@article{ca097c3ac5174dcc80faa70b6642a712,
title = "Engineering homoeologs provide a fine scale for quantitative traits in polyploid",
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.",
keywords = "agricultural improvement, homoeologous gene editing, polyploid, quantitative traits",
author = "Lee, {Eun Song} and Jung Heo and Bang, {Woo Young} and Chougule, {Kapeel M.} and Waminal, {Nomar Espinosa} and Hong, {Nguyen Thi} and Kim, {Min Ji} and Beak, {Hong Kwan} and Kim, {Yong Jun} and Priatama, {Ryza A.} and Jang, {Ji In} and Cha, {Kang Il} and Son, {Seung Han} and Sujeevan Rajendran and Choo, {Young Kug} and Bae, {Jong Hyang} and Kim, {Chul Min} and Lee, {Young Koung} and Sangsu Bae and Jones, {Jonathan D. G.} and Sohn, {Kee Hoon} and Jiyoung Lee and Kim, {Hyun Hee} and Hong, {Jong Chan} and Doreen Ware and Keunhwa Kim and Park, {Soon Ju}",
note = "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. ",
year = "2023",
month = dec,
doi = "10.1111/pbi.14141",
language = "English",
volume = "21",
pages = "2458--2472",
journal = "Plant Biotechnology Journal",
issn = "1467-7644",
publisher = "Wiley",
number = "12",
}