Potential of microsatellites to distinguish four races of Fusarium oxysporum f. sp. ciceri prevalent in India

Abstract

Fusarium oxysporum f. sp. ciceri, the causal agent of chickpea wilt, is an important fungal pathogen in India. Thirteen oligonucleotide probes complementary to microsatellite loci, in combination with 11 restriction enzymes, were used to assess the potential of such markers to study genetic variability in four Indian races of the pathogen. Hybridisation patterns, which were dependent upon both the restriction enzyme and oligonucleotide probe used, revealed the presence of different repeat motifs in the F. oxysporum f. sp. ciceri genome. Among the restriction enzymes used, hexa-cutting enzymes were more informative than tetra-and penta-cutting enzymes, whereas tetranucleotide and trinucleotide repeats yielded better hybridisation patterns than dinucleotide repeats. Dependent upon the levels of polymorphism detected, we have identified (AGT) 5 , (ATC) 5 and (GATA) 4 as the best fingerprinting probes for the F. oxysporum f. sp. ciceri races. The distribution of microsatellite repeats in the genome revealed races 1 and 4 to be closely related at a similarity index value of 76.6%, as compared to race 2 at a similarity value of 67.3%; race 3 was very distinct at a similarity value of 26.7%. Our study demonstrates the potential of oligonucleotide probes for fingerprinting and studying variability in the F. oxysporum f. sp. ciceri races and represents a step towards the identification of potential race diagnostic markers.

Current status of the taxonomic position of Fusarium oxysporum formae specialis cubense within the Fusarium oxysporum complex

“…Those that have been used to study F. oxysporum and Foc include DNA sequences (Fourie et al, 2009;O'Donnell et al, 1998), 12 restriction fragment length polymorphisms (RFLPs) (Koenig et al, 1997), random amplified polymorphic DNAs (RAPDs) (Alves-Santos et al, 1999;Bentley et al, 1994;Bentley et al, 1998), amplified fragment length polymorphisms (AFLPs) (Groenewald et al, 2006), and microsatellites or simple sequence repeats (SSRs) (Bogale et al, 2006;Brave et al, 2001).…”

“…Although they are generally expensive and time consuming to develop, significant time and cost reductions can be achieved with next generation sequencing technologies (Santana et al, 2009). Brave et al (2001) used a modified SSR technique to study F. oxysporum f. sp. ciceris isolates from India and were able to differentiate four races of the pathogen.…”

Fusarium wilt of chickpea: physiological specialization, genetics of resistance and resistance gene tagging

“…The Iranian isolates comprised at least three vegetative compatibility groups (VCGs) (Zamani et al 2004) whereas the four Indian races were phylogenetically distinct from each other (Sivaramakrishnan et al 2002;Chakrabarti et al 2001; Barve et al 2001). Indian populations of pathogen were also genetically as well as pathologically distinct from those in other countries as is evident from DNA Wngerprinting studies (Barve et al 2001) and conWnement of races 1A, 2, 3 and 4 (wilting pathotypes) to the India and 0 and 1B/C (yellowing pathotypes) to the Mediterranean region and California. Thus, atleast two diVerent populations of the pathogen exist worldwide, one native to India and another to other parts of the world.…”

Characterization of Novel Di-, Tri-, and Tetranucleotide Microsatellite Primers Suitable for Genotyping Various Plant Pathogenic Fungi with Special Emphasis on Fusaria and Mycospherella graminicola

“…ciceri races [14], Fusarium oxysporum f. sp. radicis-lycopersici , Fusarium graminearum [21], F. poae [22], Fusarium spp.…”