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

Soybean vein necrosis-associated virus has been linked to an emerging soybean disease in the United States and Canada. Virus distribution and population structure in major growing areas were evaluated. Data were employed to design and develop sensitive detection protocols, able to detect all virus isolates available in databases. The host range for the virus was assessed and several species were found to sustain virus replication, including ivyleaf morning glory, a common weed species in soybean-growing areas in the United States. Koch's postulates were fulfilled using soybean thrips and transmission efficiency was determined. This article provides significant insight into the biology of the most widespread soybean virus in the United States.

https://apsjournals.apsnet.org/doi/pdf/10.1094/PHYTO-12-12-0322-R

Epidemiology of soybean vein necrosis-associated virus.

Soybean vein necrosis virus (SVNV; genus Tospovirus; Family Bunyaviridae) is a negative-sense single-stranded RNA virus that has been detected across the United States and in Ontario, Canada. In 2013, a seed lot of a commercial soybean variety (Glycine max) with a high percentage of discolored, deformed and undersized seed was obtained. A random sample of this seed was planted in a growth room under standard conditions. Germination was greater than 90% and the resulting seedlings looked normal. Four composite samples of six plants each were tested by reverse transcription polymerase chain reaction (RT-PCR) using published primers complimentary to the S genomic segment of SVNV. Two composite leaflet samples retrieved from seedlings yielded amplicons with a size and sequence predictive of SVNV. Additional testing of twelve arbitrarily selected individual plants resulted in the identification of two SVNV positive plants. Experiments were repeated by growing seedlings from the same seed lot in an isolated room inside a thrips-proof cage to further eliminate any external source of infection. Also, increased care was taken to reduce any possible PCR contamination. Three positive plants out of forty-eight were found using these measures. Published and newly designed primers for the L and M RNAs of SVNV were also used to test the extracted RNA and strengthen the diagnosis of viral infection. In experiments, by three scientists, in two different labs all three genomic RNAs of SVNV were amplified in these plant materials. RNA-seq analysis was also conducted using RNA extracted from a composite seedling sample found to be SVNV-positive and a symptomatic sample collected from the field. This analysis revealed both sense and anti-sense reads from all three gene segments in both samples. We have shown that SVNV can be transmitted in seed to seedlings from an infected seed lot at a rate of 6%. To our knowledge this is the first report of seed-transmission of a Tospovirus.

/pdf/seed-transmission-of-soybean-vein-necrosis-virus-the-first-15nu09gz11.pdf

Seed Transmission of Soybean vein necrosis virus: The First Tospovirus Implicated in Seed Transmission

Tar spot of corn has been a major foliar disease in several Latin American countries since 1904 In 2015, tar spot was first documented in the United States and has led to significant yield losses of approximately 45 million t Tar spot is caused by an obligate pathogen, Phyllachora maydis, and thus requires a living host to grow and reproduce Due to its obligate nature, biological and epidemiological studies are limited and impact of disease in corn production has been understudied Here we present the current literature and gaps in knowledge of tar spot of corn in the Americas, its etiology, distribution, impact and known management strategies as a resource for understanding the pathosystem This will in tern guide current and future research and aid in the development of effective management strategies for this disease

Tar Spot: An Understudied Disease Threatening Corn Production in the Americas.

Tar spot is a fungal disease complex of corn that has been destructive and yield limiting in Central and South America for nearly 50 years Phyllachora maydis, the causal agent of tar spot, is an emerging corn pathogen in the United States, first reported in 2015 from major corn producing regions of the country The tar spot disease complex putatively includes Monographella maydis (syn Microdochium maydis), which increases disease damage through the development of necrotic halos surrounding tar spot lesions These necrotic halos, termed "fish-eye" symptoms, have been identified in the United States, though Monographella maydis has not yet been confirmed A recent surge in disease severity and loss of yield attributed to tar spot in the United States has led to increased attention and expanded efforts to understand the disease complex and how to manage it In this study, next-generation sequencing of the internal transcribed spacer-1 (ITS1) ribosomal DNA was used to identify fungal taxa that distinguish tar spot infections with or without fish-eye symptoms Fungal communities within tar spot only lesions were significantly different from communities having fish-eye symptoms Two low abundance OTUs were identified as Microdochium sp, however, neither were associated with fish-eye symptom development Interestingly, a single OTU was found to be significantly more abundant in fish-eye lesions compared to tar spot lesions and had a 91% ITS1 identity to Neottiosporina paspali In addition, the occurrence of this OTU was positively associated with Phyllachora maydis fish-eye symptom networks, but not in tar spot symptom networks Neottiosporina paspali has been reported to cause necrotic lesions on various monocot grasses Whether the related fungus we detected is part of the tar-spot complex of corn and responsible for fish-eye lesions remains to be tested Alternatively, many OTUs identified as Phyllachora maydis, suggesting that different isolate genotypes may be capable of causing both tar spot and fish-eye symptoms, independent of other fungi We conclude that Monographella maydis is not required for fish-eye symptoms in tar spot of corn

/pdf/identification-of-fungal-communities-within-the-tar-spot-38tyvdg77y.pdf

Identification of Fungal Communities Within the Tar Spot Complex of Corn in Michigan via Next-Generation Sequencing.

