The results show that FOLac populations in Spain are epidemiologically and biologically heterogeneous and highlight the need to integrate molecular tools and pathogenicity assays for race surveillance, breeding programs, and disease management.
Abstract
Fusarium wilt of lettuce, caused by Fusarium oxysporum forma specialis lactucae (FOLac), is an increasing constraint to lettuce production worldwide, particularly because changes in race structure and the emergence of isolates able to overcome host resistance can compromise cultivar-based management. However, information on FOLac race composition and pathogenic variation in Spain remains limited. This study characterized the race structure, molecular diversity, and pathogenic behavior of FOLac isolates collected in Spain between 2019 and 2025. A total of 81 isolates recovered from symptomatic lettuce tissues and soil samples from major lettuce-producing regions were analyzed. Race assignment was performed using race-specific PCR and detection of SIX effector genes, and phylogenetic relationships were inferred from concatenated tef-1α and rpb2 sequences. Pathogenicity assays were conducted with selected race 1 on differential lettuce cultivars to assess aggressiveness and resistance responses. Race 1 was predominant, representing 75.3% of the isolates, and showed broad geographic distribution and temporal persistence. Race 4 was less frequent, representing 9.9% of the isolates, but was detected in southeastern Spain, indicating localized occurrence in a major production area. The remaining 14.8% of the isolates, all recovered from soil samples, were not assigned to FOLac. Phylogenetic analysis separated isolates molecularly assigned to FOLac from non-assigned F. oxysporum isolates but did not resolve races 1 and 4 as distinct groups. Pathogenicity assays revealed variation in aggressiveness among race 1 isolates, including resistance-breaking behavior on `Costa Rica No. 4´ and `Palmos´. These results show that FOLac populations in Spain are epidemiologically and biologically heterogeneous and highlight the need to integrate molecular tools and pathogenicity assays for race surveillance, breeding programs, and disease management.
The results demonstrate that garlic-associated FOSC populations in Türkiye exhibit limited genetic differentiation despite considerable phenotypic variation in pathogenicity, and establishes a basis for future epidemiological, phylogenetic, and disease management studies.
Nedaa M. M. Tanina, O. Dedecan, C. Can et al.· Australasian Plant Pathology· 0 citations
Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a major constraint to wheat production in China. Although the disease occurs in Tibet every year under the favorable weather conditions, the virulence diversity and population structure of the Pst population in this region remain poorly understood. In this study, 312 Pst isolates collected in 2025 from five major wheat-growing regions of Tibet (Qamdo, Nyingchi, Lhasa, Shannan, and Shigatse) were characterized using virulence phenotyping and the Pst 5K genotyping-by-target-sequencing (GBTS) platform. Virulence testing on 19 Chinese differentials identified 139 races, including 88 previously reported and 51 novel races, with Su11-3, HY-009-1, and CYR34 being the predominant races. Testing the isolates with 18 Yr single-gene differentials identified 190 virulence phenotypes. None of the isolates were virulent to Yr5 or Yr15, whereas virulence frequencies to the remaining Yr genes ranged from 2.2% to 89.7%. Population genetic analyses using the GBTS data revealed clear regional differentiations. The Nyingchi population formed a distinct cluster with relatively low genomic diversity despite maintaining considerable virulence diversity, whereas the Lhasa and Shannan populations showed extensive admixture.The Qamdo and Shigatse populations consisted of unique genetic components and exhibited relatively high levels of virulence and genetic diversities. Combined virulence and genomic analyses indicated region-specific epidemiological characteristics and suggested that Qamdo may represent an important center of Pst diversification, whereas Lhasa and Shannan may facilitate pathogen dispersal and gene exchange. This study provides the first comprehensive assessment of Pst populations across Tibet and offers valuable information for disease surveillance, resistance breeding, and integrated management of wheat stripe rust in Tibet and neighboring wheat-growing regions.
