Natural product (NP)-based pesticides have emerged as a compelling alternative to traditional chemical fungicides, attracting substantial attention within the agrochemical industry as the world is pushing toward sustainable and environmentally friendly approaches to safeguard crops. Microbes, both bacteria and fungi, are a huge source of diverse secondary metabolites with versatile applications across pharmaceuticals, agriculture, and the food industry. Microbial genome mining has been accelerated for pesticide/drug discovery and development in recent years, driven by advancements in genome sequencing, bioinformatics, metabolomics/metabologenomics, and synthetic biology. Here, we isolated and identified Pseudomonas vancouverensis that had shown antifungal activities against crop fungal pathogens Colletotrichum fragariae, Botrytis cinerea, and Phomopsis obscurans in a dual-plate culture and bioautography assay. Further, we sequenced the whole bacterial genome and mined the genome of this bacterium to identify secondary metabolite biosynthetic gene clusters (BGCs) using antiSMASH 7.0, PRISM 4, and BAGEL 4. An in-silico analysis suggests that P. vancouverensis possesses a rich repertoire of BGCs with the potential to produce diverse and novel NPs, including non-ribosomal peptides (NRPs), polyketides (PKs), acyl homoserine lactone, cyclodipeptide, bacteriocins, and ribosomally synthesized and post-transcriptionally modified peptides (RiPPs). Bovienimide-A, an NRP, and putidacin L1, a lectin-like bacteriocin, were among the previously known predicted metabolites produced by this bacterium, suggesting that the NPs produced by this bacterium could have biological activities and be novel as well. Future studies on the antifungal activity of these compounds will elucidate the full biotechnological potential of P. vancouverensis.

Stem rust, caused by the biotrophic fungal pathogen Puccinia graminis f. sp. tritici ( Pgt), is an important disease of wheat. However, the majority of Pgt virulence/avirulence loci and underlying genes remain uncharacterized due to the constraints of developing bi-parental populations with this obligate biotroph. Genome-wide association studies (GWAS) using a sexual Pgt population mainly collected from the Pacific Northwestern United States were used to identify candidate virulence/avirulence effector genes corresponding to the six wheat Sr genes: Sr5, Sr21, Sr8a, Sr17, Sr9a, and Sr9d. The Pgt isolates were genotyped using whole-genome shotgun sequencing that identified approximately 1.2 million single nucleotide polymorphisms (SNPs) and were phenotyped at the seedling stage on six Sr gene differential lines. Association mapping analyses identified 17 Pgt loci associated with virulence or avirulence phenotypes on six Pgt resistance genes. Among these loci, 16 interacted with a specific Sr gene, indicating Sr-gene specific interactions. However, one avirulence locus interacted with two separate Sr genes ( Sr9a and Sr17), suggesting two distinct Sr genes identifying a single avirulence effector. A total of 24 unique effector gene candidates were identified, and haplotype analysis suggests that within this population, AvrSr5, AvrSr21, AvrSr8a, AvrSr17, and AvrSr9a are dominant avirulence genes, while avrSr9d is a dominant virulence gene. The putative effector genes will be fundamental for future effector gene cloning efforts, allowing for further understanding of rust effector biology and the mechanisms underlying virulence evolution in Pgt with respect to race-specific R-genes. [ ] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

