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Evolution of neutral and flowering genes along pearl millet (Pennisetum glaucum) domestication.

Lakis G, Navascués M, Rekima S, Simon M, Remigereau MS, Leveugle M, Takvorian N, Lamy F, Depaulis F, Robert T - PLoS ONE (2012)

Bottom Line: No specific polymorphisms were found either in the wild or in the domestic populations.Early and late landraces did not show significant genetic differentiation at both the neutral and the candidate loci.Reasons why these results contrast with previous results that have shown a slight but significant association between PgPHYC polymorphisms and variation in flowering time in pearl millet are discussed.

View Article: PubMed Central - PubMed

Affiliation: Laboratoire Ecologie Systématique et Evolution, UMR 8079 Université Paris-Sud, Orsay, France. ghayas.lakis@u-psud.fr

ABSTRACT

Background: Pearl millet landraces display an important variation in their cycle duration. This diversity contributes to the stability of crop production in the Sahel despite inter-annual rainfall fluctuation. Conservation of phenological diversity is important for the future of pearl millet improvement and sustainable use. Identification of genes contributing to flowering time variation is therefore relevant. In this study we focused on three flowering candidate genes, PgHd3a, PgDwarf8 and PgPHYC. We tested for signatures of past selective events within polymorphism patterns of these three genes that could have been associated with pearl millet domestication and/or landraces differentiation. In order to implement ad hoc neutrality tests, a plausible demographic history of pearl millet domestication was inferred through Approximate Bayesian Computation by using eight neutral STS loci.

Results: Domesticated pearl millet exhibited 84% of the nucleotide diversity level found in the wild population. No specific polymorphisms were found either in the wild or in the domestic populations. The bayesian approach and previous studies suggest that gene flow between wild relatives and domesticated pearl millets is a main factor explaining these results. Early and late landraces did not show significant genetic differentiation at both the neutral and the candidate loci. A positive selection was evidenced in PgHd3a and PgDwarf8 genes of domestic forms but not in the wild population.

Conclusion: Our results strongly suggest that PgHd3a and PgDwarf8 were likely targeted by selection during domestication. However, a potential role of any of the three candidate genes in the phenological differentiation between early and late landraces was not supported by our data. Reasons why these results contrast with previous results that have shown a slight but significant association between PgPHYC polymorphisms and variation in flowering time in pearl millet are discussed.

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Related in: MedlinePlus

Genetic structure of wild and domesticated populations.A. Values of ΔK calculated by using the Evanno et al. (2005) method according to the number K of clusters B. Representation of the individual assignment probabilities to each of the 2 inferred clusters; individuals were arranged according to the estimated proportion of admixture in their genome.
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pone-0036642-g001: Genetic structure of wild and domesticated populations.A. Values of ΔK calculated by using the Evanno et al. (2005) method according to the number K of clusters B. Representation of the individual assignment probabilities to each of the 2 inferred clusters; individuals were arranged according to the estimated proportion of admixture in their genome.

Mentions: Our results showed that the wild and the domestic populations are significantly genetically differentiated, as suggested by Fst values (Table S4) and by the analysis of the genetic structure within the collection of accessions. The average Fst value between the wild and the domestic populations across all STS loci was 0.12. All the Fst values estimated on each STS locus were significant, except for STS 521 and STS 738. The Bayesian analysis of the population genetic structure showed that the most likely number of groups was K = 2 (Figure 1A). Figure 1B shows that each of the two clusters was composed of both domestic and wild individuals. The wild pearl millets showed high level of genome admixture from both clusters. Genome admixture was also found for the domestic individuals, but in a lesser extent. This pattern may be due to either shared ancestral polymorphisms or migration between the two forms of pearl millet. The difference in genome admixture proportion between wild and domestic individuals suggested that the gene flow may be asymmetrical with preferential introgression of wild genotypes by genes from the domestic populations.


Evolution of neutral and flowering genes along pearl millet (Pennisetum glaucum) domestication.

Lakis G, Navascués M, Rekima S, Simon M, Remigereau MS, Leveugle M, Takvorian N, Lamy F, Depaulis F, Robert T - PLoS ONE (2012)

Genetic structure of wild and domesticated populations.A. Values of ΔK calculated by using the Evanno et al. (2005) method according to the number K of clusters B. Representation of the individual assignment probabilities to each of the 2 inferred clusters; individuals were arranged according to the estimated proportion of admixture in their genome.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3351476&req=5

pone-0036642-g001: Genetic structure of wild and domesticated populations.A. Values of ΔK calculated by using the Evanno et al. (2005) method according to the number K of clusters B. Representation of the individual assignment probabilities to each of the 2 inferred clusters; individuals were arranged according to the estimated proportion of admixture in their genome.
Mentions: Our results showed that the wild and the domestic populations are significantly genetically differentiated, as suggested by Fst values (Table S4) and by the analysis of the genetic structure within the collection of accessions. The average Fst value between the wild and the domestic populations across all STS loci was 0.12. All the Fst values estimated on each STS locus were significant, except for STS 521 and STS 738. The Bayesian analysis of the population genetic structure showed that the most likely number of groups was K = 2 (Figure 1A). Figure 1B shows that each of the two clusters was composed of both domestic and wild individuals. The wild pearl millets showed high level of genome admixture from both clusters. Genome admixture was also found for the domestic individuals, but in a lesser extent. This pattern may be due to either shared ancestral polymorphisms or migration between the two forms of pearl millet. The difference in genome admixture proportion between wild and domestic individuals suggested that the gene flow may be asymmetrical with preferential introgression of wild genotypes by genes from the domestic populations.

Bottom Line: No specific polymorphisms were found either in the wild or in the domestic populations.Early and late landraces did not show significant genetic differentiation at both the neutral and the candidate loci.Reasons why these results contrast with previous results that have shown a slight but significant association between PgPHYC polymorphisms and variation in flowering time in pearl millet are discussed.

View Article: PubMed Central - PubMed

Affiliation: Laboratoire Ecologie Systématique et Evolution, UMR 8079 Université Paris-Sud, Orsay, France. ghayas.lakis@u-psud.fr

ABSTRACT

Background: Pearl millet landraces display an important variation in their cycle duration. This diversity contributes to the stability of crop production in the Sahel despite inter-annual rainfall fluctuation. Conservation of phenological diversity is important for the future of pearl millet improvement and sustainable use. Identification of genes contributing to flowering time variation is therefore relevant. In this study we focused on three flowering candidate genes, PgHd3a, PgDwarf8 and PgPHYC. We tested for signatures of past selective events within polymorphism patterns of these three genes that could have been associated with pearl millet domestication and/or landraces differentiation. In order to implement ad hoc neutrality tests, a plausible demographic history of pearl millet domestication was inferred through Approximate Bayesian Computation by using eight neutral STS loci.

Results: Domesticated pearl millet exhibited 84% of the nucleotide diversity level found in the wild population. No specific polymorphisms were found either in the wild or in the domestic populations. The bayesian approach and previous studies suggest that gene flow between wild relatives and domesticated pearl millets is a main factor explaining these results. Early and late landraces did not show significant genetic differentiation at both the neutral and the candidate loci. A positive selection was evidenced in PgHd3a and PgDwarf8 genes of domestic forms but not in the wild population.

Conclusion: Our results strongly suggest that PgHd3a and PgDwarf8 were likely targeted by selection during domestication. However, a potential role of any of the three candidate genes in the phenological differentiation between early and late landraces was not supported by our data. Reasons why these results contrast with previous results that have shown a slight but significant association between PgPHYC polymorphisms and variation in flowering time in pearl millet are discussed.

Show MeSH
Related in: MedlinePlus