Development of DArT markers and assessment of diversity in Fusarium oxysporum f. sp. ciceris, wilt pathogen of chickpea (Cicer arietinum L.)

Abstract

BackgroundFusarium oxysporum f. sp. ciceris (Foc), the causal agent of Fusarium wilt of chickpea is highly variable and frequent recurrence of virulent forms have affected chickpea production and exhausted valuable genetic resources. The severity and yield losses of Fusarium wilt differ from place to place owing to existence of physiological races among isolates. Diversity study of fungal population associated with a disease plays a major role in understanding and devising better disease control strategies. The advantages of using molecular markers to understand the distribution of genetic diversity in Foc populations is well understood. The recent development of Diversity Arrays Technology (DArT) offers new possibilities to study the diversity in pathogen population. In this study, we developed DArT markers for Foc population, analysed the genetic diversity existing within and among Foc isolates, compared the genotypic and phenotypic diversity and infer the race scenario of Foc in India.ResultsWe report the successful development of DArT markers for Foc and their utility in genotyping of Foc collections representing five chickpea growing agro-ecological zones of India. The DArT arrays revealed a total 1,813 polymorphic markers with an average genotyping call rate of 91.16% and a scoring reproducibility of 100%. Cluster analysis, principal coordinate analysis and population structure indicated that the different isolates of Foc were partially classified based on geographical source. Diversity in Foc population was compared with the phenotypic variability and it was found that DArT markers were able to group the isolates consistent with its virulence group. A number of race-specific unique and rare alleles were also detected.ConclusionThe present study generated significant information in terms of pathogenic and genetic diversity of Foc which could be used further for development and deployment of region-specific resistant cultivars of chickpea. The DArT markers were proved to be a powerful diagnostic tool to study the genotypic diversity in Foc. The high number of DArT markers allowed a greater resolution of genetic differences among isolates and enabled us to examine the extent of diversity in the Foc population present in India, as well as provided support to know the changing race scenario in Foc population.Electronic supplementary materialThe online version of this article (doi: 10.1186/1471-2164-15-454) contains supplementary material, which is available to authorized users.

Fusarium wilt of chickpeas: Biology, ecology and management

“…ciceris included few isolates from races found in India, a significant amount of research has analyzed variability in populations from India using a variety of molecular tools (Dubey and Singh, 2008;Dubey et al, 2012Dubey et al, , 2014Durai et al, 2012;Honnareddy and Dubey, 2006;Sharma et al, 2009Sharma et al, , 2014. These studies show very high genetic diversity in F. oxysporum sampled from chickpea in India.…”

Identification of two major quantitative trait locus for fresh seed dormancy using the diversity arrays technology and diversity arrays technology‐seq based genetic map in Spanish‐type peanuts

“…) and several fungal pathogens of chickpea (Sharma et al. ) and animals (Kilian , http://www.diversityarrays.com).…”

“…In such circumstances, the use of DArT and DArT-seq genotyping platform seems to be a better option. The DArT and DArT-seq genotyping platforms manage the complexity reduction in the genome and therefore have been used in different range of crops for the genetic studies, such as rice ( (Sharma et al 2014) and animals (Kilian 2008, www.diversityarrays.com).…”

DArT-based characterisation of genetic diversity in a Miscanthus collection from Poland

“…Two replicates per clone were spotted on SuperChip poly-L-lysine slides (Thermo Scientific, Scoresby, Australia) using a MicroGrid arrayer (Genomics Solutions, Huntingdon, UK). After printing, slides were processed as described by Sharma et al (2014) to construct a DArT array. The clones were constructed using PstI and TaqI digestions according to principles described at http://www.diversityarrays.com/ dart-application-microarray-process-complexity-reduction as described by Mace et al (2008) and Heller-Uszynska et al (2011).…”