Breeding for disease resistance in soybean: a global perspective

KEY MESSAGE

This review provides a comprehensive atlas of QTLs, genes, and alleles conferring resistance to 28 important diseases in all major soybean production regions in the world. Breeding disease-resistant soybean [Glycine max (L.) Merr.] varieties is a common goal for soybean breeding programs to ensure the sustainability and growth of soybean production worldwide. However, due to global climate change, soybean breeders are facing strong challenges to defeat diseases. Marker-assisted selection and genomic selection have been demonstrated to be successful methods in quickly integrating vertical resistance or horizontal resistance into improved soybean varieties, where vertical resistance refers to R genes and major effect QTLs, and horizontal resistance is a combination of major and minor effect genes or QTLs. This review summarized more than 800 resistant loci/alleles and their tightly linked markers for 28 soybean diseases worldwide, caused by nematodes, oomycetes, fungi, bacteria, and viruses. The major breakthroughs in the discovery of disease resistance gene atlas of soybean were also emphasized which include: (1) identification and characterization of vertical resistance genes reside rhg1 and Rhg4 for soybean cyst nematode, and exploration of the underlying regulation mechanisms through copy number variation and (2) map-based cloning and characterization of Rps11 conferring resistance to 80% isolates of Phytophthora sojae across the USA. In this review, we also highlight the validated QTLs in overlapping genomic regions from at least two studies and applied a consistent naming nomenclature for these QTLs. Our review provides a comprehensive summary of important resistant genes/QTLs and can be used as a toolbox for soybean improvement. Finally, the summarized genetic knowledge sheds light on future directions of accelerated soybean breeding and translational genomics studies.

Ecology and diversity of culturable fungal species associated with soybean seedling diseases in the Midwestern United States

AIMS

To isolate and characterize fungi associated with diseased soybean seedlings in Midwestern soybean production fields and to determine the influence of environmental and edaphic factors on their incidence.

METHODS AND RESULTS

Seedlings were collected from fields with seedling disease history in 2012 and 2013 for fungal isolation. Environmental and edaphic data associated with each field was collected. 3036 fungal isolates were obtained and assigned to 76 species. The most abundant genera recovered were Fusarium (73%) and Trichoderma (11.2%). Other genera included Mortierella, Clonostachys, Rhizoctonia, Alternaria, Mucor, Phoma, Macrophomina and Phomopsis. Most recovered species are known soybean pathogens. However, non-pathogenic organisms were also isolated. Crop history, soil density, water source, precipitation and temperature were the main factors influencing the abundance of fungal species.

CONCLUSION

Key fungal species associated with soybean seedling diseases occurring in several US production regions were characterized. This work also identified major environment and edaphic factors affecting the abundance and occurrence of these species.

SIGNIFICANCE AND IMPACT OF THE STUDY

The identification and characterization of the main pathogens associated with seedling diseases across major soybean-producing areas could help manage those pathogens, and devise more effective and sustainable practices to reduce the damage they cause.

Evaluation of Commercial Soybean Cultivars for Reaction to Phomopsis Seed Decay

Phomopsis seed decay (PSD), caused by Phomopsis longicolla (syn. Diaporthe longicolla), is an economically important soybean disease causing poor seed quality. Planting resistant cultivars is one of the most effective means to control PSD. In this study, 16 commercially available maturity groups IV and V soybean cultivars, including two previously identified PSD-resistant and two PSD-susceptible checks, were evaluated for seed infection by P. longicolla in inoculated and noninoculated plots, and harvested promptly or with a 2-week delay in harvest. The test was conducted at Stoneville, Mississippi, in 2012 and 2013. Seed infection by P. longicolla ranged from 0.5 to 76%, and seed germination ranged from 18 to 97%. One MG IV cultivar (Morsoy R2 491) and five MG V cultivars (Progeny 5650, Progeny 5706, Asgrow 5606, Asgrow 5831, and Dyna-Gro33C59) had significantly (P ≤ 0.05) lower percent seed infected by P. longicolla than their respective susceptible checks and other cultivars in the same tests. Information obtained from this study will be useful for soybean growers and breeders for selection of cultivars for planting or breeding and future genetic studies in the development of cultivars with improved resistance to PSD.

Evaluation of Diverse Soybean Germplasm for Resistance to Phomopsis Seed Decay

Phomopsis seed decay (PSD), caused primarily by the fungal pathogen Phomopsis longicolla, is one of the most important diseases reducing seed quality and yield of soybean. Few cultivars have been identified as resistant. To identify new sources of resistance to PSD, 135 soybean germplasm accessions, originating from 28 countries, were field screened in Arkansas, Mississippi, and Missouri in 2009. Based on seed assays of natural field infection by P. longicolla in 2009, 42 lines, including the most resistant and susceptible lines, were reevaluated in the field in 2010, 2011, and 2012 with P. longicolla-inoculated and noninoculated treatments. Six maturity group (MG) III (PI 189891, PI 398697, PI 417361, PI 504481, PI 504488, and PI 88490), four MG IV (PI 158765, PI 235335, PI 346308, and PI 416779), and five MG V (PI 381659, PI 381668, PI 407749, PI 417567, and PI 476920) lines had significantly lower percent seed infection by P. longicolla than the susceptible checks and other lines in the same test (P ≤ 0.05). They appeared to have some levels of resistance to PSD. These new sources of PSD resistance can be used in developing soybean breeding lines or cultivars with resistance to PSD, and for genetic mapping of PSD resistance genes.

