Acid lime ( Citrus aurantifolia ) is an important commercial fruits crop, cultivated in terai to high hills of Nepal. High variation of acid lime fruits are observed in existing landraces due to crossing within the other citrus species. Determination of genetic variation is important to the plant breeders for development of high yielding variety and hybrids. Therefore, an attempt has been made to study the genetic diversity of 62 acid lime landraces, collected from different altitudinal range in the eastern part of Nepal, using SSR markers. Twelve Simple Sequence Repeat (SSR) primer pairs were used to assess the genetic diversity of acid lime. The average genetic similarity level among the 62 accessions was 0.77, ranging from 0.54 to 1.0 and separated five major cluster groups. Total of 33 alleles were detected by eleven primer pairs and size of alleles ranged from 50 to 225. Average polymorphic information content (PIC) value was 0.50, whereas highest 0.75 and lowest 0.18 was observed in CAT01 and GT03 loci respectively. The results of the study clearly indicated that, SSR markers are highly polymorphic and more informative for the assessment of genetic diversity of acid lime landraces.
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