Li Geng, Ying Li, He-Xin Chen et al.· Plant Disease· 0 citations
Fusarium oxysporum f. sp. cubense (Foc) is a soil-borne fungal pathogen responsible for fusarium wilt, which constitutes one of the major constraints in banana cultivation. Information on the occurrence and molecular characteristics of Foc in Malang Regency, one of the banana-producing areas in East Java, Indonesia, remains limited, hindering effective disease surveillance and management. This study was conducted to isolate and characterize fungal isolates associated with fusarium wilt disease in banana plants using an integrated approach combining morphological characterization, pathogenicity testing, PCR amplification, ITS sequence analysis, and phylogenetic analysis. Three fungal isolates were recovered from symptomatic banana plants collected in Donomulyo, Malang Regency, and one representative isolate (DNM) was selected for molecular characterization based on its morphological similarity to the other isolates. Morphological observations revealed characteristics typical of Fusarium oxysporum. ITS sequence analysis showed 100% query coverage and 100% sequence identity with reference Foc sequences available in GenBank, while phylogenetic analysis clustered the DNM isolate with reference Foc isolates with 94% bootstrap support. Pathogenicity assays demonstrated that the isolate induced typical fusarium wilt symptoms, resulting in an LDI of 16.39% at 14 DAI and an RDI of 41.67% at 45 DAI. These findings provide baseline information on putative Foc isolates in Malang Regency, particularly in the Donomulyo area, and establish an integrated characterization framework to support disease surveillance, early detection, and the development of integrated management strategies for fusarium wilt in banana production systems.
Akhmad Rizal Oktafian, Irisa Trianti, E. Yusnawan et al.· Agro Bali: Agricultural Jour...· 0 citations
Fusarium wilt of cotton, caused by Fusarium oxysporum f. sp. vasinfectum (Fov), remains a persistent threat to cotton production worldwide. Among the known races, Fov race 4 and its extra-virulent variants cause particularly severe losses in Upland cotton. Although several Fov genome assemblies have been assigned to races, the genomic diversity and evolutionary relationships among pathogenic and non-pathogenic isolates associated with cotton outbreaks remain poorly understood at the whole-genome level. This study addressed these gaps by generating and comparing high-quality genome assemblies of four Fusarium isolates collected from Texas cotton fields: two pathogenic (TX17-24 and TX18-9) and two non-pathogenic (TX17-6 and TX18-6). Draft assemblies were generated using Oxford Nanopore long reads and polished with Illumina reads. Comparative genomic analyses showed that pathogenic isolates possessed larger genomes and more conserved orthologous families, whereas non-pathogenic isolates contained more unique genes. Analyses of predicted secreted effectors, transposable elements, and carbohydrate-active enzymes further distinguished pathogenic and non-pathogenic lineages, suggesting roles in virulence adaptation and genome plasticity. Phylogenomic analyses using k-mer-based, assembly- and alignment-free methods incorporated all available long-read Fov genomes and revealed substantial genetic diversity within races 1 and 4, clustering isolates into multiple sublineages. These findings show that Fov race diversification is underestimated when based on traditional classification schemes and may be shaped by host specialization, geographic separation, or horizontal gene transfer. This work advances our understanding of the genomic diversity and evolutionary dynamics of Fov and establishes a foundation for improved race identification and characterization of Fusarium wilt pathogenesis in cotton.
Catherine Danmaigona Godsent-Ogbe, E. No, Lin Zhang et al.· Plant Disease· 0 citations
The current epidemic of banana Fusarium wilt is caused by Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4). Foc TR4 originates in Asia and was first reported in the early 1990s, whereafter it was restricted to five Asian countries and the Northern Territory of Australia for two decades. Since 2013, the fungus was detected in the Middle East, the Indian subcontinent, Africa and Latin America. Its recent spread may be caused by the expansion of Cavendish banana production and the movement of contaminated planting materials. Whole genome sequences of 119 Foc TR4 isolates were compared based on single nucleotide polymorphisms (SNPs) to assess the population structure, genetic diversity and relation among isolates from 20 countries to reveal the evolutionary origin and likely migration. Foc TR4 is a monophyletic lineage divided into four clusters. Two of the clusters included isolates mostly from eastern Indonesia and seem to be ancestral with many rare alleles and high genetic diversity supporting this region as centre of origin. The remaining clusters were less diverse and associated with pandemic expansion. Knowledge on Foc TR4 emergence and dispersal can be used to inform more effective biosecurity and management practice.
E. Wicker, M. Matthews, S. Ravel et al.· bioRxiv· 0 citations
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