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Anaerobic soil disinfestation (ASD) is a novel, eco-friendly method to improve soil health. This method creates oxygen-free conditions by adding organic amendments as a carbon source, saturating the soil to field capacity, and then covering it with plastic. These anaerobic conditions reduce soilborne pathogens, enhance microbial diversity, and increase crop productivity. This review provides an overview of the different organic amendments used in ASD, their impact on managing soilborne pathogens, the role of beneficial microbiomes, and the challenges associated with adopting ASD. It also emphasizes the potential benefits of ASD and the innovative approach to advancing it for sustainable agriculture. [ABSTRACT FROM AUTHOR]

Septoria tritici blotch (STB), caused by Mycosphaerella graminicola (synonym: Zymoseptoria tritici; asexual stage: Septoria tritici), is an important disease of wheat worldwide. Management of the disease usually is by host resistance or fungicides. However, M. graminicola has developed insensitivity to most commonly applied fungicides so there is a continuing need for well-characterized sources of host resistance to accelerate the development of improved wheat cultivars. Gene Stb3 has been a useful source of major resistance, but its mapping location has not been well characterized. Based on linkage to a single marker, a previous study assigned Stb3 to a location on the short arm of chromosome 6D. However, the results from the present study show that this reported location is incorrect. Instead, linkage analysis revealed that Stb3 is located on the short arm of wheat chromosome 7A, completely linked to microsatellite (SSR) locus Xwmc83 and flanked by loci Xcfa2028 (12.4 cM distal) and Xbarc222 (2.1 cM proximal). Linkage between Stb3 and Xwmc83 was validated in BC1F3 progeny of other crosses, and analyses of the flanking markers with deletion stocks showed that the gene is located on 7AS between fraction lengths 0.73 and 0.83. This revised location of Stb3 is different from those for other STB resistance genes previously mapped in hexaploid wheat but is approximately 20 cM proximal to an STB resistance gene mapped on the short arm of chromosome 7Am in Triticum monococcum. The markers described in this study are useful for accelerating the deployment of Stb3 in wheat breeding programs.

Alternaria linariae is an economically important foliar pathogen that causes early blight disease in tomatoes. Understanding genetic diversity, population genetic structure, and evolutionary potential is crucial to contemplating effective disease management strategies. We leveraged genotyping-by-sequencing (GBS) technology to compare genome-wide variation in 124 isolates of Alternaria spp. (A. alternata, A. linariae, and A. solani) for comparative genome analysis and to test the hypotheses of genetic differentiation and linkage disequilibrium (LD) in A. linariae collected from tomatoes in western North Carolina. We performed a pangenome-aware variant calling and filtering with GBSapp and identified 53,238 variants conserved across the reference genomes of three Alternaria spp. The highest marker density was observed on chromosome 1 (7 Mb). Both discriminant analysis of principal components and Bayesian model-based STRUCTURE analysis of A. linariae isolates revealed three subpopulations with minimal admixture. The genetic differentiation coefficients (FST) within A. linariae subpopulations were similar and high (0.86), indicating that alleles in the subpopulations are fixed and the genetic structure is likely due to restricted recombination. Analysis of molecular variance indicated higher variation among populations (89%) than within the population (11%). We found long-range LD between pairs of loci in A. linariae, supporting the hypothesis of low recombination expected for a fungal pathogen with limited sexual reproduction. Our findings provide evidence of a high level of population genetic differentiation in A. linariae, which reinforces the importance of developing tomato varieties with broad-spectrum resistance to various isolates of A. linariae. [ABSTRACT FROM AUTHOR]

ABSTRACT Breeding wheat for resistance is the most effective means to control Septoria tritici blotch (STB), caused by the ascomycete Mycosphaerella graminicola (anamorph Septoria tritici). At least eight genes that confer resistance to STB in wheat have been identified. Among them, the Stb4 locus from the wheat cv. Tadinia showed resistance to M. graminicola at both seedling and adult-plant stages. However, no attempt has been made to map the Stb4 locus in the wheat genome. A mapping population of 77 F10 recombinant-inbred lines (RILs) derived from a three-way cross between the resistant cv. Tadinia and the susceptible parent (Yecora Rojo x UC554) was evaluated for disease resistance and molecular mapping. The RILs were tested with Argentina isolate I 89 of M. graminicola for one greenhouse season in Brazil during 1999, with an isolate from Brazil (IPBr1) for one field season in Piracicaba (Brazil) during 2000, and with Indiana tester isolate IN95-Lafayette-1196-WW-1-4 in the greenhouse during 2000 and 2001. The ratio of resistant:susceptible RILs was 1:1 in all three tests, confirming the single-gene model for control of resistance to STB in Tadinia. However, the patterns of resistance and susceptibility were different between the Indiana isolate and those from South America. For example, the ratio of RILs resistant to both the Indiana and Argentina isolates, resistant to one but susceptible to the other, and susceptible to both isolates was approximately 1:1:1:1, indicating that Tadinia may contain at least two genes for resistance to STB. A similar pattern was observed between the Indiana and Brazil isolates. The gene identified with the Indiana tester isolate was assumed to be the same as Stb4, whereas that revealed by the South American isolates may be new. Bulked-segregant analysis was used to identify amplified fragment length polymorphism (AFLP) and microsatellite markers linked to the presumed Stb4 gene. The AFLP marker EcoRI-ACTG/MseI-CAAA5 and microsatellite Xgwm111 were closely linked to the Stb4 locus in coupling at distances of 2.1 and 0.7 centimorgans (cM), respectively. A flanking marker, AFLP EAGG/ M-CAT10, was 4 cM from Stb4. The Stb4 gene was in a potential supercluster of resistance genes near the centromere on the short arm of wheat chromosome 7D that also contained Stb5 plus five previously identified genes for resistance to Russian wheat aphid. The microsatellite marker Xgwm111 identified in this study may be useful for facilitating the transfer of Stb4 into improved cultivars of wheat.

