SSR data for maize landraces from Central Italy

SSR data for maize landraces from Central Ital

BLASTn analysis.

<p>Alignment of the 26d locus sequence and the four best matching sequences from BLASTn searches. Grey, <i>Eco</i>RI restriction site; yellow, <i>Mse</i>I restriction site.</p

Introgression from modern maize into landraces.

<p>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.</p

IMPACT : Un modèle de performance pour l’évaluation des potentielles conséquences d’un changement sur la sécurité d’une organisation

<div><p>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 <i>in situ</i> 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 <i>in situ</i> 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 <i>Misfit</i> 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.</p></div

Genetic diversity estimates for the populations analysed using the SSR and AFLP datasets.

<p>n_e, Effective number of alleles per locus [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0121381#pone.0121381.ref029" target="_blank">29</a>]; He, Unbiased expected heterozygosity [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0121381#pone.0121381.ref030" target="_blank">30</a>]; F_IS, Inbreeding coefficient [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0121381#pone.0121381.ref033" target="_blank">33</a>].</p><p>Subgroups of the RL population as determined by the population STRUCTURE analysis:</p><p>^aRL_A, accessions showing no or low level of introgression from modern maize;</p><p>^bRL_B, accessions showing high level of introgression from modern maize.</p><p>For further population codes, see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0121381#pone.0121381.t001" target="_blank">Table 1</a>.</p><p>Genetic diversity estimates for the populations analysed using the SSR and AFLP datasets.</p

Number of accessions and genotypes analysed in this study.

<p>^aThe control accession ANGRMC13 (4 genotypes) was included in the RL population.</p><p>Number of accessions and genotypes analysed in this study.</p

Variations in the genetic diversity (He) between the populations (ΔH), computed for the neutral and outlier loci detected in the given comparisons.

<p>^aSignificance between ΔH values for neutral and outlier loci (Wilcoxon–Kruskal–Wallis non-parametric test).</p><p>For population codes, see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0121381#pone.0121381.t001" target="_blank">Table 1</a>.</p><p>Variations in the genetic diversity (He) between the populations (ΔH), computed for the neutral and outlier loci detected in the given comparisons.</p

Frequency of the AFLP fragment (presence of the band) and unbiased expected heterozygosity (He) of the AFLP loci detected as outliers.

<p>^aComparison in which the loci were detected as outliers.</p><p>^bRL_A, accessions showing no or low level of introgression from modern maize;</p><p>^cRL_B, accessions showing high level of introgression from modern maize.</p><p>For further population codes, see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0121381#pone.0121381.t001" target="_blank">Table 1</a>.</p><p>Frequency of the AFLP fragment (presence of the band) and unbiased expected heterozygosity (He) of the AFLP loci detected as outliers.</p

Average membership coefficients to each of the two identified clusters for the populations analysed using the SSR and AFLP datasets.

<p>q₁, Average percentage of membership to Cluster 1; q₂, Average percentage of membership to Cluster 2.</p><p>^aThe control accession ANGRMC13 was excluded by this computation.</p><p>For population codes, see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0121381#pone.0121381.t001" target="_blank">Table 1</a>.</p><p>Average membership coefficients to each of the two identified clusters for the populations analysed using the SSR and AFLP datasets.</p

Divergence between populations.

<p>Pairwise F_ST 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 <b>(a)</b> and AFLP <b>(b)</b> molecular markers.</p