Characterization and genetics of multiple soybean aphid biotype resistance in five soybean plant introductions

Key message

Five soybean plant introductions expressed antibiosis resistance to multiple soybean aphid biotypes. Two introductions had resistance genes located in the Rag1, Rag2, and Rag3 regions; one introduction had resistance genes located in the Rag1, Rag2, and rag4 regions; one introduction had resistance genes located in the Rag1 and Rag2 regions; and one introduction had a resistance gene located in the Rag2 region.

Abstract

Soybean aphid (Aphis glycines Matsumura) is the most important soybean [Glycine max (L.) Merr.] insect pest in the USA. The objectives of this study were to characterize the resistance expressed in five plant introductions (PIs) to four soybean aphid biotypes, determine the mode of resistance inheritance, and identify markers associated with genes controlling resistance in these accessions. Five soybean PIs, from an initial set of 3000 PIs, were tested for resistance against soybean aphid biotypes 1, 2, 3, and 4 in choice and no-choice tests. Of these five PIs, PI 587663, PI 587677, and PI 587685 expressed antibiosis against all four biotypes, while PI 587972 and PI 594592 expressed antibiosis against biotypes 1, 2, and 3. F₂ populations derived from PI 587663 and PI 587972 were evaluated for resistance against soybean aphid biotype 1, and populations derived from PIs 587677, 587685, and 594592 were tested against biotype 3. In addition, F_2:3 plants were tested against biotypes 2 and 3. Genomic DNA from F₂ plants was screened with markers linked to Rag1, Rag2, Rag3, and rag4 soybean aphid-resistance genes. Results showed that PI 587663 and PI 594592 each had three genes with variable gene action located in the Rag1, Rag2, and Rag3 regions. PI 587677 had three genes with variable gene action located in the Rag1, Rag2 and rag4 regions. PI 587685 had one dominant gene located in the Rag1 region and an additive gene in the Rag2 region. PI 587972 had one dominant gene located in the Rag2 region controlling antixenosis- or antibiosis-type resistance to soybean aphid biotypes 1, 2, or 3. PIs 587663, 587677, and 587685 also showed antibiosis-type resistance against biotype 4. Information on multi-biotype aphid resistance and resistance gene markers will be useful for improving soybean aphid resistance in commercial soybean cultivars.

     

Physiological and molecular responses to drought and salinity in soybean

Drought and salinity are severe environmental stresses and limit soybean growth. In this study, a comparative analysis of physiological and molecular responses of two soybean (Glycine max L.) genotypes to these stresses was carried out. Plants of drought-tolerant genotype RD (cv. FD92) and sensitive genotype SD (cv. Z1303) were exposed to 15 % (m/v) PEG 6000, which simulated drought stress, or 150 mM NaCl. The RD plants maintained larger leaf area and higher net photosynthetic rate, chlorophyll content, stomatal conductance, and relative water content compared with the SD plants. Leaf proline content increased under both stresses more in RD than in SD. The drought tolerance of RD plants was also correlated with greater antioxidant activity and lower content of hydrogen peroxide and malondialdehyde under stress conditions. Amounts of abscisic acid, jasmonic acid, and salicylic acid under stress increased to a greater extent in RD than in SD plants. At the molecular level, the effects of 20-d stress treatments were manifested by relatively higher expression of drought- or salt-related genes: GmP5CS, GmDREB1a, GmGOLS, GmBADH, and GmNCED1 in RD plants than in SD plants. These results form the basis for understanding the mechanisms of the drought- and salt-stress tolerance in soybean.     

Electroporation-mediated RNA interference reveals a role of the multicopper oxidase 2 gene in dragonfly cuticular pigmentation

