Phylogeny, phylogeography and genetic diversity of the Pisum genus

Petr Smykal, Gregory Kenicer, Andrew J. Flavell, Jukka Corander, Oleg Kosterin, Robert J. Redden, Rebecca Ford, Clarice J. Coyne, Nigel Maxted, Mike J. Ambrose, Noel T. H. Ellis

    Research output: Contribution to journalArticle

    62 Citations (Scopus)

    Abstract

    The tribe Fabeae (formerly Vicieae) contains some of humanity's most important grain legume crops, namely Lathyrus (grass pea/sweet pea/chickling vetches; about 160 species); Lens (lentils; 4 species); Pisum (peas; 3 species); Vicia (vetches; about 140 species); and the monotypic genus Vavilovia. Reconstructing the phylogenetic relationships within this group is essential for understanding the origin and diversification of these crops. Our study, based on molecular data, has positioned Pisum genetically between Vicia and Lathyrus and shows it to be closely allied to Vavilovia. A study of phylogeography, using a combination of plastid and nuclear markers, suggested that wild pea spread from its centre of origin, the Middle East, eastwards to the Caucasus, Iran and Afghanistan, and westwards to the Mediterranean. To allow for direct data comparison, we utilized model-based Bayesian Analysis of Population structure (BAPS) software on 4429 Pisum accessions from three large world germplasm collections that include both wild and domesticated pea analyzed by retrotransposon-based markers. An analysis of genetic diversity identified separate clusters containing wild material, distinguishing Pisum fulvum, P. elatius and P. abyssinicum, supporting the view of separate species or subspecies. Moreover, accessions of domesticated peas of Afghan, Ethiopian and Chinese origin were distinguished. In addition to revealing the genetic relationships, these results also provided insight into geographical and phylogenetic partitioning of genetic diversity. This study provides the framework for defining global Pisum germplasm diversity as well as suggesting a model for the domestication of the cultivated species. These findings, together with gene-based sequence analysis, show that although introgression from wild species has been common throughout pea domestication, much of the diversity still resides in wild material and could be used further in breeding. Moreover, although existing collections contain over 10,000 pea accessions, effort should be directed towards collecting more wild material in order to preserve the genetic diversity of the species.

    Original languageEnglish
    Pages (from-to)418
    Number of pages15
    JournalPlant Genetic Resources - Characterization and Utilization
    Volume9
    Issue number1
    DOIs
    Publication statusPublished - Apr 2011

    Keywords

    • Bayesian inference
    • core collection
    • domestication
    • genetic diversity
    • germplasm
    • microsatellite
    • pea
    • phylogeny
    • Pisum
    • retrotransposon
    • NUCLEAR-CYTOPLASMIC INCOMPATIBILITY
    • CONSTRUCTING CORE COLLECTIONS
    • INTERNAL TRANSCRIBED SPACER
    • MULTILOCUS GENOTYPE DATA
    • POPULATION-STRUCTURE
    • PEA PISUM
    • BAYESIAN IDENTIFICATION
    • MOLECULAR MARKERS
    • MICROSATELLITE
    • EVOLUTION

    Cite this

    Smykal, P., Kenicer, G., Flavell, A. J., Corander, J., Kosterin, O., Redden, R. J., ... Ellis, N. T. H. (2011). Phylogeny, phylogeography and genetic diversity of the Pisum genus. Plant Genetic Resources - Characterization and Utilization, 9(1), 418. https://doi.org/10.1017/S147926211000033X
    Smykal, Petr ; Kenicer, Gregory ; Flavell, Andrew J. ; Corander, Jukka ; Kosterin, Oleg ; Redden, Robert J. ; Ford, Rebecca ; Coyne, Clarice J. ; Maxted, Nigel ; Ambrose, Mike J. ; Ellis, Noel T. H. / Phylogeny, phylogeography and genetic diversity of the Pisum genus. In: Plant Genetic Resources - Characterization and Utilization. 2011 ; Vol. 9, No. 1. pp. 418.
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    author = "Petr Smykal and Gregory Kenicer and Flavell, {Andrew J.} and Jukka Corander and Oleg Kosterin and Redden, {Robert J.} and Rebecca Ford and Coyne, {Clarice J.} and Nigel Maxted and Ambrose, {Mike J.} and Ellis, {Noel T. H.}",
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    Smykal, P, Kenicer, G, Flavell, AJ, Corander, J, Kosterin, O, Redden, RJ, Ford, R, Coyne, CJ, Maxted, N, Ambrose, MJ & Ellis, NTH 2011, 'Phylogeny, phylogeography and genetic diversity of the Pisum genus', Plant Genetic Resources - Characterization and Utilization, vol. 9, no. 1, pp. 418. https://doi.org/10.1017/S147926211000033X

    Phylogeny, phylogeography and genetic diversity of the Pisum genus. / Smykal, Petr; Kenicer, Gregory; Flavell, Andrew J.; Corander, Jukka; Kosterin, Oleg; Redden, Robert J.; Ford, Rebecca; Coyne, Clarice J.; Maxted, Nigel; Ambrose, Mike J.; Ellis, Noel T. H.

