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. 

/pdf/breeding-for-disease-resistance-in-soybean-a-global-2p2dtclq.pdf

Breeding for disease resistance in soybean: a global perspective

Genetic diversity is essential for crop breeding and one way to estimate it is through the concept of genetic base, which can be defined as the number of ancestors and their relative genetic contributions (RGC) to each cultivar. The RGC can be estimated through the coefficient of parentage between the ancestors and cultivars. Previous studies determined that the genetic base of Brazilian soybean was very narrow. The objective of this work was to evaluate the pedigree of 444 Brazilian soybean cultivars to estimate their genetic base. The cultivars were divided according to their release dates and according to their origin (public or private), and the genetic base for each group was also estimated. We found 60 ancestors, of which the top four (CNS, S-100, Roanoke and Tokyo, respectively) contribute 55.3% of the genetic base. Only 14 ancestors have an RGC over 1.0%, and they represent 92.4% of the genetic base. Analysis of the release dates indicated that there has been an increase in the number of ancestors over time, but the four main ancestors were the same over all periods, and their cumulative RGC increased from 46.6% to 57.6%, indicating a narrowing of the genetic base.

/pdf/the-genetic-base-of-brazilian-soybean-cultivars-evolution-p25dcnurtq.pdf

The genetic base of Brazilian soybean cultivars: evolution over time and breeding implications

Diseases of soybean caused by Cercospora spp. are endemic throughout the world’s soybean production regions. Species diversity in the genus Cercospora has been underestimated due to overdependence on morphological characteristics, symptoms, and host associations. Currently, only two species (Cercospora kikuchii and C. sojina) are recognized to infect soybean; C. kikuchii causes Cercospora leaf blight (CLB) and purple seed stain (PSS), whereas C. sojina causes frogeye leaf spot. To assess cryptic speciation among pathogens causing CLB and PSS, phylogenetic and phylogeographic analyses were performed with isolates from the top three soybean producing countries (USA, Brazil, and Argentina; collectively accounting for ~80% of global production). Eight nuclear genes and one mitochondrial gene were partially sequenced and analyzed. Additionally, amino acid substitutions conferring fungicide resistance were surveyed, and the production of cercosporin (a polyketide toxin produced by many Cercospora spp.) was assessed. From these analyses, the long-held assumption of C. kikuchii as the single causal agent of CLB and PSS was rejected experimentally. Four cercosporin-producing lineages were uncovered with origins (about 1 Mya) predicted to predate agriculture. Some of the Cercospora spp. newly associated with CLB and PSS appear to represent undescribed species; others were not previously reported to infect soybeans. Lineage 1, which contained the ex-type strain of C. kikuchii, was monophyletic and occurred in Argentina and Brazil. In contrast, lineages 2 and 3 were polyphyletic and contained wide-host range species complexes. Lineage 4 was monophyletic, thrived in Argentina and the USA, and included the generalist Cercospora cf. flagellaris. Interlineage recombination was detected, along with a high frequency of mutations linked to fungicide resistance in lineages 2 and 3. These findings point to cryptic Cercospora species as underappreciated global considerations for soybean production and phytosanitary vigilance, and urge a reassessment of host-specificity as a diagnostic tool for Cercospora.

/pdf/more-cercospora-species-infect-soybeans-across-the-americas-5ctovidwda.pdf

More Cercospora Species Infect Soybeans across the Americas than Meets the Eye.

Cercospora kikuchii has long been considered the causal agent of Cercospora leaf blight (CLB) and purple seed stain (PSS) on soybean, but a recent study found C. cf. flagellaris associated with CLB and PSS in Arkansas (United States) and Argentina. Here, we provide a broader perspective on the distribution of C. cf. flagellaris on soybean and alternate hosts within the United States (Arkansas, Louisiana, Mississippi, Missouri, and Kansas). We used a multilocus phylogenetic approach with data from actin, calmodulin, translation elongation factor 1-α, histone 3, the internal transcribed spacer region of rDNA and the mating-type locus to determine that two species, C. cf. flagellaris (200 of 205 isolates) and C. cf. sigesbeckiae (five of 205 isolates), are associated with CLB and PSS in the United States. In our phylogenetic analyses, species-level lineages were generally well-supported, though deeper-level evolutionary relationships remained unresolved, indicating that these genes do not possess sufficient phylogenetic signal to resolve the evolutionary history of Cercospora. We also investigated the potential for sexual reproduction in C. cf. flagellaris in Louisiana by determining the frequency of MAT1-1/MAT1-2 mating-type idiomorphs within the Louisiana population of C. cf. flagellaris. Though the MAT 1-2 idiomorph was significantly more common in our collection, the presence of both mating types suggests the potential for sexual reproduction exists.

