Whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula

Antoine Branca; Timothy D Paape; Peng Zhou; Roman Briskine; Andrew D Farmer; Joann Mudge; Arvind K Bharti; Jimmy E Woodward; Gregory D May; Laurent Gentzbittel; Cécile Ben; Roxanne Denny; Michael J Sadowsky; Joëlle Ronfort; Thomas Bataillon; Nevin D Young; Peter Tiffin

doi:10.1073/pnas.1104032108

Whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula

Antoine Branca, Timothy D Paape, Peng Zhou, Roman Briskine, Andrew D Farmer, Joann Mudge, Arvind K Bharti, Jimmy E Woodward, Gregory D May, Laurent Gentzbittel, Cécile Ben, Roxanne Denny, Michael J Sadowsky, Joëlle Ronfort, Thomas Bataillon, Nevin D Young, Peter Tiffin

Department of Molecular Biology and Genetics - Bioinformatics Research Centre (BiRC)

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

Abstract

Medicago truncatula is a model for investigating legume genetics, including the genetics and evolution of legume-rhizobia symbiosis. We used whole-genome sequence data to identify and characterize sequence polymorphisms and linkage disequilibrium (LD) in a diverse collection of 26 M. truncatula accessions. Our analyses reveal that M. truncatula harbors both higher diversity and less LD than soybean (Glycine max) and exhibits patterns of LD and recombination similar to Arabidopsis thaliana. The population-scaled recombination rate is approximately one-third of the mutation rate, consistent with expectations for a species with a high selfing rate. Linkage disequilibrium, however, is not extensive, and therefore, the low recombination rate is likely not a major constraint to adaptation. Nucleotide diversity in 100-kb windows was negatively correlated with gene density, which is expected if diversity is shaped by selection acting against slightly deleterious mutations. Among putative coding regions, members of four gene families harbor significantly higher diversity than the genome-wide average. Three of these families are involved in resistance against pathogens; one of these families, the nodule-specific, cysteine-rich gene family, is specific to the galegoid legumes and is involved in control of rhizobial differentiation. The more than 3 million SNPs that we detected, approximately one-half of which are present in more than one accession, are a valuable resource for genome-wide association mapping of genes responsible for phenotypic diversity in legumes, especially traits associated with symbiosis and nodulation.

Original language	English
Journal	Proceedings of the National Academy of Sciences
Volume	108
Issue	42
Pages (from-to)	864-870
Number of pages	7
ISSN	0027-8424
DOIs	https://doi.org/10.1073/pnas.1104032108
Publication status	Published - 26 Sept 2011

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Branca, A., Paape, T. D., Zhou, P., Briskine, R., Farmer, A. D., Mudge, J., Bharti, A. K., Woodward, J. E., May, G. D., Gentzbittel, L., Ben, C., Denny, R., Sadowsky, M. J., Ronfort, J., Bataillon, T., Young, N. D., & Tiffin, P. (2011). Whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula. Proceedings of the National Academy of Sciences, 108(42), 864-870. https://doi.org/10.1073/pnas.1104032108

@article{d6afe83a68764be992454e7f4ff72785,

title = "Whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula",

abstract = "Medicago truncatula is a model for investigating legume genetics, including the genetics and evolution of legume-rhizobia symbiosis. We used whole-genome sequence data to identify and characterize sequence polymorphisms and linkage disequilibrium (LD) in a diverse collection of 26 M. truncatula accessions. Our analyses reveal that M. truncatula harbors both higher diversity and less LD than soybean (Glycine max) and exhibits patterns of LD and recombination similar to Arabidopsis thaliana. The population-scaled recombination rate is approximately one-third of the mutation rate, consistent with expectations for a species with a high selfing rate. Linkage disequilibrium, however, is not extensive, and therefore, the low recombination rate is likely not a major constraint to adaptation. Nucleotide diversity in 100-kb windows was negatively correlated with gene density, which is expected if diversity is shaped by selection acting against slightly deleterious mutations. Among putative coding regions, members of four gene families harbor significantly higher diversity than the genome-wide average. Three of these families are involved in resistance against pathogens; one of these families, the nodule-specific, cysteine-rich gene family, is specific to the galegoid legumes and is involved in control of rhizobial differentiation. The more than 3 million SNPs that we detected, approximately one-half of which are present in more than one accession, are a valuable resource for genome-wide association mapping of genes responsible for phenotypic diversity in legumes, especially traits associated with symbiosis and nodulation.",

author = "Antoine Branca and Paape, {Timothy D} and Peng Zhou and Roman Briskine and Farmer, {Andrew D} and Joann Mudge and Bharti, {Arvind K} and Woodward, {Jimmy E} and May, {Gregory D} and Laurent Gentzbittel and C{\'e}cile Ben and Roxanne Denny and Sadowsky, {Michael J} and Jo{\"e}lle Ronfort and Thomas Bataillon and Young, {Nevin D} and Peter Tiffin",

year = "2011",

month = sep,

day = "26",

doi = "10.1073/pnas.1104032108",

language = "English",

volume = "108",

pages = "864--870",

journal = "Proceedings of the National Academy of Sciences",

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publisher = "The National Academy of Sciences of the United States of America",

