Black seeds, hidden diversity: Phenotypic structure in an urban landrace of amaranth (Amaranthus spp.) in Niger

Neglected crops often harbour cryptic diversity maintained through informal seed systems, particularly in urban gardens of the Sahel. This study investigates phenotypic variation within a black-seeded Amaranthus spp. population cultivated in Niamey, Niger, where seed colour guides local selection practices despite limited scientific documentation. A total of 180 plants were evaluated at the vegetative stage for plant height and number of leaves under a randomised complete block design, with three replicates of 60 plants each. Descriptive statistics revealed considerable intra-population variability (CV = 39.4% for height; 27.2% for leaf number). Robust Principal Component Analysis (rPCA) captured 93.5% of total variance along a single axis reflecting strong trait correlation. Unsupervised clustering identified a dominant phenotypic core with peripheral structuring but no extreme outliers. This exploratory study documents the extent and internal organisation of phenotypic variation in a black-seeded landrace cultivated in Niger’s urban gardens, highlighting the contribution of farmer-maintained populations to the conservation of agrobiodiversity in underutilised crops. Conducted over a single growing season, this work provides a quantitative description of morphological variation within a Nigerien black-seeded amaranth landrace and establishes a baseline for future multi-environment or molecular studies.