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Dominance Hierarchy Arising from the Evolution of a Complex Small RNA Regulatory Network Eléonore Durand, Raphaël Méheust, Marion Soucaze, Pauline M

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Dominance Hierarchy Arising from the Evolution of a Complex Small RNA Regulatory Network Eléonore Durand, Raphaël Méheust, Marion Soucaze, Pauline M RESEARCH ◥ between S alleles (6). Selection is expected to RESEARCH ARTICLE favor genetic elements (“dominance modifiers”), which establish dominance-recessivity interac- tion rather than codominance, because individ- PLANT GENETICS uals with a codominant genotype can produce pollen rejected by more potential mates than would occur in a dominant-recessive system (7, 8). Dominance hierarchy arising from On the basis of modeling (8), the large non- recombining region composing the S locus (9–11) is a strong candidate region for hosting such ge- the evolution of a complex small netic elements. Until recently, the dominance modifiers as- RNA regulatory network sumed in models (7, 8) remained hypothetical. A particular small RNA (sRNA) has been identified Eléonore Durand,1,2* Raphaël Méheust,1* Marion Soucaze,1 Pauline M. Goubet,1† (12) within the S locus of dominant alleles in Sophie Gallina,1 Céline Poux,1 Isabelle Fobis-Loisy,2 Eline Guillon,2 Thierry Gaude,2 Brassica (called Smi). This sRNA acts as a trans- Alexis Sarazin,3 Martin Figeac,4 Elisa Prat,5 William Marande,5 Hélène Bergès,5 modifier of the gene controlling pollen specificity Xavier Vekemans,1 Sylvain Billiard,1 Vincent Castric1‡ via de novo methylation of the promoter of re- cessive alleles, which leads to transcriptional si- The prevention of fertilization through self-pollination (or pollination by a close relative) lencing of recessive alleles by dominant alleles in the Brassicaceae plant family is determined by the genotype of the plant at the (13, 14). However, the mechanism in the more self-incompatibility locus (S locus). The many alleles at this locus exhibit a dominance complex dominance-recessivity networks in spe- Downloaded from hierarchy that determines which of the two allelic specificities of a heterozygous genotype cies that have many levels in the dominance is expressed at the phenotypic level. Here, we uncover the evolution of how at least 17 small hierarchy (15, 16) is unknown. Indeed, balancing RNA (sRNA)–producing loci and their multiple target sites collectively control the selection typically leads to the maintenance of dominance hierarchy among alleles within the gene controlling the pollen S-locus a large number of S alleles in self-incompatible phenotype in a self-incompatible Arabidopsis species. Selection has created a dynamic repertoire of sRNA-target interactions by jointly acting on sRNA genes and their target http://science.sciencemag.org/ sites, which has resulted in a complex system of regulation among alleles. 1Laboratoire Génétique et Evolution des Populations Végétales, CNRS UMR 8198, Université Lille 1, F-59655 Villeneuve d’Ascq cedex, France. 2Reproduction et porophytic self-incompatibility (SI) is a stigma S-locus receptor kinase (SRK) recognition Développement des Plantes, Institut Fédératif de Recherche genetic system that evolved in hermaph- proteins, whose ligand-receptor molecular dock- 128, Centre National de la Recherche Scientifique, Institut roditic plants to enforce outcrossing (by ing leads to self-pollen rejection (1–4). The pollen National de la Recherche Agronomique, Université Claude preventing self-fertilization) and involves recognition phenotype is controlled by the dip- Bernard Lyon I, Ecole Normale Supérieure de Lyon, F-69364 S Lyon, Cedex 07, France. 3Department of Biology, Swiss Federal a polymorphism in which multiple alleles loid paternal parent’s genotype, but even though Institute of Technology Zurich, CH-8093 Zurich, Switzerland. are maintained and display dominance-recessivity most plants are heterozygous at this locus (5), the 4UDSL Université Lille 2 Droit et Santé, and Plate-forme de relations. In the genus ,SIiscon- pollen recognition phenotype is typically deter- génomique fonctionnelle et structurale IFR-114, F-59000 Lille, Arabidopsis 5 trolled by a single genomic region “the S locus,” mined by one of the two alleles only, according to France. Centre National des Ressources Génomiques Végétales, INRA UPR 1258, Castanet-Tolosan, France. which contains two tightly linked genes that en- the alleles’ relative positions in a hierarchy or *These authors contributed equally to this work. †Deceased. on July 28, 2017 code the pollen S-locus cysteine-rich (SCR) and network of dominance-recessivity interactions ‡Corresponding author. E-mail: [email protected] Fig. 1. Models for the control of dominance-recessivity by sRNA-target one assumes no correlation or allows for some level of correlated evolution interactions in a multiallelic system. (A) Two models were tested to explain between: (B) dominance and the number of sRNAs precursors expressed; (C) how a simple mechanistic model (12) can be generalized to a multiallelic system. dominance and sRNA generalism, defined as the average number of targets used Under model 1, dominant S alleles carry a larger set of sRNA precursor genes, per sRNA precursor; (D) dominance and the number of target sites; and (E) whereas, under model 2, the same linear hierarchy is achieved by a larger set of dominance and target sites generalism, defined as the average number of distinct sRNA targets carried by recessive S alleles. Under model 1, sRNA targets of sRNA precursors using each target.The Bayes factor (BF) comparing both models recessive alleles are also more “generalist” than those of dominant alleles, is given on each panel as asterisks, as well as the distribution of correlation co- whereas, under model 2, it is the sRNA precursors of the dominant alleles efficients. *BF > 2: evidence for the dependent model, **BF > 5: strong evidence, that are more generalist. (B to E) Likelihood distributions of Bayesian models if and ***BF > 10: very strong evidence (38). 