levels of introgression (RL_B). As expected, the control RL accession ANGRMC13, which was not a landrace, but a dent hybrid that had been cultivated in situ for some years, was assigned to cluster 2 (q2 = 0.99 for both SSR and AFLP; Fig. 3).


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)

Population structure at accession level.Average percentages of membership to cluster 1 (q1, red) and cluster 2 (q2, blue) for each of the 104 accessions for the SSR (a) and AFLP (b) molecular markers. Each accession is represented by a vertical bar divided into two coloured segments, the lengths of which indicate the proportions of the genome attributed to cluster 1 and cluster 2. The arrow indicates the control accession ANGRMC13.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0121381.g003: Population structure at accession level.Average percentages of membership to cluster 1 (q1, red) and cluster 2 (q2, blue) for each of the 104 accessions for the SSR (a) and AFLP (b) molecular markers. Each accession is represented by a vertical bar divided into two coloured segments, the lengths of which indicate the proportions of the genome attributed to cluster 1 and cluster 2. The arrow indicates the control accession ANGRMC13.
Mentions: The average percentages of membership at the accession level are reported in Fig. 3; the OL accessions were assigned to cluster 1 with high percentages of membership, which ranged from a minimum q1(SSR) of 0.62 and q1(AFLP) of 0.87, to a maximum q1(SSR-AFLP) of 0.99 (Fig. 3). Moreover, the average q1 values of the OL accessions were uniform (Wilcoxon–Kruskal–Wallis non-parametric test; PSSR = 0.08 and PAFLP = 0.09). Similarly, the DMM accessions were assigned to cluster 2 with high values of q2 (q2(SSR) from 0.90 to 0.99; q2(AFLP) from 0.73 to 0.99) (Fig. 3). As suggested by Bitocchi et al. [24] from their consideration of only the SSR dataset, the AFLP dataset confirmed that the applied population structure analysis can clearly discriminate between the landraces cultivated before the introduction of maize hybrids (OL) and the modern maize germplasm (DMM). This thus provides a powerful approach for the study of introgression from modern maize varieties into RL landraces, which should be proportional to the q2 values. The level of introgression of the RL accessions was highly variable, with the means of their q1 values being significantly different (Wilcoxon–Kruskal–Wallis non-parametric test; P <0.0001 for both the SSR and AFLP datasets; control accession ANGRMC13 excluded). To evaluate the different levels of introgression for the RL accessions (no/ low introgression, or admixture/ high introgression), a threshold value of q1 was defined for both of the molecular markers, as the lowest average values of q1 among the OL accessions (0.62 for SSR, and 0.87 for AFLP). Twelve of the RL accessions (63%) showed no or low introgression from modern maize (RL_A), while the remaining seven RL accessions were admixed or showed high levels of introgression (RL_B). As expected, the control RL accession ANGRMC13, which was not a landrace, but a dent hybrid that had been cultivated in situ for some years, was assigned to cluster 2 (q2 = 0.99 for both SSR and AFLP; Fig. 3).

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.