Early blight (EB), caused by Alternaria linariae (Neerg.) (syn. A. tomatophila) Simmons, is a disease that affects tomatoes (Solanum lycopersicum L.) throughout the world, with tremendous economic implications. The objective of the present study was to map the quantitative trait loci (QTL) associated with EB resistance in tomatoes. The F2 and F2:3 mapping populations consisting of 174 lines derived from NC 1CELBR (resistant) × Fla. 7775 (susceptible) were evaluated under natural conditions in the field in 2011 and in the greenhouse in 2015 by artificial inoculation. In all, 375 Kompetitive Allele Specific PCR (KASP) assays were used for genotyping parents and the F2 population. The broad-sense heritability estimate for phenotypic data was 28.3%, and 25.3% for 2011, and 2015 disease evaluations, respectively. QTL analysis revealed six QTLs associated with EB resistance on chromosomes 2, 8, and 11 (LOD 4.0 to 9.1), explaining phenotypic variation ranging from 3.8 to 21.0%. These results demonstrate that genetic control of EB resistance in NC 1CELBR is polygenic. This study may facilitate further fine mapping of the EB-resistant QTL and marker-assisted selection (MAS) to transfer EB resistance genes into elite tomato varieties, including broadening the genetic diversity of EB resistance in tomatoes. [ABSTRACT FROM AUTHOR]

Tan spot (caused by Pyrenophora triticirepentis) and Stagonospora nodorum blotch (SNB), (caused by Phaeosphaeria nodorum)are destructive diseases of wheat (Triticum aestivum L.). The majority of currently grown wheat varieties are susceptible to both diseases, presumably because of high pathogenic variability occurring in these fungi or narrow genetic background for resistance in wheat varieties. Therefore, identifying new sources of tan spot and SNB resistance in wheat is imperative. A subset of 825 wheat accessions from the core collection of the National Small Grains Collection (NSGC) of the United States Department of Agriculture, National Plant Germplasm System (NPGS) was evaluated for resistance to tan spot and SNB at seedling stage in a growth chamber. On the basis of disease reactions, 88 wheat accessions exhibited resistance to both diseases. Data from the Germplasm Resources Information Network (GRIN) were examined for the 88 accessions to identify those that also have resistance to other key diseases and on this basis 28 accessions with multiple resistances were identified. The genetic relationship among the 88 accessions was assessed using resistance gene analog polymorphism (RGAP) primers. Wheat accessions with similar growth habit were grouped together despite differences in country of origin. Associations between agronomic traits and host resistance indicated that winter wheat habit in the studied collection was strongly associated with both SNB and tan spot resistance. This study identified genetically diverse wheat accessions with broad-spectrum resistance that can be used in developing cultivars with high levels of resistance to multiple diseases in wheat breeding programs.

Septoria tritici blotch (STB) of wheat (Triticum aestivum L.), caused by the fungal pathogen Mycosphaerella graminicola (Fuckel) J. Schrot. in Cohn (anamorph: Septoria tritici Roberge in Desmaz.), occurs naturally in all wheat production areas around the world. Two genes for resistance to this disease, Stb2 and Stb3, have been identified in wheat germplasm and together confer resistance to the most prevalent strains of M. graminicola in Australia and the USA. However, so far neither gene has been mapped in the wheat genuine and their linkage relationships to other markers are not known. The objectives of this study were to identify molecular markers linked to the STB resistance genes Stb2 and Stb3 and to map these genes in the wheat genome. Genetic families of doubled-haploid populations segregating for Stb2 and Stb3 were evaluated in the greenhouse for STB reaction during the spring and fall seasons of 2002 and 2003. Genomic DNA isolated from each segregating population was analyzed with microsatellite or simple-sequence repeat (SSR) markers in bulked-segregant analysis to identify those that cosegregated with the STB phenotypas. Linkage analysis identified five SSR markers near the Stb2 gene on the distal region of the short arm of chromosome 3B. Loci Xgwm389 and Xgwm533.1 were approximately 1 cM distal to Stb2, which itself was 3.7 cM distal to Xgwm493. In addition to Stb2, this genomic region contains multiple genes conferring resistance to taxonomically diverse fungal pathogens of wheat, including a major quantitative trait locus for resistance to Fusarium head blight (caused by Fusarium graminearum Schwabe). The SSR marker Xgdm132 was linked to the Stb3 gene at a distance of approximately 3 cM on the short arm of chromosome 6D. The microsatellite markers identified in this study should facilitate marker-assisted selection and pyramiding of Stb2 and Stb3 with other STB resistance genes for more durably resistant wheat., SEPTORIA TRITICI BLOTCH, caused by the ascomycete fungus M. graminicola, is an economically important disease of wheat worldwide (Eyal et al., 1985). Yield losses as high as 60% have been [...]

