Improving plant resistance against Fusarium wilt (FW) is key to sustaining chickpea production worldwide. Given this, the current study tested a set of 75 FW-responsive chickpea breeding lines including checks in a wilt-sick plot for two consecutive years (2016 and 2017). Genetic diversity analysis using 75 simple sequence repeats (SSRs) revealed a total of 267 alleles with an average of 3.56 alleles per marker. The entire set was divided into two major classes based on clustering method and factorial analysis. Similarly, STRUCTURE analysis placed the 75 genotypes into three distinct sub-groups (K = 3). Marker-trait association (MTA) analysis using the generalized linear model approach revealed nine and eight significant MTAs for FW resistance in the years 2016 and 2017, respectively. Three significant MTAs were obtained for FW resistance following the mixed linear model approach for both years. The SSR markers CESSR433, NCPGR21 and ICCM0284 could be potentially employed for targeted and accelerated improvement of FW resistance in chickpea. To the best of our knowledge, this is the first report on association mapping of the genomic loci controlling FW (Foc2) resistance in chickpea.

Fusarium wilt caused by Fusarium oxysporum, Schlecht. emend. Snyd. & Hans. f. sp. ciceri is prevalent in most chickpea-growing countries and is a major devastating disease. Host plant resistance is the most practical method of disease management. Indigenous chickpea germplasm reveals a heterogeneous genetic make-up and the response of resistance to wilt is an unexplored potential source for disease resistance. There are 70 indigenous germplasm lines selected on the basis of their agronomic performance and diverse areas of collections in the country. Of these, four accessions had a highly resistant score of 1 and six had a score of 3 using a 1–9 rating scale, indicating their level of resistance to Fusarium wilt (race 4). Other germplasm accessions of chickpea were found to be moderately resistant to highly susceptible disease reaction. Likewise, the same set of germplasm was also screened for Meloidogyne incognita (race 1) using pot culture under controlled condition. Only one accession was found to be resistant to this pest. These resistant gene sources can be utilised effectively for race-specific chickpea wilt and root-knot resistance breeding programmes.