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Plants 2018, 7(2), 46; https://doi.org/10.3390/plants7020046

Characterization of the Genetic Diversity of Acid Lime (Citrus aurantifolia (Christm.) Swingle) Cultivars of Eastern Nepal Using Inter-Simple Sequence Repeat Markers

1
Central Department of Biotechnology, Tribhuvan University (CDBt-TU), GPO Box 44613, Kirtipur, Kathmandu, Nepal
2
Molecular Biotechnology Unit, Faculty of Science, Nepal Academy of Science and Technology (NAST), GPO Box 3323, Khumaltar, Lalitpur, Nepal
3
Nepal Agriculture Research Council (NARC), GPO Box 5459, Khumaltar, Lalitpur, Nepal
4
Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland
*
Authors to whom correspondence should be addressed.
Received: 9 May 2018 / Revised: 6 June 2018 / Accepted: 8 June 2018 / Published: 12 June 2018
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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. View Full-Text
Keywords: citrus breeding; diversity; genetic similarity; lime; molecular markers; PCR citrus breeding; diversity; genetic similarity; lime; molecular markers; PCR
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Munankarmi, N.N.; Rana, N.; Bhattarai, T.; Shrestha, R.L.; Joshi, B.K.; Baral, B.; Shrestha, S. Characterization of the Genetic Diversity of Acid Lime (Citrus aurantifolia (Christm.) Swingle) Cultivars of Eastern Nepal Using Inter-Simple Sequence Repeat Markers. Plants 2018, 7, 46.

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