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.
References
[1]
Anonymous, “National Citrus Research Program,” Annual Report, Paripatle, 2006.
[2]
MOA, “Statistical Information of Nepalese Agriculture,” Ministry of Agriculture and Cooperatives, Agri Business Promotion and Statistical Division, Singh Durbar, 2008.
[3]
FAO, “Food and Agriculture Organization of the United Nations Developments in International Citrus Trade in 2004-2005,” 2006.
[4]
R. W. Scora, “Biochemistry, Taxonomy and Evolution of Modern Cultivated Citrus,” In: R. Goren and K. Mendel, Eds., Proc Int Soc Citricult, Vol. 1, 1988, pp. 277-289.
[5]
B. S. Dhillon, and J. S. Randhawa, “Fruit growth and development in citrus,” Advance in Horticulture, Malhotra Publishing House, New Delhi, Vol. 3, 1993, pp. 1667-1683.
[6]
E. Nicolosi, Z. N. Deng, A. Gentile, S. La Malfa, G. Continella and E. Tribulato, “Citrus Phylogeny and Genetic Origin of Important Species as Investigated by Molecular Markers,” Theoretical and Applied Genetics, Vol. 100, No. 8, 2000, pp. 1155-1166. doi:10.1007/s001220051419
[7]
R. W. Scora, “On the History and Origin of Citrus,” Bulletin of the Torrey Botanical Club, Vol. 102, No. 6, 1975, pp. 369-375. doi:10.2307/2484763
[8]
H. C. Barrett and A. M. Rhodes, “A Numerical Taxonomic Study of the Affinity Relationships in Cultivated Citrus and Its Close Relatives,” Systematic Botany, Vol. 1, 1976, pp. 105-136. doi:10.2307/2418763
[9]
S. K., Verma, “A Brief Introduction to Horticulture Development Project,” Horticulture Development Follow Up Program, Kirtipur, 1999.
[10]
H. D. Upadhya, S. L. Dwivedi, C. L. L. Gowda and S. Singh, “Identification of Diverse Germplasm Line for Agronomic Traits in Chickpea (Cicer arietinum L.) Core Collection for Use in Crop Improvement,” Field Crops Research, Vol. 100, No. 2-3, 2007, pp. 230-236.
doi:10.1016/j.fcr.2006.08.008
[11]
J. Ni, P. M. Colowit and D. J. Mackill, “Evaluation of Genetic Diversity in Rice Sub Species Using Microsatellite Markers,” Crop Science, Vol. 42, No. 2, 2002, pp. 601-607. doi:10.2135/cropsci2002.0601
[12]
D. Q. Fang, M. L. Roose, R. R. Krueger and C. T. Federici, “Fingerprinting Trifoliate Orange Germplasm Accessions with Isozymes, RFLPs, and Inter-Simple Sequence Repeat Markers,” Theoretical and Applied Genetics, Vol. 95, 1997, pp. 211-219.
doi:10.1007/s001220050550
[13]
H. D. C. Filho, M. A. Machado, M. L. P. N. Targon, M. C. P. Q. D. G. Moreira and J. Pompeu, “Analysis of the Genetic Diversity among Mandarins (Citrus spp.) Using RAPD Markers,” Euphytica, Vol. 102, No. 1, 1998, pp. 133-139. doi:10.1023/A:1018300900275
[14]
V. M. Novelli, M. A. Machado and C. R. Lopes, “Isoenzymatic Polymorphism in Citrus spp and P. trifoliata (L.) Raf. (Rutaceae),” Genetics and Molecular Biology, Vol. 23, 2000, pp. 163-168.
doi:10.1590/S1415-47572000000100030
[15]
J. M. H. Kijas, M. R. Thomas, J. C. S. Fowler and M. L. Roose, “Integration of Trinucleotide Microsatellites into a Linkage Map of Citrus,” Theoretical and Applied Genetics, Vol. 94, 1997, pp. 701-706.