1200 5 DECEMBER 2014 • VOL 346 ISSUE 6214 sciencemag.org SCIENCE RESEARCH | RESEARCH ARTICLE species, and the >50 S alleles observed in out- target sequences (each targeted by a different segregating in natural populations of A. halleri crossing Arabidopsis species (17) are predicted dominant allele). (17), this is fewer than expected if dominant al- to form up to 1225 distinct heterozygous geno- leles targeted each individual recessive allele by a Results types. In Brassica, class II alleles similarly show a distinct sRNA gene (as predicted from model 1). linear dominance hierarchy that cannot be ex- Phenotypic characterization of the The17expressedmotifs(Fig.3B)canbeclas- plained by the action of Smi alone (12, 18). Under dominance network sified into eight distinct families on the basis of the mechanistic model involving sRNAs and To determine the mechanisms of S-allele domi- sequence divergence (fig. S3). Three of these their targets within the SCR gene, two hypotheses nance in the self-incompatible plant Arabidopsis families (mir1887, mir4239,andmir867)have could explain an allelic series of n distinct S alleles halleri, we first phenotypically characterized the clear homology to miRNA genes annotated in the in a linear dominance hierarchy. First, the most- dominance network between six S alleles, by cross- A. thaliana genome and are present in the miRBase dominant allele might produce n – 1distinctsRNAs, ing each of the 15 heterozygous genotypic com- database (21), although it is unclear whether they each specifically targeting a given more-recessive binations to both of its respective “tester” lines should be considered bona fide miRNA genes, S allele, whereas the next-most-dominant allele (i.e., lines that express a single S allele) (19). especially because it has been suggested that might produce sRNAs targeting all S alleles more Overall, combining these results with those from Smi might achieve silencing through a different— recessive than itself, and so on (with the bottom previous studies (16), we determined all possible largely uncharacterized—sRNA pathway (22). In recessive producing no sRNAs but having targets pairwise relations and observed dominance in A. thaliana, these miRNA genes were all in the for all more-dominant alleles). This model pre- 14 cases (93.3%) and codominance for a single region flanked by At4g21350 and At4g21380,which dicts that the top dominant allele produces the case (Fig. 2A). The resulting network is fully tran- contains the relics of the degenerate S locus (23). largest number of sRNAs and that the bottom sitive and takes the form of a simple linear hier- Although their function has not been assessed recessive allele carries the fewest but is targeted archy with two alleles at the top of the hierarchy so far, our results suggest that these motifs may by the largest number of sequences; we refer to (Ah13 and Ah20) (Fig. 2B). have served as modifiers of S-allele dominance, this as model 1 (Fig. 1A). Alternatively, the most consistent with the fact that the A. thaliana S locus Downloaded from – dominant allele might produce a single sRNA, Slocus specific sRNA hasonlyrecentlyundergonedegeneration(24). as in Brassica (12), and all subsequent more- precursor genes The five other families we identified have no ho- recessive S alleles might carry a specific target We then examined the highly differentiated mology to any sequence in miRBase. that interacts with the most-dominant allele in nonrecombining region within the S locus (9) a manner that results in nonexpression (Fig. 1A); (Fig. 3A) and deep-sequenced sRNA populations Identification and functional validation of sRNA-target interactions the next allele in the hierarchy (that is recessive of floral buds (19) from 11 individuals carrying http://science.sciencemag.org/ to the top dominant, but dominant to other clas- the six S alleles in various heterozygous combi- The model proposed in Brassica was from ob- ses) might produce a different sRNA, whose tar- nations. Applying a set of criteria for annotating servations of specific targeting of the promoter get sequence is present in all alleles recessive to plant micro-RNA (miRNA) genes (19, 20), we region of recessive SCR alleles involving sequen- itself, and so on. This model (model 2 in Fig. 1A) identified a total of 17 sRNA precursor sequences ces in recessive alleles showing similarity with predicts that only a single sRNA is produced in among the six tested alleles (Fig.
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