Dragonflies are colorful insects, and recent RNA sequencing studies have identified a number of candidate genes potentially involved in their color pattern formation and color vision. However, functional aspects of such genes have not been assessed due to the lack of molecular genetic tools applicable to dragonflies. We established an electroporation-mediated RNA interference (RNAi) procedure using the tiny dragonfly Nannophya pygmaea Rambur, 1842 (Odonata: Libellulidae) that targets the multicopper oxidase 2 gene (MCO2; also known as laccase2 gene) responsible for cuticular pigmentation in many insects. RNA sequencing of N. pygmaea and genomic survey of the dragonfly Ladona fulva identified four multicopper oxidase family genes: MCO1, MCO2, MCO3 and multicopper oxidase-related protein gene (MCORP). In N. pygmaea, MCO2 was specifically expressed around the cuticular pigmentation period, whereas MCO1 was constantly expressed. MCORP was expressed at adult stages, and MCO3 was scarcely expressed. When we applied in vivo electroporation, final instar larvae injected with MCO2 small interfering RNA became adults with patchy unpigmented regions. RNAi without in vivo electroporation did not affect cuticular pigmentation, suggesting that dragonflies do not show a systemic RNAi response. These results indicate that MCO2 is required for cuticular pigmentation across diverse insects, and highlight the usefulness of the electroporation-mediated RNAi method in dragonflies.     

Defensive Responses in Groundnut Against Chewing and Sap-Sucking Insects

Induced resistance is one of the important components of host plant resistance to insects. We studied the induced defensive responses in groundnut genotypes with different levels of resistance to the leaf defoliator Helicoverpa armigera and the sap-sucking insect Aphis craccivora to gain an understanding of the induced resistance to insects and its implications for pest management. The activity of the defensive enzymes (peroxidase, polyphenol oxidase, phenylalanine ammonia lyase, superoxide dismutase, ascorbate peroxidase, and catalase) and the amounts of total phenols, hydrogen peroxide, malondialdehyde, and proteins were recorded at 6 days after infestation. Induction of enzyme activities and the amounts of secondary metabolites were greater in the insect-resistant genotypes ICGV 86699, ICGV 86031, ICG 2271, and ICG 1697 infested with H. armigera and A. craccivora than in the susceptible check JL 24. The resistant genotypes suffered lower insect damage and resulted in lower Helicoverpa larval survival and weights than those larvae fed on the susceptible check JL 24. The number of aphids was significantly lower on insect-resistant genotypes than on the susceptible check JL 24. The results suggested that groundnut plants respond to infestation by H. armigera and A. craccivora in a similar way; however, the degree of the response differed across the genotypes and insects, and this defense response is attributed to various defensive enzymes and secondary metabolites.     

Molecular mapping of the genomic region conferring resistance to soybean stem canker in Hutcheson soybean

Genetic resistance to soybean stem canker, caused by the fungus Diaporthe phaseolorum var. meridionalis (Dpm), is controlled by five major, dominant, nonallelic genes Rdm1 to Rdm5. A genomic region containing the Rdm4 and Rdm5 genes was first described in Hutcheson soybean, where they were found to confer specific resistance to Argentinean physiological races of Dpm. Here, we report the genetic mapping of Rdm4 and Rdm5 loci using two pheno- and genotypically characterized F_2:3 populations derived from Hutcheson cultivar. The mapping populations were screened with amplified fragment length polymorphism (AFLP) markers using bulk segregant analysis, and with simple sequence repeat (SSR) markers. Linkage analysis indicated that the Rdm4 and Rdm5 resistance loci were located in a genomic region collinear with the molecular linkage group (MLG) A2 (chromosome 8) of the soybean genetic map. The linkage group contains two SSR markers, Sat_162 and Satt233, flanking the Rdm4 and Rdm5 loci. These SSR will be useful to increase the efficiency of selection in breeding programs aimed to incorporate Rdm4 and Rdm5 genes into soybean elite germplasm.     

A correlation between host-mediated expression of parasite genes as tandem inverted repeats and abrogation of development of female <Emphasis Type="Italic">Heterodera glycines</Emphasis> cyst formation during infection of <Emphasis Type="Italic">Glycine max</Emphasis>

