title: Genetical and comparative genomics of Brassica under altered Ca supply identifies Arabidopsis Ca-transporter orthologs.
abstract: Although Ca transport in plants is highly complex, the overexpression of vacuolar Ca(2+) 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 Ca(2+) 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.
authors.affiliation: Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, United Kingdom.
authors.forename: Neil S
authors.initials: NS
authors.lastname: Graham
authors.affiliation: School of Agriculture, Policy, and Development, University of Reading, Earley Gate, Whiteknights, Reading RG6 6AR, United Kingdom.
authors.forename: John P
authors.initials: JP
authors.lastname: Hammond
authors.affiliation: Computational and Systems Biology Department, Rothamsted Research, West Common, Harpenden AL5 2JQ, United Kingdom.
authors.forename: Artem
authors.initials: A
authors.lastname: Lysenko
authors.affiliation: Crops for the Future Research Centre, Jalan Broga, 43500 Semenyih, Selangor Darul Ehsan, Malaysia.
authors.forename: Sean
authors.initials: S
authors.lastname: Mayes
authors.affiliation: Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, United Kingdom.
authors.forename: Seosamh
authors.initials: S
authors.lastname: O Lochlainn
authors.affiliation: Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, United Kingdom.
authors.forename: Bego
authors.initials: B
authors.lastname: Blasco
authors.affiliation: Warwick HRI, University of Warwick, Wellesbourne CV35 9EF, United Kingdom.
authors.forename: Helen C
authors.initials: HC
authors.lastname: Bowen
authors.affiliation: Computational and Systems Biology Department, Rothamsted Research, West Common, Harpenden AL5 2JQ, United Kingdom.
authors.forename: Chris J
authors.initials: CJ
authors.lastname: Rawlings
authors.affiliation: Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, United Kingdom.
authors.forename: Juan J
authors.initials: JJ
authors.lastname: Rios
authors.affiliation: Computational and Systems Biology Department, Rothamsted Research, West Common, Harpenden AL5 2JQ, United Kingdom.
authors.forename: Susan
authors.initials: S
authors.lastname: Welham
authors.affiliation: Computational and Systems Biology Department, Rothamsted Research, West Common, Harpenden AL5 2JQ, United Kingdom.
authors.forename: Pierre W C
authors.initials: PW
authors.lastname: Carion
authors.affiliation: James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom.
authors.forename: Lionel X
authors.initials: LX
authors.lastname: Dupuy
authors.affiliation: Southern Cross Plant Science, Southern Cross University, Lismore, New South Wales 2480, Australia.
authors.forename: Graham J
authors.initials: GJ
authors.lastname: King
authors.affiliation: James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom College of Science, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia.
authors.forename: Philip J
authors.initials: PJ
authors.lastname: White
authors.affiliation: Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, United Kingdom martin.broadley@nottingham.ac.uk.
authors.forename: Martin R
authors.initials: MR
authors.lastname: Broadley
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D001937:Brassica / Q000235:genetics* / Q000378:metabolism; D002118:Calcium / Q000378:metabolism*; D027682:Cation Transport Proteins / Q000235:genetics* / Q000378:metabolism; D002874:Chromosome Mapping; D018556:Crops, Agricultural; D018506:Gene Expression Regulation, Plant; D059647:Gene-Environment Interaction; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D020125:Mutation, Missense; D010641:Phenotype; D018515:Plant Leaves / Q000235:genetics / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics; D018520:Plant Shoots / Q000235:genetics / Q000378:metabolism; D030821:Plants, Genetically Modified; D040641:Quantitative Trait Loci / Q000235:genetics; D014617:Vacuoles / Q000378:metabolism
chemical_list: D027682:Cation Transport Proteins; D010940:Plant Proteins; D002118:Calcium
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