    In: Plant Genetic Resources - Characterization and Utilization, Vol. 9, No. 1, 04.2011, p. 418.

    Research output: Contribution to journalArticle

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    AU - Kenicer, Gregory

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    AU - Kosterin, Oleg

    AU - Redden, Robert J.

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    AU - Coyne, Clarice J.

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    AU - Ellis, Noel T. H.

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    N2 - The tribe Fabeae (formerly Vicieae) contains some of humanity's most important grain legume crops, namely Lathyrus (grass pea/sweet pea/chickling vetches; about 160 species); Lens (lentils; 4 species); Pisum (peas; 3 species); Vicia (vetches; about 140 species); and the monotypic genus Vavilovia. Reconstructing the phylogenetic relationships within this group is essential for understanding the origin and diversification of these crops. Our study, based on molecular data, has positioned Pisum genetically between Vicia and Lathyrus and shows it to be closely allied to Vavilovia. A study of phylogeography, using a combination of plastid and nuclear markers, suggested that wild pea spread from its centre of origin, the Middle East, eastwards to the Caucasus, Iran and Afghanistan, and westwards to the Mediterranean. To allow for direct data comparison, we utilized model-based Bayesian Analysis of Population structure (BAPS) software on 4429 Pisum accessions from three large world germplasm collections that include both wild and domesticated pea analyzed by retrotransposon-based markers. An analysis of genetic diversity identified separate clusters containing wild material, distinguishing Pisum fulvum, P. elatius and P. abyssinicum, supporting the view of separate species or subspecies. Moreover, accessions of domesticated peas of Afghan, Ethiopian and Chinese origin were distinguished. In addition to revealing the genetic relationships, these results also provided insight into geographical and phylogenetic partitioning of genetic diversity. This study provides the framework for defining global Pisum germplasm diversity as well as suggesting a model for the domestication of the cultivated species. These findings, together with gene-based sequence analysis, show that although introgression from wild species has been common throughout pea domestication, much of the diversity still resides in wild material and could be used further in breeding. Moreover, although existing collections contain over 10,000 pea accessions, effort should be directed towards collecting more wild material in order to preserve the genetic diversity of the species.

    AB - The tribe Fabeae (formerly Vicieae) contains some of humanity's most important grain legume crops, namely Lathyrus (grass pea/sweet pea/chickling vetches; about 160 species); Lens (lentils; 4 species); Pisum (peas; 3 species); Vicia (vetches; about 140 species); and the monotypic genus Vavilovia. Reconstructing the phylogenetic relationships within this group is essential for understanding the origin and diversification of these crops. Our study, based on molecular data, has positioned Pisum genetically between Vicia and Lathyrus and shows it to be closely allied to Vavilovia. A study of phylogeography, using a combination of plastid and nuclear markers, suggested that wild pea spread from its centre of origin, the Middle East, eastwards to the Caucasus, Iran and Afghanistan, and westwards to the Mediterranean. To allow for direct data comparison, we utilized model-based Bayesian Analysis of Population structure (BAPS) software on 4429 Pisum accessions from three large world germplasm collections that include both wild and domesticated pea analyzed by retrotransposon-based markers. An analysis of genetic diversity identified separate clusters containing wild material, distinguishing Pisum fulvum, P. elatius and P. abyssinicum, supporting the view of separate species or subspecies. Moreover, accessions of domesticated peas of Afghan, Ethiopian and Chinese origin were distinguished. In addition to revealing the genetic relationships, these results also provided insight into geographical and phylogenetic partitioning of genetic diversity. This study provides the framework for defining global Pisum germplasm diversity as well as suggesting a model for the domestication of the cultivated species. These findings, together with gene-based sequence analysis, show that although introgression from wild species has been common throughout pea domestication, much of the diversity still resides in wild material and could be used further in breeding. Moreover, although existing collections contain over 10,000 pea accessions, effort should be directed towards collecting more wild material in order to preserve the genetic diversity of the species.

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    KW - retrotransposon

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    KW - INTERNAL TRANSCRIBED SPACER

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