Go Suzuki

Abstract Weedy rice is a major problem in paddy fields around the world. It is well known that weedy rice appears to grow faster and mature earlier than cultivated rice. It is possible that differences in the root microbial genetics are correlated with this characteristic. This study incorporated 16S rRNA amplicon sequencing to study the microbial composition in the rhizosphere and endosphere of rice root. No significant difference was found between the microbiota associated with weedy and cultivated rice lines grown in the same field. It was found that the endosphere had less microbial diversity compared to the rhizosphere. The major groups of bacteria found in the endosphere are from the phylum Proteobacteria, Myxococcota, Chloroflexota, and Actinobacteria. In addition, by analyzing the microbiome of japonica rice grown in the field in a temperate climate, we found that despite differences in genotype and location, some bacterial taxa were found to be common and these members of the putative rice core microbiome can also be detected by in situ hybridization. The delineation of a core microbiome in the endosphere of rice suggests that these bacterial taxa might be important in the life cycle of a wide range of rice types.

Abstract Key message S²⁹ haplotype does not require the MLPK function for self-incompatibility in Brassica rapa. Abstract Self-incompatibility (SI) in Brassicaceae is regulated by the self-recognition mechanism, which is based on the S-haplotype-specific direct interaction of the pollen-derived ligand, SP11/SCR, and the stigma-side receptor, SRK. M locus protein kinase (MLPK) is known to be one of the positive effectors of the SI response. MLPK directly interacts with SRK, and is phosphorylated by SRK in Brassica rapa. In Brassicaceae, MLPK was demonstrated to be essential for SI in B. rapa and Brassica napus, whereas it is not essential for SI in Arabidopsis thaliana (with introduced SRK and SP11/SCR from related SI species). Little is known about what determines the need for MLPK in SI of Brassicaceae. In this study, we investigated the relationship between S-haplotype diversity and MLPK function by analyzing the SI phenotypes of different S haplotypes in a mlpk/mlpk mutant background. The results have clarified that in B. rapa, all the S haplotypes except the S²⁹ we tested need the MLPK function, but the S²⁹ haplotype does not require MLPK for the SI. Comparative analysis of MLPK-dependent and MLPK-independent S haplotype might provide new insight into the evolution of S-haplotype diversity and the molecular mechanism of SI in Brassicaceae.

<title>Abstract</title> Self-incompatibility (SI) is a breeding system that promotes cross-fertilization. In <italic>Brassica</italic>, pollen rejection is induced by a haplotype-specific interaction between pistil determinant SRK (<italic>S</italic> receptor kinase) and pollen determinant SP11 (<italic>S</italic>-locus Protein 11, also named SCR) from the <italic>S</italic>-locus. Although the structure of the <italic>B. rapa S</italic>₉-SRK ectodomain (eSRK) and <italic>S</italic>₉-SP11 complex has been determined, it remains unclear how SRK discriminates self- and nonself-SP11. Here, we uncover the detailed mechanism of self/nonself-discrimination in <italic>Brassica</italic> SI by determining the <italic>S</italic>₈-eSRK–<italic>S</italic>₈-SP11 crystal structure and performing molecular dynamics (MD) simulations. Comprehensive binding analysis of eSRK and SP11 structures reveals that the binding free energies are most stable for cognate eSRK–SP11 combinations. Residue-based contribution analysis suggests that the modes of eSRK–SP11 interactions differ between intra- and inter-subgroup (a group of phylogenetically neighboring haplotypes) combinations. Our data establish a model of self/nonself-discrimination in <italic>Brassica</italic> SI.