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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #402028

Research Project: Mapping Crop Genome Functions for Biology-Enabled Germplasm Improvement

Location: Plant, Soil and Nutrition Research

Title: Engineering homoeologs provides a fine scale for quantitative traits in polyploid

item LEE, EUN SONG - Wonderful Orchards
item HEO, JUNG - Wonderful Orchards
item BANG, WOO YOUNG - Incheon National University
item CHOUGULE, KAPEEL - Cold Spring Harbor Laboratory
item WAMINAL, NOMAR ESPINOSA - Leibniz Institute Of Plant Genetics And Crop Plant Research
item HONG, NGUYEN THI - Saarland University
item KIM, MIN JI - Wonderful Orchards
item BEAK, HONG KWAN - Wonderful Orchards
item KIM, YONG JUN - Wonderful Orchards
item PRIATAMA, RYZA - Wonderful Orchards
item JANG, JI IN - Wonderful Orchards
item CHA, KANG - Wonderful Orchards
item SON, SUENG HAN - Wonderful Orchards
item RAJENDRAN, SUJEEVAN - Wonderful Orchards
item CHOO, YOUNG KUG - Wonderful Orchards
item BAE, JONG HYANG - Wonderful Orchards
item KIM, CHUL MIN - Wonderful Orchards
item LEE, YONG KOUNG - Institute Of Parasitology - Germany
item BAE, SANGSU - Seoul National University
item JONES, JONATHAN - Sainsbury Laboratory
item SOHN, KEE HOON - Pohang University Of Science & Technology
item KIM, HEE HYUN - Saarland University
item Ware, Doreen
item KEUNHWA, KIM - Wonderful Orchards

Submitted to: Plant Biotechnology Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/5/2023
Publication Date: 8/2/2023
Citation: Lee, E., Heo, J., Bang, W., Chougule, K., Waminal, N., Hong, N., Kim, M., Beak, H., Kim, Y., Priatama, R.A., Jang, J., Cha, K., Son, S., Rajendran, S., Choo, Y., Bae, J., Kim, C., Lee, Y., Bae, S., Jones, J., Sohn, K., Kim, H., Ware, D., Keunhwa, K. 2023. Engineering homoeologs provides a fine scale for quantitative traits in polyploid. Plant Biotechnology Journal.

Interpretive Summary: Many important crops have a complex genetic makeup that makes them difficult to modify through traditional methods. However, recent advancements in genome sequencing and editing techniques have opened up new possibilities for modifying these crops. In this study, the focus was on a particular plant called black nightshade, which has six sets of chromosomes, making it a polyploid species. The study successfully sequenced and analyzed its genome, and identified sets of genes that are similar to those found in closely related diploid plants. Using a gene editing tool called CRISPR-Cas9, introduced changes in these genes and observed various combinations of mutations. These mutations resulted in measurable changes in the plant's characteristics, such as its productivity and other traits, specifically improving the fruit productivity of a variety called Boranong, which was previously not very productive. These findings suggest that modifying specific sets of genes in polyploid crops can be a useful strategy for improving their agricultural traits.

Technical 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 S. 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.