Integrated phenotypic and metabolomic analyses identify elite chickpea haplotypes under water limitation

Chickpea ( Cicer arietinum ) is a globally important legume crop whose productivity is frequently constrained by terminal drought, particularly in rainfed systems. We used high-throughput phenotyping of 35 diverse chickpea haplotypes at contrasting watering regimes (80% and 40% field capacity) to identify superior haplotypes. Significant haplotype:watering interactions were observed for water-use dynamics, growth rates, biomass accumulation and nodulation, indicating strong genetic control over drought responses. Certain haplotypes (e.g., ICC2210 and ICC18839) maintained relatively high water-use efficiency and growth under stress, while others exhibited pronounced reductions in biomass and nodulation. Principal Component Analyses (PCA) were used to identify haplotypes associated with tolerant and sensitive stress phenotypes.

Metabolomic profiling revealed widespread reprogramming of metabolism under water limitation, with 57 of 82 metabolites significantly affected by treatment. A consistent decrease in tricarboxylic acid intermediates, including succinic acid, indicated altered energy metabolism, while accumulation of osmoprotectants such as proline and sucrose reflected adaptive responses to osmotic stress. Multivariate and ANOVA Simultaneous Component Analyses (ASCA) identified key metabolites as major contributors to haplotype-specific drought responses. These metabolites are linked to nitrogen metabolism, stress signalling and cellular protection mechanisms. These results demonstrate substantial variation in drought adaptation among chickpea haplotypes and confirm that the integration of phenotypic and metabolomic traits is a powerful approach to identify drought-resilient genotypes.