Genetical and comparative genomics of Brassica under altered Ca supply identifies Arabidopsis Ca-transporter orthologs

Neil S. Graham, John P. Hammond, Artem Lysenko, Sean Mayes, Seosamh O Lochlainn, Bego Blasco, Helen C. Bowen, Chris J. Rawlings, Juan J. Rios, Susan Welham, Pierre W. C. Carion, Lionel X. Dupuy, Graham J. King, Philip J. White, Martin R. Broadley

    Research output: Contribution to journalArticle

    14 Citations (Scopus)

    Abstract

    Although Ca transport in plants is highly complex, the overexpression of vacuolar Ca2+ transporters in crops is a promising new technology to improve dietary Ca supplies through biofortification. Here, we sought to identify novel targets for increasing plant Ca accumulation using genetical and comparative genomics. Expression quantitative trait locus (eQTL) mapping to 1895 cis- and 8015 trans-loci were identified in shoots of an inbred mapping population of Brassica rapa (IMB211 × R500); 23 cis- and 948 trans-eQTLs responded specifically to altered Ca supply. eQTLs were screened for functional significance using a large database of shoot Ca concentration phenotypes of Arabidopsis thaliana. From 31 Arabidopsis gene identifiers tagged to robust shoot Ca concentration phenotypes, 21 mapped to 27 B. rapa eQTLs, including orthologs of the Ca2+ transporters At-CAX1 and At-ACA8. Two of three independent missense mutants of BraA.cax1a, isolated previously by targeting induced local lesions in genomes, have allele-specific shoot Ca concentration phenotypes compared with their segregating wild types. BraA.CAX1a is a promising target for altering the Ca composition of Brassica, consistent with prior knowledge from Arabidopsis. We conclude that multiple-environment eQTL analysis of complex crop genomes combined with comparative genomics is a powerful technique for novel gene identification/prioritization.

    Original languageEnglish
    Pages (from-to)2818-2830
    Number of pages13
    JournalPlant Cell
    Volume26
    Issue number7
    Early online date31 Jul 2014
    DOIs
    Publication statusPublished - 2014

    Fingerprint

    Brassica
    Genomics
    Arabidopsis
    transporters
    Brassica rapa
    Quantitative Trait Loci
    Phenotype
    genomics
    shoots
    phenotype
    Genome
    quantitative trait loci
    biofortification
    calcium
    lesions (plant)
    Genes
    genome
    prioritization
    crops
    Alleles

    Cite this

    Graham, N. S., Hammond, J. P., Lysenko, A., Mayes, S., O Lochlainn, S., Blasco, B., ... Broadley, M. R. (2014). Genetical and comparative genomics of Brassica under altered Ca supply identifies Arabidopsis Ca-transporter orthologs. Plant Cell, 26(7), 2818-2830. https://doi.org/10.1105/tpc.114.128603
    Graham, Neil S. ; Hammond, John P. ; Lysenko, Artem ; Mayes, Sean ; O Lochlainn, Seosamh ; Blasco, Bego ; Bowen, Helen C. ; Rawlings, Chris J. ; Rios, Juan J. ; Welham, Susan ; Carion, Pierre W. C. ; Dupuy, Lionel X. ; King, Graham J. ; White, Philip J. ; Broadley, Martin R. / Genetical and comparative genomics of Brassica under altered Ca supply identifies Arabidopsis Ca-transporter orthologs. In: Plant Cell. 2014 ; Vol. 26, No. 7. pp. 2818-2830.
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    abstract = "Although Ca transport in plants is highly complex, the overexpression of vacuolar Ca2+ transporters in crops is a promising new technology to improve dietary Ca supplies through biofortification. Here, we sought to identify novel targets for increasing plant Ca accumulation using genetical and comparative genomics. Expression quantitative trait locus (eQTL) mapping to 1895 cis- and 8015 trans-loci were identified in shoots of an inbred mapping population of Brassica rapa (IMB211 × R500); 23 cis- and 948 trans-eQTLs responded specifically to altered Ca supply. eQTLs were screened for functional significance using a large database of shoot Ca concentration phenotypes of Arabidopsis thaliana. From 31 Arabidopsis gene identifiers tagged to robust shoot Ca concentration phenotypes, 21 mapped to 27 B. rapa eQTLs, including orthologs of the Ca2+ transporters At-CAX1 and At-ACA8. Two of three independent missense mutants of BraA.cax1a, isolated previously by targeting induced local lesions in genomes, have allele-specific shoot Ca concentration phenotypes compared with their segregating wild types. BraA.CAX1a is a promising target for altering the Ca composition of Brassica, consistent with prior knowledge from Arabidopsis. We conclude that multiple-environment eQTL analysis of complex crop genomes combined with comparative genomics is a powerful technique for novel gene identification/prioritization.",
    author = "Graham, {Neil S.} and Hammond, {John P.} and Artem Lysenko and Sean Mayes and {O Lochlainn}, Seosamh and Bego Blasco and Bowen, {Helen C.} and Rawlings, {Chris J.} and Rios, {Juan J.} and Susan Welham and Carion, {Pierre W. C.} and Dupuy, {Lionel X.} and King, {Graham J.} and White, {Philip J.} and Broadley, {Martin R.}",
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    Graham, NS, Hammond, JP, Lysenko, A, Mayes, S, O Lochlainn, S, Blasco, B, Bowen, HC, Rawlings, CJ, Rios, JJ, Welham, S, Carion, PWC, Dupuy, LX, King, GJ, White, PJ & Broadley, MR 2014, 'Genetical and comparative genomics of Brassica under altered Ca supply identifies Arabidopsis Ca-transporter orthologs', Plant Cell, vol. 26, no. 7, pp. 2818-2830. https://doi.org/10.1105/tpc.114.128603

    Genetical and comparative genomics of Brassica under altered Ca supply identifies Arabidopsis Ca-transporter orthologs. / Graham, Neil S.; Hammond, John P.; Lysenko, Artem; Mayes, Sean; O Lochlainn, Seosamh; Blasco, Bego; Bowen, Helen C.; Rawlings, Chris J.; Rios, Juan J.; Welham, Susan; Carion, Pierre W. C.; Dupuy, Lionel X.; King, Graham J.; White, Philip J.; Broadley, Martin R.

    In: Plant Cell, Vol. 26, No. 7, 2014, p. 2818-2830.

    Research output: Contribution to journalArticle

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    AU - Graham, Neil S.

    AU - Hammond, John P.

    AU - Lysenko, Artem

    AU - Mayes, Sean

    AU - O Lochlainn, Seosamh

    AU - Blasco, Bego

    AU - Bowen, Helen C.

    AU - Rawlings, Chris J.

    AU - Rios, Juan J.

    AU - Welham, Susan

    AU - Carion, Pierre W. C.

    AU - Dupuy, Lionel X.

    AU - King, Graham J.

    AU - White, Philip J.

    AU - Broadley, Martin R.

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    PY - 2014

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