Early blight (EB) and leaf blight are two destructive diseases of tomato in North Carolina (NC), caused by Alternaria linariae and A. altemata, respectively. During the last decade, EB caused by A. solani has increased in potato-producing areas in Wisconsin (WI). We collected 152 isolates of three Alternaria spp. associated with tomato and potato in NC and WI and used the gene genealogical approach to compare the genetic relationships among them. Two nuclear genes: the glyceraldehyde-3-phosphate dehydrogenase (GPDH), RNA polymerase second largest subunit (RPB2), and the rDNA internal transcribed spacer (ITS) region of these isolates were sequenced. Besides, sequences of the GPDH locus from international isolates described in previous studies were included for comparison purposes. A set of single nucleotide polymorphisms was assembled to identify locus-specific and species-specific haplotypes. Nucleotide diversity varied among gene sequences and species analyzed. For example, the estimates of nucleotide diversity and Watterson's theta were higher in A. altemata than in A. linariae and A. solani. There was little or no polymorphisms in the ITS sequences and thus restricted haplotype placement. The RPB2 sequences were less informative to detect haplotype diversity in A. linariae and A. solani, yet six haplotypes were detected in A. altemata. The GPDH sequences enabled strongly supported phylogenetic inferences with the highest haplotype diversity and belonged to five haplotypes (AaH1 to AaH5), which consisted of only A. altemata from NC. However, 13 haplotypes were identified within and among A. linariae and A. solani sequences. Among them, six (AsAlHI to AsAlH6) were identical to previously reported haplotypes in global samples and the remaining were new haplotypes. The most divergent haplotypes were AaHl, AsAlH2/ AsAlH3, and AsAlH4 and consisted exclusively of A. altemata, A. linariae, and A. solani, respectively. Neutrality tests suggested an excess of mutations and population expansion, and selection may play an important role in nucleotide diversity of Alternaria spp. [ABSTRACT FROM AUTHOR]

A trichothecene biosynthesis gene (TRI)-based PCR assay is employed to analyze a collection of 336 isolates from Gibberella zeae from barley, wheat, potatoes, and sugar beets and determine the toxigenic potential of G. zeae. The findings from the studies might be applied to monitor mycotoxin contamination and to formulate Fusarium head blight (FHB) management strategies for these crops.

Bacterial spot caused by Xanthomonas spp. is one of the most devastating diseases of tomato in North Carolina (NC). In total, 290 strains of Xanthomonas spp. from tomato in NC collected over 2 years (2015 and 2016) were analyzed for phenotypic and genetic diversity. In vitro copper and streptomycin sensitivity assays revealed that >95% (n = 290) of the strains were copper tolerant in both years, whereas 25% (n = 127) and 46% (n = 163) were streptomycin tolerant in 2016 and 2015, respectively. Using BOX repetitive element PCR assay, fingerprint patterns showed four haplotypes (HI, H2, H3, and H4) among the strains analyzed. The multiplex real-time quantitative PCR on a subset of representative strains (n = 45) targeting the highly conserved hrcN gene identified Xanthomonas strains from tomato in NC that belonged to X. perforans. Race profiling of the representative strains (n = 45) on tomato and pepper differentials confirmed that ~9 and 91% of strains are tomato races T3 and T4, respectively. Additionally, PCR assays and sequence alignments confirmed that the copL, copA, copB (copLAB copper tolerance gene cluster), and avrXv4 genes are present in the strains analyzed. Phylogenetic and comparative sequence analyses of six genomic regions (elongation factor G |fusA], glyceraldehyde-3-phosphate dehydrogenase A [gapA], citrate synthase [gltA], gyrase subunit B [gyrB], ABC transporter sugar permease [IcicF], and GTP binding protein [lepA]) suggested that 13 and 74% of X. perforans strains from NC were genetically similar to races T3 and T4 from Florida, respectively. Our results provide insights that bacterial spot management practices in tomato should focus on deploying resistance genes to combat emerging pathogenic races of X. perforans and overcome the challenges currently posed by intense use of copper-based bactericides. [ABSTRACT FROM AUTHOR]