Novel Mutations Detected in Avirulence Genes Overcoming Tomato Cf Resistance Genes in Isolates of a Japanese Population of Cladosporium fulvum

Abstract

Leaf mold of tomato is caused by the biotrophic fungus Cladosporium fulvum which complies with the gene-for-gene system. The disease was first reported in Japan in the 1920s and has since been frequently observed. Initially only race 0 isolates were reported, but since the consecutive introduction of resistance genes Cf-2, Cf-4, Cf-5 and Cf-9 new races have evolved. Here we first determined the virulence spectrum of 133 C. fulvum isolates collected from 22 prefectures in Japan, and subsequently sequenced the avirulence (Avr) genes Avr2, Avr4, Avr4E, Avr5 and Avr9 to determine the molecular basis of overcoming Cf genes. Twelve races of C. fulvum with a different virulence spectrum were identified, of which races 9, 2.9, 4.9, 4.5.9 and 4.9.11 occur only in Japan. The Avr genes in many of these races contain unique mutations not observed in races identified elsewhere in the world including (i) frameshift mutations and (ii) transposon insertions in Avr2, (iii) point mutations in Avr4 and Avr4E, and (iv) deletions of Avr4E, Avr5 and Avr9. New races have developed by selection pressure imposed by consecutive introductions of Cf-2, Cf-4, Cf-5 and Cf-9 genes in commercially grown tomato cultivars. Our study shows that molecular variations to adapt to different Cf genes in an isolated C. fulvum population in Japan are novel but overall follow similar patterns as those observed in populations from other parts of the world. Implications for breeding of more durable C. fulvum resistant varieties are discussed.

Specific Hypersensitive Response–Associated Recognition of New Apoplastic Effectors from Cladosporium fulvum in Wild Tomato

“…This reemergence is due to the intensive year-round cultivation of resistant tomato cultivars, which have selected for natural strains of this fungus, capable of overcoming, for example, one or more of all cloned Cf immune receptor genes (Hubbeling 1978;Iida et al 2015;Laterrot 1986;Li et al 2015). To combat these strains, new Cf immune receptor genes need to be identified.…”

“…Based on this knowledge, Cf immune receptor genes were introgressed from wild Solanum species and landraces into cultivated tomato by breeders over several decades (Kerr and Bailey 1964). While largely effective, intensive year-round cultivation of these plants has led to the emergence of natural C. fulvum strains capable of overcoming one or more of all cloned Cf immune receptor genes (Hubbeling 1978;Iida et al 2015;Laterrot 1986;Li et al 2015). Several types of sequence modification have been shown to occur in Avr effector genes that permit the evasion of Cf immune receptor gene-mediated resistance by C. fulvum.…”

Evaluation of the potential biocontrol activity of Dicyma pulvinata against Cladosporium fulvum, the causal agent of tomato leaf mould

“…Although single resistance genes ( Cf‐2 , Cf‐4 , Cf‐5 and Cf‐9 ) have been introduced into many tomato cultivars, over‐reliance on resistant cultivars enhances physiological race differentiation and thus the complexity of the race composition. Selection pressure imposed by Cf resistance genes leads to the evolution of new C. fulvum races that overcome the activities of the products of the introduced Cf genes (Westerink et al ., ; Stergiopoulos et al ., ; Iida et al ., ).…”

“…The 12 races of C. fulvum that occur in Japan have overcome all commercial resistant cultivars (Iida et al ., , ; Kubota et al ., ). Consequently, leaf mould of tomato has become a severe problem for greenhouse production.…”

The Evolution of Orphan Regions in Genomes of a Fungal Pathogen of Wheat

“…Hence, pathogens expressing detected effectors (i.e., avirulence effectors) suffer a strong fitness penalty in host populations expressing the corresponding receptor. In turn, pathogen populations can rapidly escape host recognition through selection favoring mutations that enable effectors to escape recognition or selection favoring effector gene deletion (10, 11). …”