A diverse sexual population of wheat stem rust, Puccinia graminis f. sp. tritici, exists in the Pacific Northwest region of the United States because of the natural presence of Mahonia spp. that serves as alternate hosts to complete its sexual life cycle. The region appears to be a center of stem rust diversity in North America where novel virulence gene combinations can emerge that could overcome deployed barley and wheat stem rust resistances. A total of 100 single pustule isolates derived from stem rust samples collected from barley in Eastern Washington during the 2019 growing season were assayed for virulence on the two known effective barley stem rust resistance genes/loci, Rpg1 and the rpg4/5-mediated resistance locus (RMRL) at the seedling stage. Interestingly, 99% of the P. graminis f. sp. tritici isolates assayed were virulent on barley variety Morex carrying the Rpg1 gene, and 62% of the isolates were virulent on the variety Golden Promise transformant (H228.2c) that carries a single-copy insertion of the Rpg1 gene from Morex and is more resistant than Morex to many Rpg1 avirulent isolates. Also, 16% of the isolates were virulent on the near isogenic line HQ-1, which carries the RMRL introgression from the barley line Q21861 in the susceptible Harrington background. Alarmingly, 10% of the isolates were virulent on barley line Q21861, which contains both Rpg1 and RMRL. Thus, we report on the first P. graminis f. sp. tritici isolates worldwide with virulence on both Rpg1 and RMRL when stacked together, representing the most virulent P. graminis f. sp. tritici isolates reported on barley.

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a destructive disease of wheat worldwide. William Som (WS), an Argentinian spring wheat landrace, has consistently exhibited high-level resistance to stripe rust for over 20 years in our field evaluations in Washington state, USA. A previous study showed high-temperature adult-plant (HTAP) resistance in WS. To map the HTAP resistance quantitative trait loci (QTL) in WS, 114 F_5-8 recombinant inbred lines (RILs) from the cross AvS/WS were evaluated for their stripe rust response in seven field environments in Washington. The RILs and parents were genotyped with the Infinium 90K SNP chip. Four stable QTL, QYrWS.wgp-1BL on chromosome 1B (669–682 Mb), QyrWS.wgp-2AL on 2A (611–684 Mb), QyrWS.wgp-3AS on 3A (9–13 Mb), and QyrWS.wgp-3BL on 3B (476–535 Mb), were identified, and they explained 10.0–19.0%, 10.2–16.7%, 7.0–15.9%, and 12.0–27.8% of the phenotypic variation, respectively. The resistance in WS was found to be due to additive interactions of the four QTL. For each QTL, two Kompetitive allele-specific PCR (KASP) markers were developed, and these markers should facilitate the introgression of the HTAP resistance QTL into new wheat cultivars.

Wheat stem rust, caused by the obligate biotrophic fungal pathogen Puccinia graminis f. sp. tritici ( Pgt), is an important disease of barley and wheat worldwide. Alarmingly, the Pacific Northwest contains a highly virulent Pgt population on barley. This population includes the Pgt isolate Lsp21, which is virulent on the barley stem rust resistance genes Rpg1, Rpg2, Rpg3, rpg4, Rpg5, and rpg8. The virulence on barley lines containing Rpg1 and the rpg4/ Rpg5-mediated resistance locus, when stacked together, is a Pgt virulence profile on barley not previously reported. Thus, this population contains the most virulent Pgt isolates on barley resistance genes characterized worldwide. The Elliot line (PI 592261) was identified from the world barley core collection as containing effective seedling resistance to Pgt isolate Lsp21. To genetically characterize the resistance present in Elliot, 129 recombinant inbred lines were developed by advancing a population from the cross Elliot (resistant) × Palmer (susceptible) to the F₆ generation. The population was phenotyped with Pgt isolate Lsp21 at the seedling stage and genotyped with the Illumina 50K bead express single-nucleotide polymorphism chip, resulting in 7,284 high-quality single-nucleotide polymorphism markers. Two significant resistance quantitative trait loci (QTLs) (EP Rpg_4H-1 and EP Rpg_5H-1) contributed by Elliot were identified on chromosomes 4H and 5H, respectively. The major QTL, EP Rpg_4H-1, is novel, whereas EP Rpg_5H-1 localized to a region approximately 9 Mbp distal of the rpg4/ Rpg5-mediated resistance locus within a region of the barley genome that contains previously identified stem rust resistance loci. These QTLs should be useful in developing barley cultivars with resistance to the virulent Pacific Northwest Pgt population.