Genome scan detection of selective sweeps among biotypes of the soybean aphid, Aphis glycines, with differing virulence to resistance to A. glycines (Rag) traits in soybean, Glycine max

Coates, Brad S.; Hohenstein, Jessica D.; Giordano, Rosanna; Donthu, Ravi Kiran; Michel, Andrew P.; Hodgson, Erin W.; O’Neal, Matthew E.

doi:10.1016/j.ibmb.2020.103364

Cited by 8 publications

(4 citation statements)

References 106 publications

(116 reference statements)

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“…In order to overcome the unique response deployed by Rag1/2 , aphids would need to evolve virulence factors that can overcome not only the individual Rag1 and Rag2 mechanisms, but also the Rag1/2 synergistic response. This is in part corroborated by the recent finding that the genome structure (SNPs) of soybean aphid biotype 4 (virulent on Rag1 , Rag2 , and Rag1/2 ) is not simply the additive effect of biotype 2 and biotype 3 (virulent on Rag1 and Rag2 , respectively), but rather the majority of the sequence variation in its genome was unique to biotype 4 [ 104 ]. This may suggest that alternative mechanisms are needed for overcoming pyramided resistance.…”

Section: Discussionmentioning

confidence: 62%

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

Natukunda

Hohenstein

McCabe³

et al. 2021

BMC Genomics

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Background 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, aphid resistance is conferred by Rag genes. We compared the transcriptional response of four soybean genotypes to aphid feeding to assess how the combination of Rag genes enhanced the soybean resistance to aphid infestation. Results A strong synergistic interaction between Rag1 and Rag2, defined as genes differentially expressed only in the pyramid genotype, was identified. This synergistic effect in the Rag1/2 phenotype was very evident early (6 h after infestation) and involved unique biological processes. However, the response of susceptible and resistant genotypes had a large overlap 12 h 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. Conclusions The synergistic interaction between Rag1 and Rag2 in the Rag1/2 genotype can explain its enhanced resistance phenotype. Understanding molecular mechanisms that support enhanced resistance in pyramid genotypes could facilitate more directed approaches for crop improvement.

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Section: Discussionmentioning

confidence: 62%

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

Natukunda

Hohenstein

McCabe³

et al. 2021

BMC Genomics

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“…After 15 years of heavy, and 135 sometimes unwarranted, insecticide use against soybean 136 aphid in the US, insecticide resistance has evolved [11 ] 137 and is expanding across four major soybean-producing There may be multiple causes for virulence [18]. Genomic re-sequencing revealed between 167 000 and 217 000 single nucleotide polymorphisms (SNPs) among all four soybean aphid biotypes [19 ]. Based on the complete genome, a putative glycoprotein effector occurs near a genomic area with evidence of recent selection.…”

Section: Current Opinion In Insect Sciencementioning

confidence: 99%

Aphid resistance is the future for soybean production, and has been since 2004: efforts towards a wider use of host plant resistance in soybean

Tilmon

Michel

O’Neal

2021

Current Opinion in Insect Science

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“…FST genome-scan is based on neutral theory, assuming that polymorphisms are selectively neutral and random genetic drift is the main driver of allele frequencies in populations without selection (Booker et al, 2020). This approach to detect selection signals in small samples has been insightfull in ecological and evolutionary settings (Barr et al, 2021;Van Bocxlaer, 2017), for crops including rice (Oryza sativa), wheat and chickpea (Jordan et al, 2015;Li et al, 2017;Sadras et al, 2016;Xu et al, 2012), and for crop pests such as the soybean aphid, Aphis glycines (Coates et al, 2020). The reliability of FST genome scan is particularly apparent in a comparison between FST genome scan and genome-wide association (GWAS), with both returning a common 100 kb region (AB4.1) on chromosome 4 associated with Ascochyta blight resistance in chickpea (Li et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

Genetic basis and adaptive implications of temperature-dependent and temperature-independent effects of drought on chickpea phenology

Lake

Chauhan³

et al. 2022

Preprint

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Water deficit often hastens flowering of pulses partially because droughted plants are hotter. Separating temperature-independent and temperature-dependent effects of drought is important to understand, model and manipulate phenology genetically and agronomically. We define a new trait, drought effect on phenology (DEP = difference in flowering time between irrigated and rainfed crops), and use FST genome scan to probe for genomic regions under selection for this trait. Genomic regions overlapping for early- and late-sown crops would associate with temperature-independent effects and non-overlapping genomic regions would associate with temperature-dependent effects. Time to flowering shortened with increasing water stress quantified with carbon isotope composition. Genomic regions on chromosomes 4, 5, 7 and 8 were under selection for DEP. An overlapping region for early and late sowing on chromosome 8 revealed a temperature-independent effect with four candidate genes: BAM1, BAM2, HSL2 and ANT. The non-overlapping regions included six candidate genes: EMF1, EMF2, BRC1/TCP18, BZR1, NPGR1 and ERF1. Modelling to assess DEP adaptive value showed it reduces the likelihood of drought and heat stress at the expense of cold risk. Accounting for DEP would improve phenology models to predict adaptation to future climates and breeding against the combined risks of drought, heat, and cold stress.

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Genome scan detection of selective sweeps among biotypes of the soybean aphid, Aphis glycines, with differing virulence to resistance to A. glycines (Rag) traits in soybean, Glycine max

Cited by 8 publications

References 106 publications

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

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

Aphid resistance is the future for soybean production, and has been since 2004: efforts towards a wider use of host plant resistance in soybean

Genetic basis and adaptive implications of temperature-dependent and temperature-independent effects of drought on chickpea phenology

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