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Nat Plants. 2016 Dec 22;3:16206. doi: 10.1038/nplants.2016.206.

A complex dominance hierarchy is controlled by polymorphism of small RNAs and their targets.

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Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan.
Division of Vegetable Breeding, Institute of Vegetable and Floriculture Science, NARO, Tsu, Mie 514-2392, Japan.
Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8577, Japan.
Graduate School of Agricultural Science, Kobe University, Kobe, Hyogo 657-8501, Japan.
Division of Natural Science, Osaka Kyoiku University, Kashiwara, Osaka 582-8582, Japan.
Department of Applied Biological Chemistry, The University of Tokyo, Tokyo 113-8657, Japan.


In diploid organisms, phenotypic traits are often biased by effects known as Mendelian dominant-recessive interactions between inherited alleles. Phenotypic expression of SP11 alleles, which encodes the male determinants of self-incompatibility in Brassica rapa, is governed by a complex dominance hierarchy1-3. Here, we show that a single polymorphic 24 nucleotide small RNA, named SP11 methylation inducer 2 (Smi2), controls the linear dominance hierarchy of the four SP11 alleles (S44 > S60 > S40 > S29). In all dominant-recessive interactions, small RNA variants derived from the linked region of dominant SP11 alleles exhibited high sequence similarity to the promoter regions of recessive SP11 alleles and acted in trans to epigenetically silence their expression. Together with our previous study4, we propose a new model: sequence similarity between polymorphic small RNAs and their target regulates mono-allelic gene expression, which explains the entire five-phased linear dominance hierarchy of the SP11 phenotypic expression in Brassica.


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