Host-mediated (hm) expression of parasite genes as tandem inverted repeats was investigated as a means to abrogate the formation of mature Heterodera glycines (soybean cyst nematode) female cysts during its infection of Glycine max (soybean). A Gateway^®-compatible hm plant transformation system was developed specifically for these experiments in G. max. Three steps then were taken to identify H. glycines candidate genes. First, a pool of 150 highly conserved H. glycines homologs of genes having lethal mutant phenotypes or phenocopies from the free living nematode Caenorhabditis elegans were identified. Second, annotation of those 150 genes on the Affymetrix^® soybean GeneChip^® allowed for the identification of a subset of 131 genes whose expression could be monitored during the parasitic phase of the H. glycines life cycle. Third, a microarray analyses identified a core set of 32 genes with induced expression (>2.0-fold, log base 2) during the parasitic stages of infection. H. glycines homologs of small ribosomal protein 3a and 4 (Hg-rps-3a [accession number CB379877] and Hg-rps-4 [accession number CB278739]), synaptobrevin (Hg-snb-1 [accession number BF014436]) and a spliceosomal SR protein (Hg-spk-1 [accession number BI451523.1]) were tested for functionality in hm expression studies. Effects on H. glycines development were observed 8 days after infection. Experiments demonstrated that 81–93% fewer females developed on transgenic roots containing the genes engineered as tandem inverted repeats. The effect resembles RNA interference. The methodology has been used here as an alternative approach to engineer resistance to H. glycines.     

Herbivore- and MeJA-induced volatile emissions from the redroot pigweed <Emphasis Type="Italic">Amaranthus retroflexus</Emphasis> Linnaeus: their roles in attracting <Emphasis Type="Italic">Microplitis mediator</Emphasis> (Haliday) parasitoids

The redroot pigweed Amaranthus retroflexus Linnaeus (Caryophyllales: Amaranthaceae), an annual weed, is a host plant of the cotton bollworm Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae). Microplitis mediator (Haliday) (Hymenoptera: Braconidae) is a parasitoid of H. armigera. Here, the electrophysiological and behavioral responses of M. mediator to induced redroot pigweed volatiles were investigated. Female parasitoids were significantly attracted to odors from plants induced by H. armigera damage, H. armigera continuous feeding, and 10 mM methyl jasmonate (MeJA) spray. The gas chromatography–mass spectrometry (GC–MS) results demonstrated that there were significant changes in volatiles from these three treatments in comparison with the control. When the constitutive compound 6-methyl-5-hepten-2-one was emitted in significant amounts from treated plants, it could elicit a medium electrophysiological response (0.2?≤?value?<?0.8) , a significant behavioral response of M. mediator females. β-Elemene, emitted from two treatments (plants damaged by H. armigera, plants with H. armigera continuous feeding), showed a very weak electrophysiological response (value?<?0.2), but was significantly attractive to M. mediator. The results showed that 6-methyl-5-hepten-2-one and β-elemene might play important roles in mediating the foraging behavior of M. mediator. Further work will be conducted to evaluate the function of these two compounds under semi-field and field conditions and exploit them as attractants for M. mediator to control H. armigera.     

Pyramiding different aphid-resistance genes in elite soybean germplasm to combat dynamic aphid populations

The soybean aphid (Aphis glycines Matsumura), an invasive species, has posed a significant threat to soybean [Glycine max (L.) Merr.] production in North America since 2001. Use of resistant cultivars is an effective tactic to protect soybean yield. However, the variability and dynamics of aphid populations could limit the effectiveness of host-resistance gene(s). Gene pyramiding is a promising way to sustain host-plant resistance. The objectives of this study were to determine the prevalent aphid biotypes in Michigan and to assess the effectiveness of different combinations of aphid-resistance genes. A total of 11 soybean genotypes with known resistance gene(s) were used as indicator lines. Based on their responses, Biotype 3 was a major component of Michigan aphid populations during 2015–2016. The different performance of Rag-“Jackson” and Rag1-“Dowling” along with the breakdown of resistance in plant introductions (PIs) 567301B and 567324 may be explained by Biotype 3 or an unknown virulent biotype establishing in Michigan. With the assistance of flanking markers, 12 advanced breeding lines carrying different aphid-resistance gene(s) were developed and evaluated for effectiveness in five trials across 2015 to 2017. Lines with rag1c, Rag3d, Rag6, Rag3c?+?Rag6, rag1b?+?rag3, rag1c?+?rag4, rag1c?+?rag3?+?rag4, rag1c?+?Rag2?+?rag3?+?rag4, and rag1b?+?rag1c?+?rag3?+?rag4 demonstrated strong and consistent resistance. Due to the variability of virulent aphid populations, different combinations of Rag genes may perform differently across geographies. However, advanced breeding lines pyramided with three or four Rag genes likely will provide broader and more durable resistance to diverse and dynamic aphid populations.     