Screening a Diverse Soybean Germplasm Collection for Reaction to Purple Seed Stain Caused by Cercospora kikuchii

Purple seed stain (PSS), caused by Cercospora kikuchii, is a prevalent soybean disease that causes latent seed infection, seed decay, purple seed discoloration, and overall quality deterioration. The objective of this research was to screen soybean accessions from the United States Department of Agriculture germplasm collection for resistance to PSS. In total, 123 plant introductions (PI) from 28 different countries, representing maturity groups (MG) III, IV, and V, were screened. Incidence of Cercospora leaf blight (% CLB), visual PSS (% PSS), and seed infected by C. kikuchii (% C. kikuchii) in harvested seed were determined. In 2007, % C. kikuchii was 2 to 51% for MG III, 2 to 35% for MG IV, and 0 to 33% for MG V. In 2008, % C. kikuchii was 0 to 45% for MG III, 1 to 71% for MG IV, and 0 to 15% for MG V. In total, four and ten PI from MG III and IV, respectively, were identified as resistant to PSS in both years. Highly positive correlations were found for inoculated versus noninoculated treatments and for % PSS versus % C. kikuchii infection. The PSS-resistant PI identified in this study will be valuable to breeders in developing resistant cultivars.

A Coordinated Effort to Manage Soybean Rust in North America: A Success Story in Soybean Disease Monitoring

Existing crop monitoring programs determine the incidence and distribution of plant diseases and pathogens and assess the damage caused within a crop production region. These programs have traditionally used observed or predicted disease and pathogen data and environmental information to prescribe management practices that minimize crop loss. Monitoring programs are especially important for crops with broad geographic distribution or for diseases that can cause rapid and great economic losses. Successful monitoring programs have been developed for several plant diseases, including downy mildew of cucurbits, Fusarium head blight of wheat, potato late blight, and rusts of cereal crops. A recent example of a successful disease-monitoring program for an economically important crop is the soybean rust (SBR) monitoring effort within North America. SBR, caused by the fungus Phakopsora pachyrhizi, was first identified in the continental United States in November 2004. SBR causes moderate to severe yield losses globally. The fungus produces foliar lesions on soybean (Glycine max) and other legume hosts. P. pachyrhizi diverts nutrients from the host to its own growth and reproduction. The lesions also reduce photosynthetic area. Uredinia rupture the host epidermis and diminish stomatal regulation of transpiration to cause tissue desiccation and premature defoliation. Severe soybean yield losses can occur if plants defoliate during the mid-reproductive growth stages. The rapid response to the threat of SBR in North America resulted in an unprecedented amount of information dissemination and the development of a real-time, publicly available monitoring and prediction system known as the Soybean Rust-Pest Information Platform for Extension and Education (SBR-PIPE). The objectives of this article are (i) to highlight the successful response effort to SBR in North America, and (ii) to introduce researchers to the quantity and type of data generated by SBR-PIPE. Data from this system may now be used to answer questions about the biology, ecology, and epidemiology of an important pathogen and disease of soybean.

Effect of Lactofen, Azoxystrobin, and Genotypes on Charcoal Rot, Phomopsis Seed Decay, and Pod and Stem Blight in Soybean

Yield-limiting diseases such as charcoal rot and Phomopsis seed decay have a significant impact on the economic potential for soybean because there are few methods for management of these diseases. The objectives of this study were to determine the development of charcoal rot, infection of seed by Phomopsis spp., and severity of pod and stem blight on Asgrow 4403, Delta Pine 5806, United States Department of Agriculture-introduced DT 97-4290 and plant introduction (PI) number PI 567562A, and Asgrow 4403 treated and not treated with lactofen or azoxystrobin. This is the first report of high levels of resistance in PI 567562A to charcoal rot, and resistance in this PI was greater than for DT 97-4290. Application of lactofen at growth stage R1 and azoxystrobin at either planting, R3, or R6 had no significant impact on severity of charcoal rot, percentage of harvested seed infected by Phomopsis spp., or severity of pod and stem blight on genotype Asgrow 4403. Of four genotypes evaluated, none were resistant to infection by Phomopsis spp. The genotypes Asgrow 4403, DP 5806, and DT 97-4290 were susceptible to pod and stem blight and PI 567562A was resistant.