Interaction between Rag genes results in a unique synergistic transcriptional response that enhances soybean resistance to soybean aphids

Authors: NATUKUNDA, MARTHA - Iowa State University; HOHENSTEIN, JESSICA - Iowa State University; McCabe, Chantal; Graham, Michelle; QI, YUNHUI - Iowa State University; SINGH, ASHEESH - Iowa State University; MACINTOSH, GUSTAVO - Iowa State University

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/3/2021
Publication Date: 12/11/2021
Citation: Natukunda, M.I., Hohenstein, J.D., McCabe, C.E., Graham, M.A., Qi, Y., Singh, A.K., MacIntosh, G.C. 2021. Interaction between Rag genes results in a unique synergistic transcriptional response that enhances soybean resistance to soybean aphids. BMC Genomics. 22. Article 887. https://doi.org/10.1186/s12864-021-08147-3.
DOI: https://doi.org/10.1186/s12864-021-08147-3

Interpretive Summary: Throughout history, plant breeders have stacked multiple resistance genes targeting specific pathogens or pests within a single line. Stacked resistance lines offer more robust and durable resistance compared to lines with individual resistance genes. In soybean, aphid resistance is conferred by Rag genes. Plants containing the Rag1/Rag2 double stack are significantly more resistant to aphid attack than plants containing either Rag1 or Rag2 alone. To understand how stacking resistance genes enhances resistance, researchers from Iowa State University and the USDA-ARS conducted whole genome expression analyses of four soybean lines (aphid-susceptible line, Rag1 line, Rag2 line and line containing the Rag1/Rag2 double stack), collecting samples six and 12 hours after infestation or mock infestation with soybean aphids. We identified 1000 genes specifically expressed in response to aphids in the double stack line, but not in either of the single resistance gene lines. Many of the 1000 response unique to the double stack line had functions related to defense including modification of cell walls, detection of pests and pathogens and defense signaling. The data was also used to identify a strong candidate for the Rag1 resistance gene. Understanding how stacking resistance genes results in enhanced resistance is essential for future crop improvement.

Technical Abstract: Pyramiding different resistance genes into one plant genotype confers enhanced resistance at the phenotypic level, but the molecular mechanisms underlying this effect are not well-understood. In soybean, resistance to aphids (Aphis glycines) is conferred by Rag genes. We analyzed the effect of pyramiding Rag genes at the transcriptome level by comparing the response to aphids in four soybean genotypes, aphid-susceptible (no Rag gene), monogenic aphid resistance (Rag1 or Rag2 alone), and pyramid (Rag1/2), at 6 and 12 hours after infestation. A strong synergistic interaction was identified between Rag1 and Rag2 in the Rag1/2 genotype, resulting in differential expression of large gene sets unique to the pyramid. This synergistic effect was very evident early (6 hours after infestation) and involved biological processes unique to the pyramid. However, the response of all four genotypes shared more commonalities 12 hours after aphid infestation. Transcription factor (TF) analyses identified a network of interacting TF that potentially integrates signaling from Rag1 and Rag2 to produce the unique Rag1/2 response. Pyramiding resulted in rapid induction of phytochemicals production and deposition of lignin to strengthen the secondary cell wall, while repressing photosynthesis. We also identified Glyma.07G063700 as a novel, strong candidate for the Rag1 gene. The synergistic interaction between Rag1 and Rag2 in the Rag1/2 genotype can explain its enhanced resistance phenotype. This synergistic effect can change the selective pressure on colonizing aphids, impacting the durability of resistance. Understanding molecular mechanisms that support enhanced resistance in pyramid genotypes could also facilitate more directed approaches for crop improvement.