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A Multi-Year, Multi-Cultivar Approach to Differential Expression Analysis of High- and Low-Protein Soybean (Glycine max)

Soybean (Glycine max (L.) Merr.) is among the most valuable crops based on its nutritious seed protein and oil. Protein quality, evaluated as the ratio of glycinin (11S) to β-conglycinin (7S), can play a role in food and feed quality. To help uncover the underlying differences between high and low p...

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Autores principales: Hooker, Julia C., Nissan, Nour, Luckert, Doris, Charette, Martin, Zapata, Gerardo, Lefebvre, François, Mohr, Ramona M., Daba, Ketema A., Warkentin, Thomas D., Hadinezhad, Mehri, Barlow, Brent, Hou, Anfu, Golshani, Ashkan, Cober, Elroy R., Samanfar, Bahram
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9820483/
https://www.ncbi.nlm.nih.gov/pubmed/36613666
http://dx.doi.org/10.3390/ijms24010222
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author Hooker, Julia C.
Nissan, Nour
Luckert, Doris
Charette, Martin
Zapata, Gerardo
Lefebvre, François
Mohr, Ramona M.
Daba, Ketema A.
Warkentin, Thomas D.
Hadinezhad, Mehri
Barlow, Brent
Hou, Anfu
Golshani, Ashkan
Cober, Elroy R.
Samanfar, Bahram
author_facet Hooker, Julia C.
Nissan, Nour
Luckert, Doris
Charette, Martin
Zapata, Gerardo
Lefebvre, François
Mohr, Ramona M.
Daba, Ketema A.
Warkentin, Thomas D.
Hadinezhad, Mehri
Barlow, Brent
Hou, Anfu
Golshani, Ashkan
Cober, Elroy R.
Samanfar, Bahram
author_sort Hooker, Julia C.
collection PubMed
description Soybean (Glycine max (L.) Merr.) is among the most valuable crops based on its nutritious seed protein and oil. Protein quality, evaluated as the ratio of glycinin (11S) to β-conglycinin (7S), can play a role in food and feed quality. To help uncover the underlying differences between high and low protein soybean varieties, we performed differential expression analysis on high and low total protein soybean varieties and high and low 11S soybean varieties grown in four locations across Eastern and Western Canada over three years (2018–2020). Simultaneously, ten individual differential expression datasets for high vs. low total protein soybeans and ten individual differential expression datasets for high vs. low 11S soybeans were assessed, for a total of 20 datasets. The top 15 most upregulated and the 15 most downregulated genes were extracted from each differential expression dataset and cross-examination was conducted to create shortlists of the most consistently differentially expressed genes. Shortlisted genes were assessed for gene ontology to gain a global appreciation of the commonly differentially expressed genes. Genes with roles in the lipid metabolic pathway and carbohydrate metabolic pathway were differentially expressed in high total protein and high 11S soybeans in comparison to their low total protein and low 11S counterparts. Expression differences were consistent between East and West locations with the exception of one, Glyma.03G054100. These data are important for uncovering the genes and biological pathways responsible for the difference in seed protein between high and low total protein or 11S cultivars.
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spelling pubmed-98204832023-01-07 A Multi-Year, Multi-Cultivar Approach to Differential Expression Analysis of High- and Low-Protein Soybean (Glycine max) Hooker, Julia C. Nissan, Nour Luckert, Doris Charette, Martin Zapata, Gerardo Lefebvre, François Mohr, Ramona M. Daba, Ketema A. Warkentin, Thomas D. Hadinezhad, Mehri Barlow, Brent Hou, Anfu Golshani, Ashkan Cober, Elroy R. Samanfar, Bahram Int J Mol Sci Article Soybean (Glycine max (L.) Merr.) is among the most valuable crops based on its nutritious seed protein and oil. Protein quality, evaluated as the ratio of glycinin (11S) to β-conglycinin (7S), can play a role in food and feed quality. To help uncover the underlying differences between high and low protein soybean varieties, we performed differential expression analysis on high and low total protein soybean varieties and high and low 11S soybean varieties grown in four locations across Eastern and Western Canada over three years (2018–2020). Simultaneously, ten individual differential expression datasets for high vs. low total protein soybeans and ten individual differential expression datasets for high vs. low 11S soybeans were assessed, for a total of 20 datasets. The top 15 most upregulated and the 15 most downregulated genes were extracted from each differential expression dataset and cross-examination was conducted to create shortlists of the most consistently differentially expressed genes. Shortlisted genes were assessed for gene ontology to gain a global appreciation of the commonly differentially expressed genes. Genes with roles in the lipid metabolic pathway and carbohydrate metabolic pathway were differentially expressed in high total protein and high 11S soybeans in comparison to their low total protein and low 11S counterparts. Expression differences were consistent between East and West locations with the exception of one, Glyma.03G054100. These data are important for uncovering the genes and biological pathways responsible for the difference in seed protein between high and low total protein or 11S cultivars. MDPI 2022-12-23 /pmc/articles/PMC9820483/ /pubmed/36613666 http://dx.doi.org/10.3390/ijms24010222 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Hooker, Julia C.
Nissan, Nour
Luckert, Doris
Charette, Martin
Zapata, Gerardo
Lefebvre, François
Mohr, Ramona M.
Daba, Ketema A.
Warkentin, Thomas D.
Hadinezhad, Mehri
Barlow, Brent
Hou, Anfu
Golshani, Ashkan
Cober, Elroy R.
Samanfar, Bahram
A Multi-Year, Multi-Cultivar Approach to Differential Expression Analysis of High- and Low-Protein Soybean (Glycine max)
title A Multi-Year, Multi-Cultivar Approach to Differential Expression Analysis of High- and Low-Protein Soybean (Glycine max)
title_full A Multi-Year, Multi-Cultivar Approach to Differential Expression Analysis of High- and Low-Protein Soybean (Glycine max)
title_fullStr A Multi-Year, Multi-Cultivar Approach to Differential Expression Analysis of High- and Low-Protein Soybean (Glycine max)
title_full_unstemmed A Multi-Year, Multi-Cultivar Approach to Differential Expression Analysis of High- and Low-Protein Soybean (Glycine max)
title_short A Multi-Year, Multi-Cultivar Approach to Differential Expression Analysis of High- and Low-Protein Soybean (Glycine max)
title_sort multi-year, multi-cultivar approach to differential expression analysis of high- and low-protein soybean (glycine max)
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9820483/
https://www.ncbi.nlm.nih.gov/pubmed/36613666
http://dx.doi.org/10.3390/ijms24010222
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