Identification and Characterization of Fusarium nirenbergiae Associated with Saffron Corm Rot Disease

Abstract

Saffron (Crocus sativus L.) is the most expensive spice plant and is distributed widely around the world. However, its production is limited by corm rot, a disastrous disease, attributed to Fusarium oxysporum in many regions of the world. In 2020, extensive surveys were carried out in Zhejiang, Shanghai, Anhui, and Guizhou provinces as saffron growing areas of China. Fourteen single-spore isolates were obtained from rotted corms and identified as F. nirenbergiae according to morphological appearance and multilocus phylogenetic analysis with translation elongation factor 1-α (tef1), DNA-directed RNA polymerase II largest subunit (rpb2), and β-tubulin (tub2). Results of the pathogenicity assay supported the conclusion that F. nirenbergiae is the pathogen responsible for corm rot. In this study, we obtained the whole genome sequence of two highly virulent F. nirenbergiae strains via the Illumina HiSeq platform. Genome sequence assemblies of approximately 52.7 and 52.2 Mb were generated for isolates WY5 and SH1, respectively. To the best of our knowledge, this is the first report of F. nirenbergiae causing C. sativus corm rot in China and indeed worldwide. Results from this research contribute to our understanding of genetic diversity, genomic information, and host determination, which will enable researchers to design appropriate management measures for this hazardous disease.

Molecular and Pathogenic Characterization of Fusarium Species Associated with Corm Rot Disease in Saffron from China

“…The isolation frequency of F. nirenbergiae (58.2%) was greater than F. commune (26.8%), and F. annulatum (14.9%). The ability of F. nirenbergiae to cause corm rot has been previously established [ 10 ], and was therefore not further examined in the current study. Here, we focused on thirteen representative isolates of F. annulatum , and F. commune , chosen based on geographical regions and identified using sequences of tef1 and ITS (internal transcribed spacer).…”

“…Fusarium species are among the most severe pathogens that affect a broad range of crops worldwide. We previously established that F. nirenbergiae is a causative agent of corm rot on saffron [ 10 ]. In the current study, we isolated and identified two further species from saffron growing regions, namely Fusarium annulatum and F. commune , based on morphological criteria and multilocus (two-gene) phylogenetic analyses.…”

“…The genomic DNA of thirteen representative isolates was extracted using a Plant Genomic DNA kit (Tiangen, China) according to the company’s protocols. Portions of nuclear translation elongation factor 1-alpha ( tef1 ), second largest subunit of RNA polymerase II gene ( rpb2 ), and internal transcribed spacer ( ITS ) genes were amplified from the thirteen representative isolates using the primers EF-1/EF-2, RPB2-5f2/RPB2-7cr, and ITS1/ITS4, respectively [ 10 , 11 ]. Polymerase chain reaction (PCR) was conducted with 1 μL forward primer (10 μM), 1 μL reverse primer (10 μM), 0.5 μL DNTPs (10 mM), 12.5 μL of 2× Rapid Taq Master Mix (Vazyme, Nanjing, China), 1 µL of genomic DNA, and 9.5 μL of DNase-free water.…”

“…Growth of a saffron crop is hampered by biotic agents, such as insects, fungi, viruses, and bacteria. Various pathogens affect corm, including Aspergillus niger , A. terreus , A. flavus , A. flavipes , Bacillus croci , Burkholderia gladioli , Fusarium spp., Macrophomina phaseolina , Mucor sp., Penicillium solitum , P. cyclopium , P. corymbiferum , Phoma crocophila , Pythium spp., Rhizoctonia crocorum , R. violacea , Rhizopus nigricans , Sclerotium rolfsii , Stromatinia gladioli , and Uromyces croci [ 6 , 7 , 8 , 9 , 10 ]. Among them, Fusarium corm rot is one of the most destructive belowground fungal diseases in saffron that causes significant economic losses.…”

“…Previous investigators have reported that corm rot is caused by various F. oxysporum formae speciales such, as gladioli , iridiacearum , and saffrani [ 7 , 8 , 9 ]. Recently, Mirghasempour et al [ 10 ] identified F. nirenbergiae as the predominant agent of corm rot in China.…”