Deep learning analysis of soybean cyst nematode effectors to proven soybean resistance genes and homolog identification in the sugar beet-sugar beet root maggot plant pathosystem

Authors: RAHIM, SIDRA - Towson University; LEE, YERANG - Towson University; ALKHAROUF, NADIM - Towson University; Chu, Chenggen; Klink, Vincent

Submitted to: Data in Brief
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/1/2026
Publication Date: 4/11/2026
Citation: Rahim, S.S., Lee, Y., Alkharouf, N.W., Chu, C.N., Klink, V.P. 2026. Deep learning analysis of soybean cyst nematode effectors to proven soybean resistance genes and homolog identification in the sugar beet-sugar beet root maggot plant pathosystem. Data in Brief. 66. Article e112749. https://doi.org/10.1016/j.dib.2026.112749.
DOI: https://doi.org/10.1016/j.dib.2026.112749

Interpretive Summary: Pathogenic insects cause $80B in economic losses, annually. The sugar beet root maggot (SBRM), Tetanops myopaeformis, is among them, and the most significant pathogen of sugar beet, Beta vulgaris ssp vulgaris, its obligate crop host. SBRM causes $1B in damage, annually, in the U.S. to a crop with a global value of $4.6B. A gene known as Kunitz trypsin inhibitor (KTI) has been identified that undergoes expression during the sugar beet resistance response to SBRM. KTIs target pathogen trypsin (TRP) and inactivates it to effect resistance. KTI is hypothesized to perform an important function during the sugar beet resistance response to SBRM because its composition resembles other genes identified in other crop plants and through transgenic studies shown to function in resistance. Transgenic experiments used to demonstrate KTI resistance in sugar beet are problematic so other important crop plants are used to examine a potential resistance role because the experimental procedures have been developed. Soybean, Glycine max, the most important U.S. export crop ($31B, U.S., $155B, globally), and top U.S. export crop ($27B) is the obligate crop host that undergoes infection by its most significant root pathogen the soybean cyst nematode, Heterodera glycines (a plant parasitic nematode) is a genetic model for demonstrating the role of genes during resistance to root pathogens. Plant parasitic nematodes are devastating pathogens causing cause $187B in economic losses, annually, globally, with SCN causing $1.5B, U.S., $23B, globally. Consequently, resistance can be studied in two very important crop pathosystems, the sugar beet-SBRM pathosystem and the soybean-SCN pathosystem. Computer-aided analyses identified the soybean cyst nematode proteins that are inhibited by the soybean KTI resistance protein found in soybean, aiding in the discovery of a solution to the soybean cyst nematode problem of soybean with that information being translated to sugar beet, aiding in the development of management strategies, engineering resistance, and breeding programs aimed at controlling SBRM as well as SCN.

Technical Abstract: Sugar beet (Beta vulgaris ssp. vulgaris) is one of two plants from which sugar is broadly produced, accounting for 55% of U.S. sugar ($1B, U.S.) and 35% global raw sugar ($4.6B), annually. The sugar beet root maggot (Tetanops myopaeformis) is its top pathogen in the U.S., and capable of causing total crop failure, making its study of urgent need. A B. vulgaris protease inhibitor, BvSTI (DV501688), one of 22 of its Kunitz trypsin inhibitors (KTIs) was shown through deep learning analyses to bind 9 different T. myopaeformis trypsins (Trps). As a surrogate crop experimental system to understand resistance in the B. vulgaris-T. myopaeformis pathosystem, transgenic analysis identified homologous Glycine max (soybean) KTIs expressed in root cells undergoing resistance to its most important pathogen, Heterodera glycines and suppresses parasitism by greater than 80%. The study adds to a list of 114 soybean genes identified in laser microdissection-assisted analyses whose expression suppresses H. glycines parasitism.