Next-generation sequencing to identify candidate genes and develop diagnostic markers for a novel Phytophthora resistance gene, <Emphasis Type="Italic">RpsHC18</Emphasis>, in soybean

Key message

A novel Phytophthora sojae resistance gene RpsHC18 was identified and finely mapped on soybean chromosome 3. Two NBS–LRR candidate genes were identified and two diagnostic markers of RpsHC18 were developed.

Abstract

Phytophthora root rot caused by Phytophthora sojae is a destructive disease of soybean. The most effective disease-control strategy is to deploy resistant cultivars carrying Phytophthora-resistant Rps genes. The soybean cultivar Huachun 18 has a broad and distinct resistance spectrum to 12 P. sojae isolates. Quantitative trait loci sequencing (QTL-seq), based on the whole-genome resequencing (WGRS) of two extreme resistant and susceptible phenotype bulks from an F_2:3 population, was performed, and one 767-kb genomic region with ΔSNP-index ≥ 0.9 on chromosome 3 was identified as the RpsHC18 candidate region in Huachun 18. The candidate region was reduced to a 146-kb region by fine mapping. Nonsynonymous SNP and haplotype analyses were carried out in the 146-kb region among ten soybean genotypes using WGRS. Four specific nonsynonymous SNPs were identified in two nucleotide-binding sites–leucine-rich repeat (NBS–LRR) genes, RpsHC18-NBL1 and RpsHC18-NBL2, which were considered to be the candidate genes. Finally, one specific SNP marker in each candidate gene was successfully developed using a tetra-primer ARMS-PCR assay, and the two markers were verified to be specific for RpsHC18 and to effectively distinguish other known Rps genes. In this study, we applied an integrated genomic-based strategy combining WGRS with traditional genetic mapping to identify RpsHC18 candidate genes and develop diagnostic markers. These results suggest that next-generation sequencing is a precise, rapid and cost-effective way to identify candidate genes and develop diagnostic markers, and it can accelerate Rps gene cloning and marker-assisted selection for breeding of P. sojae-resistant soybean cultivars.

     

Discovery of a seventh <Emphasis Type="Italic">Rpp</Emphasis> soybean rust resistance locus in soybean accession PI 605823

Key message

A novel Rpp gene from PI 605823 for resistance to Phakopsora pachyrhizi was mapped on chromosome 19.

Abstract

Soybean rust, caused by the obligate biotrophic fungal pathogen Phakopsora pachyrhizi Syd. & P. Syd, is a disease threat to soybean production in regions of the world with mild winters. Host plant resistance conditioned by resistance to P. pachyrhizi (Rpp) genes has been found in numerous soybean accessions, and at least 10 Rpp genes or alleles have been mapped to six genetic loci. Identifying additional disease-resistance genes will facilitate development of soybean cultivars with durable resistance. PI 605823, a plant introduction from Vietnam, was previously identified as resistant to US populations of P. pachyrhizi in greenhouse and field trials. In this study, bulked segregant analysis using an F₂ population derived from ‘Williams 82’ × PI 605823 identified a genomic region associated with resistance to P. pachyrhizi isolate GA12, which had been collected in the US State of Georgia in 2012. To further map the resistance locus, linkage mapping was carried out using single-nucleotide polymorphism markers and phenotypic data from greenhouse assays with an F_2:3 population derived from Williams 82 × PI 605823 and an F_4:5 population derived from ‘5601T’ × PI 605823. A novel resistance gene, Rpp7, was mapped to a 154-kb interval (Gm19: 39,462,291–39,616,643 Glyma.Wm82.a2) on chromosome 19 that is different from the genomic locations of any previously reported Rpp genes. This new gene could be incorporated into elite breeding lines to help provide more durable resistance to soybean rust.

