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ToolsLee, Eun Song, Heo, Jung, Bang, Woo Young, Chougule, Kapeel M., Waminal, Nomar Espinosa, Hong, Nguyen Thi, Kim, Min Ji, Beak, Hong Kwan, Kim, Yong Jun, Priatama, Ryza A., Jang, Ji In, Cha, Kang Il, Son, Seung Han, Rajendran, Sujeevan, Choo, Young Kug, Bae, Jong Hyang, Kim, Chul Min, Lee, Young Koung, Bae, Sangsu, Jones, Jonathan D. G., Sohn, Kee Hoon, Lee, Jiyoung, Kim, Hyun Hee, Hong, Jong Chan, Ware, Doreen, Kim, Keunhwa and Park, Soon Ju (2023) Engineering homoeologs provide a fine scale for quantitative traits in polyploid. Plant Biotechnology Journal, 21 (12). pp. 2458-2472. ISSN 1467-7644
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Abstract
Numerous staple crops exhibit polyploidy and are difficult to genetically modify. However, recent advances in genome sequencing and editing have enabled polyploid genome engineering. The hexaploid black nightshade species Solanum nigrum has immense potential as a beneficial food supplement. We assembled its genome at the scaffold level. After functional annotations, we identified homoeologous gene sets, with similar sequence and expression profiles, based on comparative analyses of orthologous genes with close diploid relatives Solanum americanum and S. lycopersicum. Using CRISPR-Cas9-mediated mutagenesis, we generated various mutation combinations in homoeologous genes. Multiple mutants showed quantitative phenotypic changes based on the genotype, resulting in a broad-spectrum effect on the quantitative traits of hexaploid S. nigrum. Furthermore, we successfully improved the fruit productivity of Boranong, an orphan cultivar of S. nigrum suggesting that engineering homoeologous genes could be useful for agricultural improvement of polyploid crops.
| Item Type: | Article |
|---|---|
| Additional Information: | Data availability statement: All the raw sequencing data generated in this study have been deposited at the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) with BioProject accession number PRJNA946382. The assembled genomes and annotations are available at Figshare (https://figshare.com/articles/dataset/Genome_assembly_and_annotation_for_Solanum_americanum_and_Solanum_nigrum/22316296). Funding Information: This work was supported by a grant from the New Breeding Technologies Development Program (project no. PJ01653802) to S.J.P., also supported by the National Research Foundation of Korea grant numbers 2020R1A6A1A03044344, 2021R1C1C2006483 and 2020R1A2C1101915 to J.-C.H., K.K. and S.J.P., respectively, and supported by the USDA ARS 80622100 044 000D to K.M.C. and D.W. |
| Uncontrolled Keywords: | agricultural improvement,homoeologous gene editing,polyploid,quantitative traits,biotechnology,agronomy and crop science,plant science ,/dk/atira/pure/subjectarea/asjc/1300/1305 |
| Faculty \ School: | Faculty of Science > School of Biological Sciences Faculty of Science > The Sainsbury Laboratory |
| UEA Research Groups: | Faculty of Science > Research Groups > Plant Sciences |
| Related URLs: | |
| Depositing User: | LivePure Connector |
| Date Deposited: | 25 Oct 2024 14:30 |
| Last Modified: | 12 Nov 2024 14:30 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/97222 |
| DOI: | 10.1111/pbi.14141 |
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