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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

Posterior probability density distribution of the parameters of the demographic model inferred by ABC estimation.Data shown was obtained for the scenario “with migration”. The prior (black line) is used as a reference for the posterior distribution (blue lines) obtained from the rejection followed by the non linear regression. Parameters T, M and rho are scaled to the wild population effective size New.
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pone-0036642-g002: Posterior probability density distribution of the parameters of the demographic model inferred by ABC estimation.Data shown was obtained for the scenario “with migration”. The prior (black line) is used as a reference for the posterior distribution (blue lines) obtained from the rejection followed by the non linear regression. Parameters T, M and rho are scaled to the wild population effective size New.

Mentions: The posterior density probability distributions, of the parameters included in the model, were different from the prior distributions with clearly identified modes (Figure 2). This allowed point estimations of these parameters except for rho, the effective migration rates (Figure 2) and t, the time of domestication in generation units (not shown). Indeed, the posterior distributions of these parameters were very similar to their prior distributions. Thus, our data was not informative enough to get reliable estimates of these parameters.


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)

Posterior probability density distribution of the parameters of the demographic model inferred by ABC estimation.Data shown was obtained for the scenario “with migration”. The prior (black line) is used as a reference for the posterior distribution (blue lines) obtained from the rejection followed by the non linear regression. Parameters T, M and rho are scaled to the wild population effective size New.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0036642-g002: Posterior probability density distribution of the parameters of the demographic model inferred by ABC estimation.Data shown was obtained for the scenario “with migration”. The prior (black line) is used as a reference for the posterior distribution (blue lines) obtained from the rejection followed by the non linear regression. Parameters T, M and rho are scaled to the wild population effective size New.
Mentions: The posterior density probability distributions, of the parameters included in the model, were different from the prior distributions with clearly identified modes (Figure 2). This allowed point estimations of these parameters except for rho, the effective migration rates (Figure 2) and t, the time of domestication in generation units (not shown). Indeed, the posterior distributions of these parameters were very similar to their prior distributions. Thus, our data was not informative enough to get reliable estimates of these parameters.

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