Genetic architecture and evolution of the s locus supergene in primula vulgaris

ABSTRACT Darwin's studies on heterostyly in _Primula_ described two floral morphs, pin and thrum, with reciprocal anther and stigma heights that promote insect-mediated

cross-pollination. This key innovation evolved independently in several angiosperm families. Subsequent studies on heterostyly in _Primula_ contributed to the foundation of modern genetic

theory and the neo-Darwinian synthesis. The established genetic model for _Primula_ heterostyly involves a diallelic _S_ locus comprising several genes, with rare recombination events that

result in self-fertile homostyle flowers with anthers and stigma at the same height. Here we reveal the _S_ locus supergene as a tightly linked cluster of thrum-specific genes that are

absent in pins. We show that thrums are hemizygous not heterozygous for the _S_ locus, which suggests that homostyles do not arise by recombination between _S_ locus haplotypes as previously

proposed. Duplication of a floral homeotic gene 51.7 million years (Myr) ago, followed by its neofunctionalization, created the current _S_ locus assemblage which led to floral heteromorphy

in _Primula._ Our findings provide new insights into the structure, function and evolution of this archetypal supergene. Access through your institution Buy or subscribe This is a preview

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Scholar  Download references ACKNOWLEDGEMENTS We thank M. Lappage, M. Hughes and P. Wells for horticultural support; colleagues at TGAC for Illumina sequencing; A. Thanki for TGAC Browser

support; O. Kent for _P. elatior_ _GLO_ and _GLO__T_ sequences; Norfolk Wildlife Trust, Suffolk Wildlife Trust and Norfolk County Council for permission to sample _P. veris_, _P. elatior_

and _P. vulgaris_ respectively; M. Gage, B. Davies and D. Bowles for comments on the manuscript; W. Wang for advice on _k_-means analysis; BBSRC for funding via grant BB/H019278/2, and prior

awards G11027 and P11021; The Gatsby Foundation for early stage funding; University of Leeds, Durham University and University of East Anglia for support to P.M.G. over several years of the

project. CvO was funded by the Earth & Life Systems Alliance (ELSA). P.M.G.'s laboratory is hosted at the John Innes Centre under the UEA-JIC Norwich Research Park collaboration.

AUTHOR INFORMATION Author notes * Sarah Dyer & Mario Caccamo Present address: †Present address: National Institute for Agricultural Botany, Huntingdon Road, Cambridge CB3 0LE, UK, *

Jinhong Li and Jonathan M. Cocker: These authors contributed equally to this work. AUTHORS AND AFFILIATIONS * School of Biological Sciences, University of East Anglia, Norwich Research Park,

Norwich, NR4 7TJ, UK Jinhong Li, Jonathan M. Cocker, Margaret A. Webster & Philip M. Gilmartin * John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK Jinhong Li, Jonathan M.

Cocker, Margaret A. Webster & Philip M. Gilmartin * The Earlham Institute, Norwich Research Park, Norwich, NR4 7UH, UK Jonathan Wright, Mark McMullan, Sarah Dyer, David Swarbreck & 

Mario Caccamo * School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK Cock van Oosterhout Authors * Jinhong Li View author publications You

can also search for this author inPubMed Google Scholar * Jonathan M. Cocker View author publications You can also search for this author inPubMed Google Scholar * Jonathan Wright View

author publications You can also search for this author inPubMed Google Scholar * Margaret A. Webster View author publications You can also search for this author inPubMed Google Scholar *

Mark McMullan View author publications You can also search for this author inPubMed Google Scholar * Sarah Dyer View author publications You can also search for this author inPubMed Google

Scholar * David Swarbreck View author publications You can also search for this author inPubMed Google Scholar * Mario Caccamo View author publications You can also search for this author

inPubMed Google Scholar * Cock van Oosterhout View author publications You can also search for this author inPubMed Google Scholar * Philip M. Gilmartin View author publications You can also

search for this author inPubMed Google Scholar CONTRIBUTIONS J.L. contributed to project design, performed all molecular analyses, generated the _S_ locus assembly, manually annotated the

_S_ locus gene structures and undertook data analysis. J.M.C. carried out bioinformatic analyses, including automated annotation of the _S_ locus region, undertook _in silico_ gene

expression and _k_-means clustering analyses, assembled genome sequences and library scaffolds, generated the molecular phylogeny, undertook recombination analysis of the _S_ locus flanking

regions and contributed to project design. J.W. assembled genome sequences and library scaffolds, contributed to genome annotation and generated the automated gene model predictions across

the _S_ locus, aligned sequencing reads to the _S_ locus assembly and contributed to project design. M.A.W. contributed the inbred long homostyle line, other genetic resources and classical

genetics, identified the short homostyle mutant and generated the three-point cross used to demonstrate linkage. M.M. and C.v.O. contributed to the molecular phylogeny construction,

evolutionary data analysis and recombination analysis. S.A., D.S. and M.C. contributed to the genome sequencing strategy, assembly and annotation that underpins this project. P.M.G.

conceived, designed and directed the project, contributed to data analysis, prepared the figures and drafted the manuscript, with revision input from C.v.O.; all authors contributed to

editing the manuscript. CORRESPONDING AUTHOR Correspondence to Philip M. Gilmartin. ETHICS DECLARATIONS COMPETING INTERESTS The authors declare no competing financial interests.

SUPPLEMENTARY INFORMATION SUPPLEMENTARY INFORMATION Supplementary Methods, Supplementary References, Supplementary Figures 1–4, Supplementary Tables 1–6, Supplementary Sequence Analyses 1–3.

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locus supergene in _Primula vulgaris_. _Nature Plants_ 2, 16188 (2016). https://doi.org/10.1038/nplants.2016.188 Download citation * Received: 08 September 2015 * Accepted: 31 October 2016 *

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