Acid lime (<i>Citrus aurantifolia</i>) fruits are cultivated in terai, mid hill and high hill districts of Nepal. It is cross-pollinated crop and has a high variation in fruit characters within the species. Fruit character is the main basis of genotype selection. Study of fruit diversity is of utmost importance to select the elite genotypes for breeding and variety development program. Therefore, total of 620 fruit samples were collected and evaluated in the main production season of the year 2010 and 2011, from 62 bearing trees. Samples were collected from three agro-ecological domains, representing terai, mid hill and high hill areas of eastern Nepal. Elite landraces were selected on the basis of scoring fruit characters. High variation in vitamin C was observed between the terai (57.4 mg) and high hill (72.5 mg) samples. Amount of juice was 36.8% in mid hill and 44.1% in terai samples. Higher percent of juice and total soluble solids (TSS) observed in terai samples but tritable acidity (TA) and vitamin C was low as compare to high hills. There was significantly negative correlation found in fruit weight, fruit diameter, juice percent and seed number, whereas significantly positive correlation was in pulp and vitamin C, with altitude range. Total landraces were separated in five major cluster group. Variation in the level of similarity was observed among the cluster groups. The variability distance of fruit characters was highest in cluster group II (–17.45%) and lowest in cluster group V (58.5%). On the basis of scoring number of fruit characters, total four elite genotypes i.e. LD-49 from mid hills, LD-23 and LT-17 from higher hills and LM-44 from terai were selected for conservation, breeding and variety development purpose
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