Abstract
Acid lime (Citrus aurantifolia (Christm.) Swingle) is an important fruit crop, which has high commercial value and is cultivated in 60 out of the 77 districts representing all geographical landscapes of Nepal. A lack of improved high-yielding varieties, infestation with various diseases, and pests, as well as poor management practices might have contributed to its extremely reduced productivity, which necessitates a reliable understanding of genetic diversity in existing cultivars. Hereby, we aim to characterize the genetic diversity of acid lime cultivars cultivated at three different agro-ecological gradients of eastern Nepal, employing PCR-based inter-simple sequence repeat (ISSR) markers. Altogether, 21 polymorphic ISSR markers were used to assess the genetic diversity in 60 acid lime cultivars sampled from different geographical locations. Analysis of binary data matrix was performed on the basis of bands obtained, and principal coordinate analysis and phenogram construction were performed using different computer algorithms. ISSR profiling yielded 234 amplicons, of which 87.18% were polymorphic. The number of amplified fragments ranged from 7–18, with amplicon size ranging from ca. 250–3200 bp. The Numerical Taxonomy and Multivariate System (NTSYS)-based cluster analysis using the unweighted pair group method of arithmetic averages (UPGMA) algorithm and Dice similarity coefficient separated 60 cultivars into two major and three minor clusters. Genetic diversity analysis using Popgene ver. 1.32 revealed the highest percentage of polymorphic bands (PPB), Nei’s genetic diversity (H), and Shannon’s information index (I) for the Terai zone (PPB = 69.66%; H = 0.215; I = 0.325), and the lowest of all three for the high hill zone (PPB = 55.13%; H = 0.173; I = 0.262). Thus, our data indicate that the ISSR marker has been successfully employed for evaluating the genetic diversity of Nepalese acid lime cultivars and has furnished valuable information on intrinsic genetic diversity and the relationship between cultivars that might be useful in acid lime breeding and conservation programs in Nepal.
Highlights
Citrus, an important genus from Rutaceae family [1], is an ancient perennial crop more often cultivated in tropical and sub-tropical parts of the globe [2]
Our objectives were to employ an inter-simple sequence repeat (ISSR) marker system to evaluate the genetic diversity of the same acid lime germplasm sampled from different agro-ecological zones of Eastern Nepal that were used previously with two other two marker systems, viz., RAPDs and simple sequence repeats (SSRs), and to perform a comparative discussion based on the results obtained from all three different marker systems: RAPD, SSRs, and ISSRs [41,43]
ISSR primers across the cultivars fromAltogether, 7–18, with 234 variation in amplicon ranging from 250–3200 bp
Summary
An important genus from Rutaceae family [1], is an ancient perennial crop more often cultivated in tropical and sub-tropical parts of the globe [2]. F.) are important fruit crops in Asia, and India is the largest producer of lime and lemon [6]. As lemon and lime juices have profound amounts of citric acid, comprising 1.38 and 1.44 g/oz, respectively [8], beverages with citric acid are reported to reduce the content of calcium, and enhancing an excretion of urinary citrates. It could be a good dietary supplement for preventing and managing calcium urolithiasis (kidney stone) [7,9]
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