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Pathogen-derived 9-methyl sphingoid base is perceived by a lectin receptor kinase in Arabidopsis

Kato, H., Nemoto, K., Shimizu, M., Abe, A., Asai, S., Ishihama, N., Daimon, T., Ojika, M., Kawakita, K., Onai, K., Shirasu, K., Ishiura, M., Takemoto, D., Takano, Y. and Terauchi, R. (2021). Pathogen-derived 9-methyl sphingoid base is perceived by a lectin receptor kinase in Arabidopsis. BioRxiv, 2021.10.18.464766. https://doi.org/10.1101/2021.10.18.464766

Abstruct

In plants, many invading microbial pathogens are recognized by cell-surface pattern recognition receptors (PRRs), inducing defense responses; yet how PRRs perceive pathogen sphingolipids remains unclear. Here, we show that the ceramide Pi-Cer D from a plant pathogenic oomycete Phytophthora infestans triggers defense responses in Arabidopsis. Pi-Cer D is cleaved by an Arabidopsis apoplastic ceramidase, NCER2, and the resulting 9-methyl-branched sphingoid base is recognized by a plasma membrane lectin receptor-like kinase, RDA2. Importantly, 9-methyl-branched sphingoid base, which is unique to microbes, induces plant immune responses by interacting with RDA2. Loss of RDA2 or NCER2 function compromised Arabidopsis resistance against an oomycete pathogen, indicating that these are crucial for defense. We provide new insights that help elucidate the recognition mechanisms of pathogen-derived lipid molecules in plants.

Fig. 4. A model for the recognition of pathogen-derived ceramide in plants. Pi-Cer D is cleaved by plant apoplastic ceramidase NCER2 into 9-methyl sphingoid base. 9-methyl sphingoid base is recognized by a lectin-receptor kinase, RDA2/SphingR, which then induces defense responses that include WRKY33 gene expression and enhances immunity against pathogen infection.
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Population Genomics of Yams: Evolution and Domestication of Dioscorea Species

Sugihara, Y., Kudoh, A., Oli, M. T., Takagi, H., Natsume, S., Shimizu, M., Abe, A., Asiedu, R., Asfaw, A., Adebola, R. & Terauchi, R. (2021). Population Genomics of Yams: Evolution and Domestication of Dioscorea Species. In: Population Genomics. Springer, Cham. https://doi.org/10.1007/13836_2021_94

Abstruct

Yam is a collective name of tuber crops belonging to the genus Dioscorea. Yam is important not only as a staple food crop but also as an integral component of society and culture of the millions of people who depend on it. However, due to its regional importance, yam has long been regarded as an “orphan crop” lacking a due global attention. Although this perception is changing with recent advances in genomics technologies, domestication processes of most yam species are still ambiguous. This is mainly due to the complicated evolutionary history of Dioscorea species caused by frequent hybridization and polyploidization, which is possibly caused by dioecy that imposed obligate outcrossing to the species of Dioscorea. In this chapter, we provide an overview of the evolution of Dioscorea and address the domestication of yam from population genomics perspectives by focusing on the processes of hybridization and polyploidization. A review is given to the recent population genomics studies on the hybrid origin of D. rotundata in West and Central Africa, the global dispersion of D. alata through human migrations, and the whole-genome duplication of the South America species of D. trifida. In the end, we give a summary of current understanding of sex-determination system in Dioscorea.

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RIL-StEp: epistasis analysis of recombinant inbred lines (RILs) reveals candidate interacting genes that control rice seed hull color and leaf chlorophyll content

Toshiyuki Sakai, Abe, A., Shimizu, M., Terauchi, R. (2021). RIL-StEp: epistasis analysis of rice recombinant inbred lines (RILs) reveals candidate interacting genes that control seed hull color and leaf chlorophyll content. G3 Genes|Genomes|Genetics, https://doi.org/10.1093/g3journal/jkab130

Abstract

Characterizing epistatic gene interactions is fundamental for understanding the genetic architecture of complex traits. However, due to the large number of potential gene combinations, detecting epistatic gene interactions is computationally demanding. A simple, easy-to-perform method for sensitive detection of epistasis is required. Due to their homozygous nature, use of recombinant inbred lines excludes the dominance effect of alleles and interactions involving heterozygous genotypes, thereby allowing detection of epistasis in a simple and interpretable model. Here, we present an approach called RIL-StEp (recombinant inbred lines stepwise epistasis detection) to detect epistasis using single-nucleotide polymorphisms in the genome. We applied the method to reveal epistasis affecting rice (Oryza sativa) seed hull color and leaf chlorophyll content and successfully identified pairs of genomic regions that presumably control these phenotypes. This method has the potential to improve our understanding of the genetic architecture of various traits of crops and other organisms.