Comparison of phenotypic and marker-assisted selection in Turkish cultivars and global genotypes of chickpea for resistance to pathotypes of Ascochyta rabiei (Pass.) Labr.

The pathotypes of Ascochyta rabiei, which causes ascochyta blight, show a high pathogenic variation. Forty-four chickpeas, including 26 cultivars commonly cultivated in Turkey and 18 global genotypes, were characterized for resistance status to ascochyta blight following inoculation with four pathotypes of A. rabiei. The pathogenicity experiments were conducted using the whole-plant inoculation method and completely randomized designs with three replicates. The pathogenicity tests revealed that 32, 17, 3, and 1 chickpea showed resistance reactions to pathotypes I, II, III, and IV, respectively. These chickpeas were genotyped with STMS (GAA47, TA146, and TA194), SCAR (SCK13603, SCAE19336, and SCY17590), and an allele-specific (CaETR) MAS markers closely linked to QTLs located on linkage groups 2 and 4 for ascochyta blight resistance. QTLAR1 predicted blight resistance to pathotype I with a rate of 65.9%. Strong correlations at P < 0.01 were found between resistance reactions of chickpeas to pathotype II and QTLAR2, which made it possible to predict resistance in 79.55%–81.82% of studied chickpeas. A significant association was found between QTLAR3 and resistance to pathotypes III and IV, which are the most aggressive groups among A. rabiei isolates. Three chickpea genotypes (ICC 3996, ICC 12004, and ICC 4475) showed a high level of resistance to pathotypes I, II, and III. ICC 3996 was the only genotype with resistance to pathotype IV. This study is the most comprehensive phenotypic study yet for determining the resistance status of chickpeas against pathotype IV, and the first study showing a significant association between a MAS marker linked to QTLAR3 and blight resistance to pathotypes III and IV. Breeders should include the isolates in pathotype III and IV groups into pathogenicity tests due to the increase in their prevalence. The markers linked to QTLs determining the resistance to these pathotypes should be emphasized, and the efficiency of the use of these markers in breeding programmes should be increased.

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