Genetic resources and genes/QTLs for gram pod borer (Helicoverpa armigera Hübner) resistance in chickpea from the Western Himalayas

Helicoverpa armigera (also known as gram pod borer) is a serious threat to chickpea production in the world. A set of 173 chickpea genotypes were evaluated for H. armigera resistance, including mean larval population (MLP), percentage pod damage (PPD), and pest resistance (PR) for 2 consecutive years (year 2020 and 2021). The same core set was also genotyped with 50K Axiom CicerSNP Array. The trait data and 50,000 single nucleotide polymorphism genotypic data were used together to work out marker–trait associations (MTAs) using different genome‐wide association studies models. For MLP, a total of 53 MTAs were identified, including 25 MTAs in year 2020 and 28 MTAs in year 2021. A set of three MTAs was found common in both environments. For PPD, two MTAs in year 2020 and five MTAs in year 2021 were identified. A set of two MTAs were common in both environments. Similarly, for PR, only two MTAs common in both environments were identified. Interestingly, a common MTA (Affx_123255526) on chromosome 2 (Ca2) was found to be associated with all the three component traits (MLP, PPD, and PR) of pod borer resistance in chickpea. Further, we report key genes that encode SCAMPs (that facilitates the secretion of defense‐related molecules), quinone oxidoreductase (enables the production of reactive oxygen species that promotes diapause of gram pod borer), and NB‐LRR proteins that have been implicated in plant defense against H. armigera. The resistant chickpea genotypes, MTAs, and key genes reported in the present study may prove useful in the future for developing pod borer–resistant chickpea varieties. Core Ideas A core set of 173 chickpea genotypes was evaluated for Helicoverpa armigera resistance for 2 years. Pod borer–resistant genotypes were identified. Genotyping of core set with Axiom CicerSNP Array has ∼50,000 single nucleotide polymorphisms. A total of 53 significant marker–trait associations/genes/quantitative trait loci conferring resistance to H. armigera were identified. Candidate gene analysis identified key genes responsible for plant defense against H. armigera (mean larval population) in chickpea. Plain Language Summary Chickpea is one of the important crops for diet diversity in the Western Himalayas of Jammu and Kashmir. However, its production and productivity are badly challenged by the pod borer (Helicoverpa armigera). We made efforts to develop a diverse collection of chickpea and evaluated the same for pod borer resistance for 2 years. The core