Cargando…

Molecular adaptation in flowering and symbiotic recognition pathways: insights from patterns of polymorphism in the legume Medicago truncatula

BACKGROUND: We studied patterns of molecular adaptation in the wild Mediterranean legume Medicago truncatula. We focused on two phenotypic traits that are not functionally linked: flowering time and perception of symbiotic microbes. Phenology is an important fitness component, especially for annual...

Descripción completa

Detalles Bibliográficos
Autores principales: De Mita, Stéphane, Chantret, Nathalie, Loridon, Karine, Ronfort, Joëlle, Bataillon, Thomas
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3199773/
https://www.ncbi.nlm.nih.gov/pubmed/21806823
http://dx.doi.org/10.1186/1471-2148-11-229
_version_ 1782214593221754880
author De Mita, Stéphane
Chantret, Nathalie
Loridon, Karine
Ronfort, Joëlle
Bataillon, Thomas
author_facet De Mita, Stéphane
Chantret, Nathalie
Loridon, Karine
Ronfort, Joëlle
Bataillon, Thomas
author_sort De Mita, Stéphane
collection PubMed
description BACKGROUND: We studied patterns of molecular adaptation in the wild Mediterranean legume Medicago truncatula. We focused on two phenotypic traits that are not functionally linked: flowering time and perception of symbiotic microbes. Phenology is an important fitness component, especially for annual plants, and many instances of molecular adaptation have been reported for genes involved in flowering pathways. While perception of symbiotic microbes is also integral to adaptation in many plant species, very few reports of molecular adaptation exist for symbiotic genes. Here we used data from 57 individuals and 53 gene fragments to quantify the overall strength of both positive and purifying selection in M. truncatula and asked if footprints of positive selection can be detected at key genes of rhizobia recognition pathways. RESULTS: We examined nucleotide variation among 57 accessions from natural populations in 53 gene fragments: 5 genes involved in nitrogen-fixing bacteria recognition, 11 genes involved in flowering, and 37 genes used as control loci. We detected 1757 polymorphic sites yielding an average nucleotide diversity (pi) of 0.003 per site. Non-synonymous variation is under sizable purifying selection with 90% of amino-acid changing mutations being strongly selected against. Accessions were structured in two groups consistent with geographical origins. Each of these two groups harboured an excess of rare alleles, relative to expectations of a constant-sized population, suggesting recent population expansion. Using coalescent simulations and an approximate Bayesian computation framework we detected several instances of genes departing from selective neutrality within each group and showed that the polymorphism of two nodulation and four flowering genes has probably been shaped by recent positive selection. CONCLUSION: We quantify the intensity of purifying selection in the M. truncatula genome and show that putative footprints of natural selection can be detected at different time scales in both flowering and symbiotic pathways.
format Online
Article
Text
id pubmed-3199773
institution National Center for Biotechnology Information
language English
publishDate 2011
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-31997732011-10-24 Molecular adaptation in flowering and symbiotic recognition pathways: insights from patterns of polymorphism in the legume Medicago truncatula De Mita, Stéphane Chantret, Nathalie Loridon, Karine Ronfort, Joëlle Bataillon, Thomas BMC Evol Biol Research Article BACKGROUND: We studied patterns of molecular adaptation in the wild Mediterranean legume Medicago truncatula. We focused on two phenotypic traits that are not functionally linked: flowering time and perception of symbiotic microbes. Phenology is an important fitness component, especially for annual plants, and many instances of molecular adaptation have been reported for genes involved in flowering pathways. While perception of symbiotic microbes is also integral to adaptation in many plant species, very few reports of molecular adaptation exist for symbiotic genes. Here we used data from 57 individuals and 53 gene fragments to quantify the overall strength of both positive and purifying selection in M. truncatula and asked if footprints of positive selection can be detected at key genes of rhizobia recognition pathways. RESULTS: We examined nucleotide variation among 57 accessions from natural populations in 53 gene fragments: 5 genes involved in nitrogen-fixing bacteria recognition, 11 genes involved in flowering, and 37 genes used as control loci. We detected 1757 polymorphic sites yielding an average nucleotide diversity (pi) of 0.003 per site. Non-synonymous variation is under sizable purifying selection with 90% of amino-acid changing mutations being strongly selected against. Accessions were structured in two groups consistent with geographical origins. Each of these two groups harboured an excess of rare alleles, relative to expectations of a constant-sized population, suggesting recent population expansion. Using coalescent simulations and an approximate Bayesian computation framework we detected several instances of genes departing from selective neutrality within each group and showed that the polymorphism of two nodulation and four flowering genes has probably been shaped by recent positive selection. CONCLUSION: We quantify the intensity of purifying selection in the M. truncatula genome and show that putative footprints of natural selection can be detected at different time scales in both flowering and symbiotic pathways. BioMed Central 2011-08-01 /pmc/articles/PMC3199773/ /pubmed/21806823 http://dx.doi.org/10.1186/1471-2148-11-229 Text en Copyright ©2011 De Mita et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
De Mita, Stéphane
Chantret, Nathalie
Loridon, Karine
Ronfort, Joëlle
Bataillon, Thomas
Molecular adaptation in flowering and symbiotic recognition pathways: insights from patterns of polymorphism in the legume Medicago truncatula
title Molecular adaptation in flowering and symbiotic recognition pathways: insights from patterns of polymorphism in the legume Medicago truncatula
title_full Molecular adaptation in flowering and symbiotic recognition pathways: insights from patterns of polymorphism in the legume Medicago truncatula
title_fullStr Molecular adaptation in flowering and symbiotic recognition pathways: insights from patterns of polymorphism in the legume Medicago truncatula
title_full_unstemmed Molecular adaptation in flowering and symbiotic recognition pathways: insights from patterns of polymorphism in the legume Medicago truncatula
title_short Molecular adaptation in flowering and symbiotic recognition pathways: insights from patterns of polymorphism in the legume Medicago truncatula
title_sort molecular adaptation in flowering and symbiotic recognition pathways: insights from patterns of polymorphism in the legume medicago truncatula
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3199773/
https://www.ncbi.nlm.nih.gov/pubmed/21806823
http://dx.doi.org/10.1186/1471-2148-11-229
work_keys_str_mv AT demitastephane molecularadaptationinfloweringandsymbioticrecognitionpathwaysinsightsfrompatternsofpolymorphisminthelegumemedicagotruncatula
AT chantretnathalie molecularadaptationinfloweringandsymbioticrecognitionpathwaysinsightsfrompatternsofpolymorphisminthelegumemedicagotruncatula
AT loridonkarine molecularadaptationinfloweringandsymbioticrecognitionpathwaysinsightsfrompatternsofpolymorphisminthelegumemedicagotruncatula
AT ronfortjoelle molecularadaptationinfloweringandsymbioticrecognitionpathwaysinsightsfrompatternsofpolymorphisminthelegumemedicagotruncatula
AT bataillonthomas molecularadaptationinfloweringandsymbioticrecognitionpathwaysinsightsfrompatternsofpolymorphisminthelegumemedicagotruncatula