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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.


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.
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pone.0121381.g006: 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.

Mentions: Through BLASTn [55] searches against the nucleotide collection (nr/nt) database (NCBI/GenBank), we identified four Zea mays sequences that showed high similarity with the 26d locus sequence (Fig. 6 and S4 Table). This analysis indicated that the 26d AFLP fragment is part of a DNA transposon, which is a member of the CACTA family, known as Misfit [56]. The sequences of the lines W22 [57] and McC [56] were from the genomic region characterised by the bronze (bz) locus in maize, which is located on the short arm of chromosome 9 (9S). The Misfit transposon sequence of the A654 line is from a genomic region that is characterised by the delta zein (dzs10) gene, which is located on chromosome 9 [58]. In contrast, as showed by Fu and Dooner [56], the B73 line does not carry the corresponding genomic region with the Misfit transposon in the bronze locus; however, for the 26d fragment, we found correspondence in the B73 line (identity, 99%; e-value, 7e-81), with a region located on chromosome 1: the so-called pcluster [59]. Several hits for all of the chromosomes characterised by high e-values (from 3.49e-80 to 3.47e-85) were found by the BLASTn analysis performed against the B73 Reference Genome sequence database. This was expected, considering that the 26d fragment is a partial sequence of a transposable element. As for four sequences found in the NCBI nr/nt database and the B73 Reference Genome, the 26d fragment that was characteristic of individuals from the OL and RL populations was characterised by two mutations (Fig. 6). One mutation was within the restriction site of MseI (‘TTAA’ for 26d, and ‘TTAT’ for all of the other sequences found by BLASTn analysis); this explains the presence of the band for 100% and 96% of the OL and RL individuals, respectively, and its absence in 96% of the DMM varieties and lines. The other polymorphism was a mutation 3 bp upstream of the MseI restriction site (a ‘C’ base, instead of ‘T’).


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)

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.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0121381.g006: 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.
Mentions: Through BLASTn [55] searches against the nucleotide collection (nr/nt) database (NCBI/GenBank), we identified four Zea mays sequences that showed high similarity with the 26d locus sequence (Fig. 6 and S4 Table). This analysis indicated that the 26d AFLP fragment is part of a DNA transposon, which is a member of the CACTA family, known as Misfit [56]. The sequences of the lines W22 [57] and McC [56] were from the genomic region characterised by the bronze (bz) locus in maize, which is located on the short arm of chromosome 9 (9S). The Misfit transposon sequence of the A654 line is from a genomic region that is characterised by the delta zein (dzs10) gene, which is located on chromosome 9 [58]. In contrast, as showed by Fu and Dooner [56], the B73 line does not carry the corresponding genomic region with the Misfit transposon in the bronze locus; however, for the 26d fragment, we found correspondence in the B73 line (identity, 99%; e-value, 7e-81), with a region located on chromosome 1: the so-called pcluster [59]. Several hits for all of the chromosomes characterised by high e-values (from 3.49e-80 to 3.47e-85) were found by the BLASTn analysis performed against the B73 Reference Genome sequence database. This was expected, considering that the 26d fragment is a partial sequence of a transposable element. As for four sequences found in the NCBI nr/nt database and the B73 Reference Genome, the 26d fragment that was characteristic of individuals from the OL and RL populations was characterised by two mutations (Fig. 6). One mutation was within the restriction site of MseI (‘TTAA’ for 26d, and ‘TTAT’ for all of the other sequences found by BLASTn analysis); this explains the presence of the band for 100% and 96% of the OL and RL individuals, respectively, and its absence in 96% of the DMM varieties and lines. The other polymorphism was a mutation 3 bp upstream of the MseI restriction site (a ‘C’ base, instead of ‘T’).

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.