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Branca, A, Paape, TD, Zhou, P, Briskine, R, Farmer, AD, Mudge, J, Bharti, AK, Woodward, JE, May, GD, Gentzbittel, L, Ben, C, Denny, R, Sadowsky, MJ, Ronfort, J, Bataillon, T, Young, ND & Tiffin, P 2011, 'Whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula', Proceedings of the National Academy of Sciences, vol. 108, no. 42, pp. 864-870. https://doi.org/10.1073/pnas.1104032108

Whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula. / Branca, Antoine; Paape, Timothy D; Zhou, Peng et al.
In: Proceedings of the National Academy of Sciences, Vol. 108, No. 42, 26.09.2011, p. 864-870.

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

TY - JOUR

T1 - Whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula

AU - Branca, Antoine

AU - Paape, Timothy D

AU - Zhou, Peng

AU - Briskine, Roman

AU - Farmer, Andrew D

AU - Mudge, Joann

AU - Bharti, Arvind K

AU - Woodward, Jimmy E

AU - May, Gregory D

AU - Gentzbittel, Laurent

AU - Ben, Cécile

AU - Denny, Roxanne

AU - Sadowsky, Michael J

AU - Ronfort, Joëlle

AU - Bataillon, Thomas

AU - Young, Nevin D

AU - Tiffin, Peter

PY - 2011/9/26

Y1 - 2011/9/26

N2 - Medicago truncatula is a model for investigating legume genetics, including the genetics and evolution of legume-rhizobia symbiosis. We used whole-genome sequence data to identify and characterize sequence polymorphisms and linkage disequilibrium (LD) in a diverse collection of 26 M. truncatula accessions. Our analyses reveal that M. truncatula harbors both higher diversity and less LD than soybean (Glycine max) and exhibits patterns of LD and recombination similar to Arabidopsis thaliana. The population-scaled recombination rate is approximately one-third of the mutation rate, consistent with expectations for a species with a high selfing rate. Linkage disequilibrium, however, is not extensive, and therefore, the low recombination rate is likely not a major constraint to adaptation. Nucleotide diversity in 100-kb windows was negatively correlated with gene density, which is expected if diversity is shaped by selection acting against slightly deleterious mutations. Among putative coding regions, members of four gene families harbor significantly higher diversity than the genome-wide average. Three of these families are involved in resistance against pathogens; one of these families, the nodule-specific, cysteine-rich gene family, is specific to the galegoid legumes and is involved in control of rhizobial differentiation. The more than 3 million SNPs that we detected, approximately one-half of which are present in more than one accession, are a valuable resource for genome-wide association mapping of genes responsible for phenotypic diversity in legumes, especially traits associated with symbiosis and nodulation.

AB - Medicago truncatula is a model for investigating legume genetics, including the genetics and evolution of legume-rhizobia symbiosis. We used whole-genome sequence data to identify and characterize sequence polymorphisms and linkage disequilibrium (LD) in a diverse collection of 26 M. truncatula accessions. Our analyses reveal that M. truncatula harbors both higher diversity and less LD than soybean (Glycine max) and exhibits patterns of LD and recombination similar to Arabidopsis thaliana. The population-scaled recombination rate is approximately one-third of the mutation rate, consistent with expectations for a species with a high selfing rate. Linkage disequilibrium, however, is not extensive, and therefore, the low recombination rate is likely not a major constraint to adaptation. Nucleotide diversity in 100-kb windows was negatively correlated with gene density, which is expected if diversity is shaped by selection acting against slightly deleterious mutations. Among putative coding regions, members of four gene families harbor significantly higher diversity than the genome-wide average. Three of these families are involved in resistance against pathogens; one of these families, the nodule-specific, cysteine-rich gene family, is specific to the galegoid legumes and is involved in control of rhizobial differentiation. The more than 3 million SNPs that we detected, approximately one-half of which are present in more than one accession, are a valuable resource for genome-wide association mapping of genes responsible for phenotypic diversity in legumes, especially traits associated with symbiosis and nodulation.

U2 - 10.1073/pnas.1104032108

DO - 10.1073/pnas.1104032108

M3 - Journal article

C2 - 21949378

SN - 0027-8424

VL - 108

SP - 864

EP - 870

JO - Proceedings of the National Academy of Sciences

JF - Proceedings of the National Academy of Sciences

IS - 42

ER -

Whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula

Abstract

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