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

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.

Fig 1. Divergence between populations.

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 (a) and AFLP (b) molecular markers.

Fig 2. Population structure at individual level.

Percentages of membership to cluster 1 (q₁, red) and cluster 2 (q₂, blue) for each of the 218 genotypes for the SSR (a) and AFLP (b) molecular markers. Each genotype 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 four genotypes of the control accession ANGRMC13.

Fig 3. 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.

Fig 4. Pairwise comparisons performed with DFDIST using the AFLP markers.

Plot of F_ST 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).

Fig 5. 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.

Fig 6. BLASTn analysis.

Alignment of the 26d locus sequence and the four best matching sequences from BLASTn searches. Grey, EcoRI restriction site; yellow, MseI restriction site.