     

Translationally controlled tumor protein GmTCTP interacts with GmCDPKSK5 in response to high temperature and humidity stress during soybean seed development

The developing seed of soybean is susceptible to high temperature and humidity (HTH) stress, resulting in pre-harvest seed deterioration in the field. Many genes are found to respond to the stress. Based on our previous proteomics study, an HTH-responsive gene, GmCDPKSK5, was isolated from soybean seed. GmCDPKSK5 encodes a cytoplasm- and membrane-associated protein, which belongs to Group I of the CDPK family. By yeast two-hybrid (Y2H) from soybean seed cDNA library, GmTCTP was screened as a GmCDPKSK5-interacting protein. The interaction between GmCDPKSK5 and GmTCTP was further verified using bimolecular fluorescence complementation and GST pull down assays. Expression levels of both GmCDPKSK5 and GmTCTP were induced by HTH stress in soybean seed. Our results indicated that GmCDPKSK5 and GmTCTP interact with each other and may function in responses to HTH stress in soybean developing seed.     

A novel alphabaculovirus isolated from the cotton bollworm, <Emphasis Type="Italic">Helicoverpa armigera</Emphasis> (Hubner) (Lepidoptera: Noctuidae): characterization and pathogenicity

The cotton bollworm, Helicoverpa armigera (Hubner) (Lepidoptera: Noctuidae) is a polyphagous pest that exist all over the world. It is also very destructive in Turkey on various agricultural products. In this study, we have detected an alphabaculovirus from Helicoverpa armigera larvae collected from cotton field. The virus isolate was named as Helicoverpa armigera nucleopolyhedrovirus (HearNPV-O1) based on morphological and molecular properties. This is the first record of baculovirus from H. armigera in Eurasia region. Scanning electron microscopy examinations of polyhedral inclusion bodies (PIBs) showed their irregular morphology with average diameter of 0.85 to 1.25 μm. Transmission electron microscopy studies revealed that the nucleocapsids were multiple enveloped and bacilliform shaped. The size of nucleocapsid was found as 279 nm with a width of 56 nm. Digestion of viral genome by PstI generated 8 fragments with total size of 130.9 kbp. According to the phylogenetic analysis of the partial polyhedrin (polh), late expression factor 8 (lef8) and late expression factor 9 (lef9) genes, HearNPV-O1 isolate is very close to H. armigera MNPV Indian isolate-443. Five different concentrations of HearNPV-O1 between 10³ and 10⁷ were used in dose-response test on neonate, 3rd and 5th instars larvae of H. armigera. The highest dose (10⁷) showed 92%, 88% and 57% mortality, respectively within 14 days. LC₅₀ values of HearNPV-O1 isolate were calculated as 6?×?10⁴, 7?×?10⁴ and 8?×?10⁶ PIBs/mL^?1 against neonate, 3rd and 5th instars larval stages, respectively. These results demonstrate that HearNPV-O1 isolate may be a potential biocontrol agent to be utilized against H. armigera.     

Cytochrome P<Subscript>450</Subscript>, CYP93A1, as defense marker in soybean

Cytochrome P₄₅₀, CYP93A1, is involved in the synthesis of the phytoalexin glyceollin in soybean (Glycine max L. Merr). The gene encoding CYP93A1 has been used as defense marker in soybean cell cultures, however, little is known regarding how this gene is expressed in the intact plant. To further understand the tissue-specific role of CYP93A1 in soybean defense, we analyzed the expression of this gene in mechanically damaged leaves and stems. In leaves, CYP93A1 was constitutively expressed; its expression did not change in response to mechanical damage. In stems, however, expression of CYP93A1 was induced as quickly as 4 h after mechanical damage and remained upregulated for at least 48 h. The induction of CYP93A1 was associated with the synthesis of glyceollins. In comparison to several other defense-related genes encoding cysteine protease inhibitors L1 and R1 and storage proteins vspA and vspB, CYP93A1 was the most strongly induced by stem wounding. The induction of CYP93A1 was observed only locally, not systemically. Similar stem expression patterns were consistently observed among three different soybean genotypes. The strong induction of CYP93A1 in mechanically damaged stems suggests an important role in the soybean stem defense response; therefore, this study expands the use of CYP93A1 as a defense response marker to stems, not just soybean cell cultures.     