https://apsjournals.apsnet.org/doi/pdf/10.1094/PHYTO-12-15-0332-R

Cercospora cf. flagellaris and Cercospora cf. sigesbeckiae Are Associated with Cercospora Leaf Blight and Purple Seed Stain on Soybean in North America

Defense-related gene expression in soybean leaves and seeds inoculated with Cercospora kikuchii and Diaporthe phaseolorum var. meridionalis

Purple seed stain (PSS) of soybean [Glycine max (L.) Merr.], caused by Cercospora kikuchii (T. Matsu. & Tomoyasu) Gardner, is favored by high moisture and warm temperatures during early pod development. PSS can significantly reduce seed and grain quality. Characterizing genetic resistance to PSS would be valuable in the development of resistant lines and varieties. PI 80837 has a high level of resistance to PSS and also good resistance to Phomopsis seed decay (PSD) caused primarily by Phomopsis longicolla Hobbs. Resistance to PSD in PI 80837 is conferred by a single dominant gene. The research reported here genetically characterizes PSS resistance in PI 80837 and examines if genes for PSS and PSD resistances are linked. Crosses were made between PI 80837 and ‘Agripro 350’ (AP 350) (susceptible to PSS and PSD), PI 91113 (susceptible to PSS and PSD), and line MO/PSD-0259 (susceptible to PSS but resistant to PSD). Populations and lines were grown in the field and C. kikuchii infection was assayed by plating seed. Cercospora seed infection of F1 plants from reciprocal crosses of AP 350 3 PI 80837 was not significantly different from that of PI 80837, indicating that resistance is under nuclear control. Segregation data from each of four F2 populations fit a single dominant gene model for resistance. Data from F2:3 lines of AP 350 3 PI 80837 and PI 80837 3 MO/PSD-0259 fit the model for a single dominant gene for PSS resistance. A linkage test for reaction to Cercospora and Phomopsis seed infection in F2:3 lines of AP 350 3 PI 80837 showed that the genes for PSS and PSD resistances in PI 80837 are not linked.

Inheritance of Resistance to Purple Seed Stain Caused by Cercospora kikuchii in PI 80837 Soybean

The suitability of adult male the navel orangeworm, Amyelois transitella (Walker) for Sterile Insect Technique (SIT) has been reported for both high energy gamma (>1 MeV) and low energy x-ray (90 keV) sterilization. However, research regarding sterilization of NOW larvae and pupae by gamma irradiation indicated nonsuitability due to high mortality. Here, NOW larvae and pupae were irradiated to doses up to 50 Gy with 90 keV x-rays, then paired with nonirradiated colony mates. Sterility of surviving insects was determined by the presence or absence of hatched neonates. While presence of offspring does not guarantee viability, the absence does guarantee sterility (as is appropriate for SIT) and was thus the measure used here. Early stage larvae experienced 77% mortality at a dose of 30 Gy, versus 20% for nonirradiated control. At 40 Gy, mortality reached 98%. Of surviving early stage larvae at 30 Gy, 29% of moth pairs produced offspring. For late stage larvae, no offspring were produced at 40 Gy, but mortality was 73%. For pupae, mortality reached 53% at 30 Gy with 13% still producing neonates, while mortality reached 98% at 40 Gy. These results are consistent with reported results for gamma irradiation of NOW larvae where sterility was observed somewhere between the 30 Gy and 60 Gy data points, but mortality was high. This further confirms the lack of suitability of NOW irradiated in the larval stage, whether by gamma or x-ray, and supports the hypothesis that x-ray and gamma treatments are biologically equivalent at equal doses.

X-Ray-Based Irradiation of Larvae and Pupae of the Navel Orangeworm (Lepidoptera: Pyralidae).

Building lab-scale x-ray tube based irradiators

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Inheritance of Resistance to Purple Seed Stain Caused by Cercospora kikuchii in PI 80837 Soybean

X-Ray-Based Irradiation of Larvae and Pupae of the Navel Orangeworm (Lepidoptera: Pyralidae).

Building lab-scale x-ray tube based irradiators