Leaf lesions typical of those reported for tar spot of corn caused by Phyllachora maydis Maubl. were observed in commercial corn hybrids (Zea mays L.). In 2016, symptoms were observed in Jones County, IA, Palm Beach County, FL, Allegan County, MI, and in Green and Iowa counties, WI. In 2017, symptoms were observed again in Allegan County, MI, and in Grant and Lafayette counties, WI. Leaf signs and symptoms included ascomata, often surrounded by a narrow necrotic halo, on both healthy and senescent leaf material. Disease severity and incidence varied by location. Some fields had few infected plants (<1%), with some infected leaves only exhibiting a single ascoma, whereas in 2017 one field in Michigan had up to 90% infected plants with up to 80% disease severity on individual leaves. Morphological characteristics of the pathogen from all examined leaves from all locations were similar and consistent with the description of P. maydis (Parbery 1967). Ascomata, single or grouped with a clypeus, contained numerous paraphyses, with cylindrical asci containing hyaline, ellipsoid, aseptate ascospores 5.5 to 8 × 9.5 to 14 µm (n = 30). DNA was extracted from ascomata aseptically removed from leaves collected in each state. Voucher samples from each state were deposited in the U.S. National Fungus Collections (BPI). The internal transcribed spacer (ITS) regions of the ribosomal RNA gene were sequenced using primer pair ITS1F/ITS4A (Larena et al. 1999) for Iowa and Michigan samples and ITS4/ITS5 for Wisconsin (White et al. 1990). Sequences from Iowa, Michigan, and Wisconsin were identical and showed a 97% sequence homology to GenBank deposit accession KU184459.1, with a 90% query cover. A representative sequence from each state was deposited: Iowa (BPI 910561) GenBank MG881848, Michigan (BPI 910562) GenBank MG881847, and Wisconsin (BPI 910560) GenBank MG881846. Sequences were not obtained from the Florida sample (BPI 910568). Koch’s postulates were not performed given the obligate nature of the pathogen (Muller and Samuels 1984). This report documents the first confirmation of tar spot on corn in Iowa, Michigan, and Wisconsin (three states surrounding Indiana and Illinois, where it was first reported in 2015; Ruhl et al. 2016) and Florida. It has been reported in Central and South America that when coinfection of P. maydis and Monographella maydis occurs there can be significant yield loss. However, M. maydis has not yet been documented within the United States. There may currently be no significant losses in grain production; however, this disease could potentially affect silage corn production for which early dry-down is not desired, and it may increase lodging.

First Report of Tar Spot on Corn (Zea mays) Caused by Phyllachora maydis in Florida, Iowa, Michigan, and Wisconsin

Several viral diseases of soybean (Glycine max) have been identified in the north-central U.S. soybean production area, which includes Wisconsin and Iowa (2). Previously, Soybean vein necrosis disease (SVND) caused by Soybean vein necrosis-associated virus was reported in Arkansas, Tennessee, and other southern states (4). In September 2012, soybean plants with symptoms similar to those reported for SVND (4) were observed in fields across Wisconsin and Iowa. Symptoms included leaf-vein and leaf chlorosis, followed by necrosis of the leaf veins and eventually necrosis of the entire leaf. Six samples with symptoms indicative of SVNaV were collected from research plots located at the West Madison Agricultural Research Station located in Madison, WI. An additional three samples were collected from three locations in central Iowa. Total RNA extracted from each sample using the Trizol Plus RNA purification kit (Invitrogen, Carlsbad, CA) was used to generate complementary DNA (cDNA) using the iScript cDNA synthe...

https://lib.dr.iastate.edu/cgi/viewcontent.cgi?article=1076&context=plantpath_pubs

First Report of Soybean Vein Necrosis Disease Caused by Soybean vein necrosis-associated virus in Wisconsin and Iowa

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First Report of Tar Spot on Corn (Zea mays) Caused by Phyllachora maydis in Florida, Iowa, Michigan, and Wisconsin

First Report of Soybean Vein Necrosis Disease Caused by Soybean vein necrosis-associated virus in Wisconsin and Iowa