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

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

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. We define a new trait, drought effect on phenology (DEP), as the difference in flowering time between irrigated and rainfed crops, and use FST genome scanning to probe for genomic regions under selection for this trait in chickpea (Cicer arietinum). Owing to the negligible variation in daylength in our dataset, variation in phenology with sowing date was attributed to temperature and water; hence, 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. Thermal-time to flowering was shortened with increasing water stress, as quantified with carbon isotope composition. Genomic regions on chromosomes 4-8 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 showed that DEP reduces the likelihood of drought and heat stress at the expense of increased likelihood of cold stress. Accounting for DEP would improve genetic and phenotypic models of phenology.

Association of voltage-gated sodium channel mutations with field-evolved pyrethroid resistant phenotypes in soybean aphid and genetic markers for their detection

The frequent use of insecticides to manage soybean aphids, Aphis glycines (Hemiptera: Aphididae), in the United States has contributed to field-evolved resistance. Pyrethroid-resistant aphids have nonsynonymous mutations in the voltage-gated sodium channel (vgsc). We identified a leucine to phenylalanine mutation at position 1014 (L1014F) and a methionine to isoleucine mutation (M918I) of the A. glycines vgsc, both suspected of conferring knockdown resistance (kdr) to lambda-cyhalothrin. We developed molecular markers to identify these mutations in insecticide-resistant aphids. We determined that A. glycines which survived exposure to a diagnostic concentration of lambda-cyhalothrin and bifenthrin via glass-vial bioassays had these mutations, and showed significant changes in the resistance allele frequency between samples collected before and after field application of lambda-cyhalothrin. Thus, a strong association was revealed between aphids with L1014F and M918I vgsc mutations and survival following exposure to pyrethroids. Specifically, the highest survival was observed for aphids with the kdr (L1014F) and heterozygote super-kdr (L1014F + M918I) genotypes following laboratory bioassays and in-field application of lambda-cyhalothrin. These genetic markers could be used as a diagnostic tool for detecting insecticide-resistant A. glycines and monitoring the geographic distribution of pyrethroid resistance. We discuss how generating these types of data could improve our efforts to mitigate the effects of pyrethroid resistance on crop production.

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

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.

Variation in Soybean Aphid (Hemiptera: Aphididae) Biotypes Within Fields

Soybean aphid (Aphis glycines Matsumura (Hemiptera: Aphididae)) has been a major pest of soybean in North America since its detection in this continent in 2000 and subsequent spread. Although several aphid resistance genes have been identified, at least four soybean aphid biotypes have been discovered, with three of them being virulent on soybean cultivars with certain soybean aphid resistance genes. These biotypes are known to vary across years and locations, but information on their variation within single fields is limited. An investigation was conducted to study the variation of soybean aphid biotypes within single townships and fields in Minnesota. Screening of 28 soybean aphid isolates collected from seven soybean fields (six soybean fields in Cairo and Wellington Townships of Renville County, MN and one field in Wilmar Township of Kandiyohi County, MN) revealed the existence of multiple known biotypes of soybean aphid within single fields of soybean. We found up to three biotypes of soybean aphid in a single field. Two biotypes were found in five fields while only one field had only a single biotype. Three isolates presented reactions on a panel of resistant and susceptible indicator lines that were different from known biotypes. These results highlight the importance of characterizing soybean aphid biotypes in small geographical areas and utilizing generated knowledge to develop soybean cultivars pyramided with multiple resistance genes. The outcome will be decreased use of insecticides, thereby improving economic and environmental sustainability of soybean production.

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

The soybean aphid (Aphis glycines) is an important pest of soybeans in the Midwestern US. The first aphid resistance genes were identified in the early 21st century and resistant varieties have been commercially available for 10 years, but have been very underutilized. Major seed companies have avoided commercializing aphid resistant soybean varieties for conventional farmers (i.e., not organic), in part because of the discovery of virulent biotypes in North America. The emergence of soybean aphid populations resistant to insecticides creates a greater incentive for the use of host plant resistance. New research on aphid genetics and markers, plant gene expression and in-plant refuges, suggest important avenues for insect resistance management (IRM) which may encourage more widescale commercialization of this valuable pest management tool.

The Resistant Soybean-Aphis glycines Interaction: Current Knowledge and Prospects

Soybean aphids (Aphis glycines Matsumura) are invasive insect pests of soybean, and they cause significant yield losses. Resistance to soybean aphids is conferred by Resistance to Aphis glycines (Rag) genes. Since the first discovery of aphid-resistant soybean genotypes in 2004, several studies have attempted to characterize Rag genes from aphid-resistant soybean genotypes. To date, 12 Rag genes and four quantitative trait loci for aphid resistance have been reported on soybean chromosomes 07, 08, 13, 16, and 17. Although candidate genes have been proposed for several discovered Rag loci, additional studies are needed to pinpoint, validate, and further explain the potential mechanisms of Rag gene action. A major challenge to utilizing host plant resistance is the discovery of virulent aphid biotypes that can colonize aphid-resistant soybean. This occurrence suggests the need for additional studies to devise strategies to enhance the effectiveness of aphid-resistant soybean. In this mini review, we discuss current knowledge on the resistant soybean-Aphis glycines interaction, potential mechanisms of Rag gene action, opportunities to discover new Rag genes, and prospects for utilization of host plant resistance to manage soybean aphids. A clearer understanding of host plant resistance to soybean aphids will guide researchers on strategies for developing soybean varieties with more durable aphid resistance, reducing the present challenge of virulent aphid biotypes.