Germplasm exploration and digital phenotyping reveal indigenous diversity and farmer preferences in pigeon pea (Cajanus cajan (L.) Millsp.) for climate-smart breeding

Pigeon pea (Cajanus cajan [L.] Millsp.) remains an underutilized legume in most African countries despite its potential to promote climate-resilient farming, diversify food sources, and enhance nutrition. Limited understanding of its indigenous diversity and farmer trait preferences hampers wider adoption, especially in the West African region. Between February and May 2025, a germplasm exploration was conducted across 18 Nigerian states, supplemented by accessions from the International Institute of Tropical Agriculture (IITA) genebank, Ghana, the Republic of Benin, and The Gambia, totaling 273 accessions. Ethnobotanical surveys documented farmer preferences, cultural uses, and local nomenclature, while seed morphometric traits were assessed using Videometerlab4 multispectral imaging. Farmer surveys revealed that cooking time (58.3%), commercial value (27.0%), and maturity cycle (14.7%) were key preferred traits. Gender and age influenced preferences; women and older farmers prioritized cooking time, whereas men and younger farmers emphasized the maturity cycle. Vernacular names (e.g., Otili, Fiofio, Waken Gwari) reflected deep cultural ties and cross-border exchange in Ogun State and the Republic of Benin, highlighting transboundary diversity. Morphometric analysis showed moderate variation in seed size, shape, and color. Seed area (14.2–46.0 mm2), compactness (0.590–0.998), and eccentricity (0–0.808) distinguished rounded from elongated seeds, while CIELab_A values (− 0.04 to 29.98) captured color differences. The first two PCA axes explained 67.1% of the total variation, and cluster analysis grouped accessions into four morphotypes. By combining genetic, morphometric, and farmer preference data, this study offers a strong basis for conserving and developing climate-resilient, fast-cooking, and market-preferred cultivars for sub-Saharan Africa.