Differential gene expression provides leads to environmentally regulated soybean seed protein content

Julia C Hooker; Myron Smith; Gerardo Zapata; Martin Charette; Doris Luckert; Ramona M Mohr; Ketema A Daba; Thomas D Warkentin; Mehri Hadinezhad; Brent Barlow; Anfu Hou; François Lefebvre; Ashkan Golshani; Elroy R Cober; Bahram Samanfar

doi:10.3389/fpls.2023.1260393

Differential gene expression provides leads to environmentally regulated soybean seed protein content

Front Plant Sci. 2023 Sep 18:14:1260393. doi: 10.3389/fpls.2023.1260393. eCollection 2023.

Authors

Julia C Hooker^{1

2}, Myron Smith², Gerardo Zapata³, Martin Charette¹, Doris Luckert¹, Ramona M Mohr⁴, Ketema A Daba⁵, Thomas D Warkentin⁵, Mehri Hadinezhad¹, Brent Barlow⁵, Anfu Hou⁶, François Lefebvre³, Ashkan Golshani², Elroy R Cober¹, Bahram Samanfar^{1

2}

Affiliations

¹ Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada.
² Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada.
³ Canadian Centre for Computational Genomics, Montréal, QC, Canada.
⁴ Brandon Research Centre, Agriculture and Agri-Food Canada, Brandon, MB, Canada.
⁵ Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada.
⁶ Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada.

Abstract

Soybean is an important global source of plant-based protein. A persistent trend has been observed over the past two decades that soybeans grown in western Canada have lower seed protein content than soybeans grown in eastern Canada. In this study, 10 soybean genotypes ranging in average seed protein content were grown in an eastern location (control) and three western locations (experimental) in Canada. Seed protein and oil contents were measured for all lines in each location. RNA-sequencing and differential gene expression analysis were used to identify differentially expressed genes that may account for relatively low protein content in western-grown soybeans. Differentially expressed genes were enriched for ontologies and pathways that included amino acid biosynthesis, circadian rhythm, starch metabolism, and lipid biosynthesis. Gene ontology, pathway mapping, and quantitative trait locus (QTL) mapping collectively provide a close inspection of mechanisms influencing nitrogen assimilation and amino acid biosynthesis between soybeans grown in the East and West. It was found that western-grown soybeans had persistent upregulation of asparaginase (an asparagine hydrolase) and persistent downregulation of asparagine synthetase across 30 individual differential expression datasets. This specific difference in asparagine metabolism between growing environments is almost certainly related to the observed differences in seed protein content because of the positive correlation between seed protein content at maturity and free asparagine in the developing seed. These results provided pointed information on seed protein-related genes influenced by environment. This information is valuable for breeding programs and genetic engineering of geographically optimized soybeans.

Keywords: RNA-seq; amino acid metabolism; asparagine; differential expression; seed protein; soybean.

Grants and funding

The authors declare financial support was received for the research, authorship, and/or publication of this article. This research was funded by Agriculture and Agri-Food Canada and the Canadian Field Crop Research Alliance (CFCRA).