Phenotypic and transcriptomic approaches to understanding natural dicamba tolerance in soybean, and an exploration of segregation distortion in SCN resistance

Ozer, Seda

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https://hdl.handle.net/2142/127482 Copy

Description

Title

Phenotypic and transcriptomic approaches to understanding natural dicamba tolerance in soybean, and an exploration of segregation distortion in SCN resistance

Author(s)

Ozer, Seda

Issue Date

2024-12-03

Director of Research (if dissertation) or Advisor (if thesis)

Diers, Brian W.

Doctoral Committee Chair(s)

Diers, Brian W.

Committee Member(s)

• Juvik, John A.
• Clough, Steven J.
• Bohn, Martin O.

Department of Study

Crop Sciences

Discipline

Crop Sciences

Degree Granting Institution

University of Illinois at Urbana-Champaign

Degree Name

Ph.D.

Degree Level

Dissertation

Keyword(s)

soybean, dicamba, vegetation indices, RNA-sequencing, differentially expressed genes, segregation distortion, rhg1-b, NSFRAN07

Abstract

Dicamba, a synthetic auxin herbicide, is widely used for postemergence weed control. However, the high potential for volatility and spray drift raises critical concerns about the impact of dicamba on non-target dicot crops lacking the dicamba monooxygenase (DMO) transgene, which provides engineered tolerance. Our objective was to improve our understanding of non-Genetically Modified (GM) tolerance to off-target dicamba injury. We conducted field experiments in 2021 and 2022 with varying rates of dicamba to test the responses of non-GM soybean lines pre-identified as naturally tolerant (T) or sensitive (S) to dicamba developed and classified for tolerance at the University of Missouri. Temporal visual ratings of dicamba damage were taken on a 0-5 scale approximately every five days after dicamba application for a 6-8 week period. The soybean injury was at its greatest level approximately three weeks after the initial spraying. S soybean lines consistently showed higher visual damage scores than T lines, especially at higher dicamba doses (1/250 and 1/500) and under weekly treatments (1/500 weekly and 1/1,000 weekly). The 1/500 dosage consistently provided the clearest distinction between T and S lines, making it the most reliable treatment for assessing dicamba effects for future studies. To augment the precision of the visual damage assessment, an Unmanned Aerial Vehicle (UAV) equipped with a multispectral camera was used to calculate four temporal vegetation indices (GLI, ExG2, NGRDI, and RENDVI) for each flight date. Strong negative correlations at each flight date were observed between visual damage ratings and VI scores across dicamba rates, indicating that these VIs captured the same variation between T and S lines that were observed visually. NGRDI was the most sensitive VI, showing the strongest ability to differentiate dicamba damage between S and T lines across treatments and time points. NGRDI had the highest negative correlation with visual damage scores, especially under 1/500 and 1/500 weekly treatments. Our results align with previous findings that observed dicamba tolerance under unknown rate conditions. Through controlled experiments, we confirmed these observations and demonstrated that natural dicamba tolerance in soybean is strongly influenced by genetics. The natural dicamba tolerance identified in soybean germplasm [Glycine max (L.) Merr.] is promising for mitigating off-target damage, though the genetic basis of this tolerance remains poorly understood. To address this gap in knowledge, we conducted a transcriptomic analysis comparing one tolerant (S17-1980) and one sensitive (S17-7688) soybean line developed and classified for tolerance at the University of Missouri. The analysis was done for lines tested under control conditions and a 1/1,000 dicamba treatment at three post-inoculation time points: 8 hours, 24 hours, and 72 hours. Gene expression in the two genotypes exhibited substantial variation across time points, with time and genotype being the primary factors influencing expression patterns, while dicamba treatment had a relatively minor effect. The tolerant line (S17-1980) showed a unique temporal response to dicamba, with an increasing number of unique differentially expressed genes (DEGs) at 24 and 72 hours. Enhanced carbon utilization suggested that tolerant soybean may optimize carbon fixation and utilization as a mechanism to mitigate dicamba-induced stress. At 24 hours, pathways related to hydrogen peroxide, reactive oxygen species, jasmonic acid, and oxidative stress were activated; by 72 hours, this shifted to cell wall modification and pectin breakdown, indicating a possible adaptive response. Protein processing in the endoplasmic reticulum was found to be more active at 24 hours in tolerant plant, aiding protein folding and stress resilience. Identified candidate genes, such as those involved in detoxification (UGTs) and vacuolar transport, provide potential targets for breeding dicamba-tolerant soybean varieties. GWAS suggested candidates showed significant regulation in time contrast analyses, indicating probable roles in temporal dicamba responses. A 1 Mbp region around GWAS significant SNPs contained genes related to hormone signaling and stress pathways as being differentially expressed, indicating a possible genetic basis for tolerance through hormonal regulation. These findings demonstrated that multiple gene responses and diverse mechanisms synergize to enhance natural dicamba tolerance in soybean, advancing our understanding of the molecular processes and establishing a foundation for future breeding strategies. Rhg1 is the most important locus conferring resistance to soybean cyst nematode (SCN; Heterodera glycine Ichinohe) in soybean [Glycine max (L.) Merr]. Previous research has shown that to obtain viable plants, the SCN resistance allele at Rhg1 on chromosome 18 needs to be paired with NSFRAN07, an atypical resistance-associated NSF allele of the NSF (N-ethylmaleimide sensitive factor) allele on chromosome 07. This causes segregation distortion in populations developed from crosses between resistant and susceptible plants. Our study aimed to improve our understanding of this segregation distortion and determine the developmental stage it occurs. DNA from developing F2 seeds and F2 plants originating from crosses between resistant and susceptible parents were genotyped with markers for the rhg1 and NSF loci using TaqMan assays. Chi-square tests revealed significant deviations from the expected Mendelian segregation ratio (1:2:1:2:4:2:1:2:1) in both F2 seeds and plants, indicating segregation distortion at these loci. The absence of rhg1-b_rhg1-b_NSFCh07_NSFCh07 genotype supports previous finding that the combination of the resistance allele rhg1-b and the commonly occurring NSFCh07 allele is lethal, apparently because the α-SNAP (GmSNAP18) proteins encoded by rhg1-b or rhg1-a interact well with NSFRAN07 protein but not the more common NSFCh07 protein. The findings indicate that segregation distortion occurs prior to seed maturation and is primarily due to zygotic selection during early seed development. The results emphasize the need to consider this genetic interaction in breeding efforts to improve soybean, since segregation distortion may affect inheritance of SCN resistance and other traits linked to Rhg1 or NSFCh07.

Graduation Semester

2024-12

Type of Resource

Thesis

Handle URL

https://hdl.handle.net/2142/127482

Copyright and License Information

Copyright 2024 Seda Ozer

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