Identification of <Emphasis Type="Italic">GmSALT3</Emphasis> haplotypes and development of molecular markers based on their diversity associated with salt tolerance in soybean

Soybean [Glycine max (L.) Merr.] is a major agricultural crop and generally known as a salt-sensitive crop. In a previous study, GmSALT3 was identified as a salt tolerance gene in soybean, and its nine haplotypes (H1 to H9) were reported in Chinese soybean accessions. In the present study, we aimed to identify new haplotypes of GmSALT3 in soybean accessions and to develop molecular markers for selection of salt-tolerant and -sensitive accessions. To do so, we examined genomic variations in the GmSALT3 coding region of 216 accessions of G. max and G. soja from Korea, China, and Japan. As a result, 40 different haplotypes, including three known haplotypes (H1, H2, and H5), were identified. Performing salt tolerance tests for the haplotypes, we were able to classify them into salt-tolerant (8) and salt-sensitive (32) categories. We also found that more variations in the haplotype composition of G. soja accessions exist than in that of G. max accessions. Quantitative expression analysis showed that almost all of the salt-tolerant haplotypes had much higher levels of GmSALT3 expression than the salt-sensitive haplotypes did. Finally, we developed molecular markers and applied them to screen salt tolerance of soybean accessions. The molecular markers performed well with an accuracy of 98.8% in identifying phenotypes of soybean accessions.     

Improved tolerance against <Emphasis Type="Italic">Helicoverpa armigera</Emphasis> in transgenic tomato over-expressing multi-domain proteinase inhibitor gene from <Emphasis Type="Italic">Capsicum annuum</Emphasis>

Plant proteinase inhibitors (PIs) are plant defense proteins and considered as potential candidates for engineering plant resistances against herbivores. Capsicum annuum proteinase inhibitor (CanPI7) is a multi-domain potato type II inhibitor (Pin-II) containing four inhibitory repeat domains (IRD), which target major classes of digestive enzymes in the gut of Helicoverpa armigera larvae. Stable integration and expression of the transgene in T1 transgenic generation, were confirmed by established molecular techniques. Protein extract of transgenic tomato lines showed increased inhibitory activity against H. armigera gut proteinases, supporting those domains of CanPI7 protein to be effective and active. When T1 generation plants were analyzed, they exhibited antibiosis effect against first instar larvae of H. armigera. Further, larvae fed on transgenic tomato leaves showed delayed growth relative to larvae fed on control plants, but did not change mortality rates significantly. Thus, better crop protection can be achieved in transgenic tomato by overexpression of multi-domain proteinase inhibitor CanPI7 gene against H. armigera larvae.     

Integration of sudden death syndrome resistance loci in the soybean genome

Key message

Complexity and inconsistencies in resistance mapping publications of soybean sudden death syndrome (SDS) result in interpretation difficulty. This review integrates SDS mapping literature and proposes a new nomenclature system for reproducible SDS resistance loci.

Abstract

Soybean resistance to sudden death syndrome (SDS) is composed of foliar resistance to phytotoxins and root resistance to pathogen invasion. There are more than 80 quantitative trait loci (QTL) and dozens of single nucleotide polymorphisms (SNPs) associated with soybean resistance to SDS. The validity of these QTL and SNPs is questionable because of the complexity in phenotyping methodologies, the disease synergism between SDS and soybean cyst nematode (SCN), the variability from the interactions between soybean genotypes and environments, and the inconsistencies in the QTL nomenclature. This review organizes SDS mapping results and proposes the Rfv (resistance to Fusarium virguliforme) nomenclature based on supporting criteria described in the text. Among ten reproducible loci receiving our Rfv nomenclature, Rfv18-01 is mostly supported by field studies and it co-localizes to the SCN resistance locus rhg1. The possibility that Rfv18-01 is a pleiotropic resistance locus and the concern about Rfv18-01 being confounded with Rhg1 is discussed. On the other hand, Rfv06-01, Rfv06-02, Rfv09-01, Rfv13-01, and Rfv16-01 were identified both by screening soybean leaves against phytotoxic culture filtrates and by evaluating SDS severity in fields. Future phenotyping using leaf- and root-specific resistance screening methodologies may improve the precision of SDS resistance, and advanced genetic studies may further clarify the interactions among soybean genotypes, F. virguliforme, SCN, and environments. The review provides a summary of the SDS resistance literature and proposes a framework for communicating SDS resistance loci for future research considering molecular interactions and genetic breeding for soybean SDS resistance.