Biology subjects

Iwai, J.

Publications and source records attributed to Iwai, J..

4 recordsLinked to original sources

bioRxiv2025

Positional identification of a candidate gene for MALE STERILITY 2 (MS2) by linkage mapping and transcriptomic data in Cryptomeria japonica D. Don

BackgroundJapanese cedar (Cryptomeria japonica D. Don) is a major plantation species in Japan, but its abundant pollen production is a primary cause of seasonal allergic rhinitis (pollinosis). To mitigate this public health issue, the use of male-sterile cultivars has been promoted. Five types of recessive male-sterile mutations (ms1-ms5) have been identified, and the causal genes and mutations for MS1 and MS4 have been elucidated. However, the gene responsible for MS2-type male sterility remains unknown. ResultsWe aimed to identify the candidate gene responsible for MS2-type male sterility using a map-based cloning strategy. High-resolution linkage mapping localized the MS2 locus to a 1.56 cM interval on linkage group 5, corresponding to an 8.64 Mb region of the reference genome. Ninety-one genes in this region were subjected to functional annotation, gene expression analysis, and mutation screening. Among these, a single gene, SUGI_0493010, encoding a GDSL-type esterase/lipase protein (GELP), fulfilled all three criteria: it showed homology to pollen development genes in Arabidopsis thaliana, was specifically expressed in male strobili, and carried a deleterious amino acid substitution (S40F) within the predicted catalytic domain in ms2 mutant. The same mutation was also detected in a heterozygous individual (Ms2/ms2) from a separate breeding population, whose genotype was confirmed through progeny testing. Structural annotation revealed that the affected serine residue lies within the conserved GDSL motif, suggesting a functional disruption of enzymatic activity. ConclusionsOur results strongly suggest that SUGI_0493010 (GELP) is the causal gene for MS2-type male sterility in C. japonica. This finding enhances our understanding of male sterility mechanisms in conifers and provides a valuable genetic resource for breeding pollen-free trees. The study also demonstrates the effectiveness of combining genetic mapping with transcriptomic and mutational data in forest tree genomics.

genomics↗

bioRxiv2022

Single-nucleotide substitution determines pollen production in Japanese cedar

Pollinosis, also known as pollen allergy or hay fever, is a global problem caused by pollen produced by various plant species1-6. The wind-pollinated Japanese cedar (Cryptomeria japonica) is the largest contributor to severe pollinosis in Japan, where increasing proportions of people have been affected in recent decades7. The MS4 (MALE STERILITY 4) locus of Japanese cedar controls pollen production, and its homozygous mutants (ms4/ms4) show abnormal pollen development after the tetrad stage and produce no mature pollen. In this study, we narrowed down the MS4 locus by fine mapping in Japanese cedar and found TKPR1 (TETRAKETIDE -PYRONE REDUCTASE) gene in this region. Transformation experiments using Arabidopsis thaliana showed that single-nucleotide substitution of CjTKPR1 determines pollen production. Broad conservation of TKPR1 beyond plant division could lead to the creation of pollen-free plant not only for Japanese cedar but also for broader plant species.

plant biology↗

bioRxiv2020

Marker-assisted selection of trees with MALE STERALITY 1 in Cryptomeria japonica D. Don

Practical use of marker-assisted selection (MAS) is limited in conifers because of the difficulty with developing markers due to a rapid decrease in linkage disequilibrium, the limited genomic information available, and the diverse genetic backgrounds among breeding material collections. First, in this study, two families were produced by artificial crossing between two male-sterile trees, Shindai11 and Shindai12, and a plus tree, Suzu-2 (Ms1/ms1) (S11-S and S12-S families, respectively). The segregation ratio between male-sterile and male-fertile trees did not deviate significantly from the expected 1:1 ratio in either family. These results clearly suggested that the male-sterile gene of Shindai11 and Shindai12 is MALE STERALITY 1 (MS1). Because some markers reported previously have not been linkage mapped, we constructed a partial linkage map of the region encompassing MS1 using the S11-S and S12-S families. For the S11-S and S12-S families, 19 and 18 markers were mapped onto the partial linkage maps of MS1 region, respectively. There was collinearity (conserved gene order) between the two partial linkage maps. Two markers (CJt020762_ms1-1 and reCj19250_2335) were mapped to the same position as the MS1 locus on both maps. Of these markers, we used CJt020762 for MAS in this study. According to the MAS results for 650 trees from six prefectures of Japan (603 trees from breeding materials and 47 trees from the Ishinomaki natural population), five trees in Niigata Prefecture and one tree in Yamagata Prefecture had heterozygous ms1-1, and three trees in Miyagi Prefecture had heterozygous ms1-2. The results obtained in this study suggested that there may be geographical hotspots for the ms1-1 and ms1-2 alleles. Because MAS can be used effectively to reduce the labor and time required for selection of trees with a male-sterile gene, the number of breeding materials should increase in the future.

genetics↗

bioRxiv2020

Inspecting abundantly expressed genes in male strobili in sugi (Cryptomeria japonica D. Don) via a highly accurate cDNA assembly

Sugi (Cryptomeria japonica D. Don) is an important conifer used for afforestation in Japan. The field of functional genomics is rapidly developing. The genomics of this gymnosperm species is currently being studied. Although its genomic size is 11 Gbps, it is still too large to assemble well within a short period of time. Transcriptomics is the one another approach to address this. Moreover, it is a necessary step in obtaining the complete genomic data. Here we designed a three stages assembling workflow using the de novo transcriptome assembly tools, Oases and Trinity. The three stages in transcriptomics are independent assembly, automatic and semi-automatic integration, and refinement by filtering out potential contamination. We found a set of 49,795 cDNA and an equal number of translated proteins (CJ3006NRE). According to the benchmark of BUSCO, 87.01 % were complete genes, including very high "Complete and single-copy" genes-78.47%. Compared to other full-length cDNA resources, the extent of the coverage in CJ3006NRE suggests that it may be used as the standard for further studies. When two tissue-specific libraries were compared, principal component analysis (PCA) showed that there were significant differences between male strobili and leaf and bark sets. The highest three upregulated transcription factors stood out as orthologs to angiosperms. The identified signature-like domain of the transcription factors demonstrated the accuracy of the assembly. Based on the evaluation of different resources, we demonstrate that our transcriptome assembly output is valuable and useful for further studies in functional genomics and evolutionary biology.

bioinformatics↗