BULLETIN 1
International Research Teams Decode Oats' Pangenome and Origin

In a breakthrough for agricultural science, an international team of researchers, led by the IPK Leibniz Institute in Germany, has successfully decoded the pangenome and pantranscriptome of the common oat (Avena sativa). Oats, prized globally for their health benefits, including high fiber and gluten-free properties, have a genome that is notoriously large and complex. This work provides a complete genetic map essential for accelerating the development of new, improved oat varieties.
The researchers established a detailed pangenome, sequenced and analysed the genomes of 33 different cultivated and wild oat lines, including genes present only in certain varieties. To create the transcriptome, they examined the gene expression patterns in six tissues and developmental stages of 23 of these oat lines. According to Dr. Martin Mascher, coordinator of the PanOat consortium, this genetic blueprint will help breeders better understand which genes are key for improving traits such as yield, adaptation, and health content in a climate-challenged world.
The deep genomic analysis also yielded surprising insights, such as finding a significant number of gene losses in one of the oat's three subgenomes, with the plant compensating by using other gene copies. Importantly, the researchers identified that structural variations within the genome affect the genes responsible for controlling flowering time, a critical trait for adapting crops to local growing conditions. The team's findings, which also included a second related study on the evolutionary origin of the oat, were published in Nature and Nature Communications.
For more details, read the press release from the IPK Leibniz Institute.
See https://www.isaaa.org/kc/cropbiotechupdate/article/default.asp?ID=21583

 

BULLETIN 2
NARO Scientists Report Successful Use of Eco CRISPR-Cas3 in Rice

Researchers from Japan's National Agriculture and Food Research Organization (NARO) reported a powerful tool for editing rice genes that can create large deletions in target sites. The findings are published in Plant and Cell Physiology.
The gene editing tool Eco CRISPR-Cas3, which comes from Escherichia coli, has been proven to be effective in deleting large portions of DNA in mammals. However, using this tool in plants has been a challenge because it requires all seven components of the system (six proteins and one guide RNA) to be active inside the cell simultaneously.
Using Agrobacterium-mediated transformation, the researchers were able to enhance Eco CRISPR-Cas3 and make it work in rice genes. With this tool, a significant number of rice calli exhibited the intended DNA deletions; up to 71% of the cells had the edit. This high success rate indicated a potential to develop edited plants. Thus, the edited cells were used to generate rice plants that showed small and large DNA deletions, which were passed down to the following generation. Base editing was also achieved using the same tool.
Based on the findings, Eco CRISPR-Cas3 is a promising genetic improvement tool in rice, including switching off genes, removing large DNA sections, and making precise single-letter edits.
Read the research article in Plant and Cell Physiology.
See https://www.isaaa.org/kc/cropbiotechupdate/article/default.asp?ID=21588

 

SCIENTIFIC NEWS

Versatile Genome Editing Using Type I-E CRISPR-Cas3 in Rice

Hiroaki Saika, Naho Hara, Shuhei Yasumoto, Toshiya Muranaka, Kazuto Yoshimi, Tomoji Mashimo, Seiichi Toki

Plant & Cell Biology; 28 October 2025; pcaf138, https://doi.org/10.1093/pcp/pcaf138

 

  

 

 

Abstract
Type I-E CRISPR-Cas3 derived from Escherichia coli (Eco CRISPR-Cas3) can introduce large deletions in target sites and is available for mammalian genome editing. The use of Eco CRISPR-Cas3 in plants is challenging because 7 CRISPR-Cas3 components (6 Cas proteins and CRISPR RNA) must be expressed simultaneously in plant cells. To date, application has been limited to maize protoplasts, and no mutant plants have been produced. In this study, we developed a genome editing system in rice using Eco CRISPR-Cas3 via Agrobacterium-mediated transformation. Deletions in the target gene were detected in 39–71% of transformed calli by PCR analysis, and the frequency of alleles lacking a region 7.0 kb upstream of the PAM sequence was estimated as 21–61% by quantifying copy number by droplet digital PCR, suggesting that mutant plants could be obtained with reasonably high frequency. Deletions were determined in plants regenerated from transformed calli and stably inherited to the progenies. Sequencing analysis showed that deletions of 0.1–7.2 kb were obtained, as reported previously in mammals. Interestingly, deletions separated by intervening fragments or with short insertion and inversion were also determined, suggesting the creation of novel alleles. Moreover, we demonstrated C to T base editing based on Type I-E CRISPR-Cas3 in rice; base editing based on Type I-C and Type I-F2 CRISPR-Cas3 has been reported previously only in human cells.
Overall, Eco CRISPR-Cas3 could be a promising genome editing tool for gene knockout, gene deletion, base editing, and genome rearrangement in plants.
See https://academic.oup.com/pcp/advance-article/doi/10.1093/pcp/pcaf138/8305110?login=false