doi:10.1007/s001220050468
[16]
A. A. Sanker and G. A. Moore, “Evaluation of Inter-Simple Sequence Repeat Analysis for Mapping in Citrus and Extension of the Genetic Linkage Map,” Theoretical and Applied Genetics, Vol. 102, No. 2, 2001, pp. 206-214.
doi:10.1007/s001220051637
[17]
J. M. H. Kijas, J. C. S. Fowler and M. R. Thomas, “An Evaluation of Sequence Tagged Microsatellite Site Markers for Genetic Analysis within Citrus and Related Species,” Genome, Vol. 38, No. 2, 1995, pp. 349-355.
doi:10.1139/g95-045
[18]
R. Herrero, M. J. Asins, E. A. Carbonell and L. Navarro, “Genetic Diversity in the Orange Subfamily Aurantioideae. I. Intraspecies and Intragenus Genetic Variability,” Theoretical and Applied Genetics, Vol. 92, No. 5, 1996, pp. 599-609. doi:10.1007/BF00224564
[19]
S. M., Brown, M. S. Hopkins, S. E. Mitchell, M. L. Senior, T. Y. Wang, R. R. Duncan, F. Gonzalez-Candelas and S. Kresovich, “Multiple Methods for the Identity Wcation of Polymorphic Simple Sequence Repeats (SSRs) in Sorghum (Sorghum spp.),” Theoretical and Applied Genetics, Vol. 93, 1996, pp. 190-198.
doi:10.1007/BF00225745
[20]
S. C. Hokanson, A. K. Szewc-McFadden, W. F. Lamboy and J. R. McFerson, “Microsatellite (SSR) Markers Reveal Genetic Identities, Genetic Diversity and Relationships in a Malus ￡ domestica Borkh,” Core Subset Collection, Theoretical and Applied Genetics, Vol. 97, No. 5, 998, pp. 671-683.
[21]
K. Liu, M. Goodman, S. Muse, J. S. Smith E. Buckler and J. Doebley, “Genetic Structure and Diversity among Maize Inbred Lines as Inferred from DNA Microsatellites,” Genetics, Vol. 165, No. 4, 2003, pp. 2117-2128.
[22]
P. K. Gupta, H. S. Balyan, P. C. Sharma and B. Ramesh, “Microsatellites in Plants: A New Class of Molecular Markers,” Current Science, Vol. 70, No. 1, 1996, pp. 45-54.
[23]
D. Tautz, “Hypervariability of Simple Sequences as a General Source of Polymorphic DNA Markers,” Nucleic Acids Research, Vol. 17, 1989, pp. 6463-6471.
doi:10.1093/nar/17.16.6463
[24]
B. Golein, A. Talaie, Z. Zamani, A. Ebadiand and A. Behjatnia, “Assessment of Genetic Variability in Some Iranian Sweet Oranges (Citrus sinensis [L.] Osbeck) and Mandarins (Citrus reticulata Blanco) Using SSR markers,” International Journal of Agriculture and Biology, Vol. 7, No. 2, 2005, pp. 167-170.
[25]
K. Weising and R. C. Gardner, “A Set of Conserved PCR Primers for the Analysis of Simple Sequence Repeat Polymorphism in Chloroplast Genomes of Dicotyledonous Angiosperm,” Genome, Vol. 42, No. 1, 1999, pp. 9-19. doi:10.1139/g98-104
[26]
M. J. C. Nunes, M. A. Machado, W. M. C. Nunes, M. Cristofania and M. L. P. N. Targon, “Assessment of Genetic Variability in Grapefruits (Citrusparadisi Macf.) and Pummelos (C. maxima (Burn.) Merr.) Using RAPD and SSR Markers,” Euphytica, Vol. 126, 2000, pp. 169-176.
doi:10.1023/A:1016332030738
[27]
P. Guilford, S. Parkash, J. M. Zhu, E. Rikkerink, S. Gardiner, H. Bassett and R. Forster, “Microsatellite in Apple (Malus domestica), Abundance, Polymorphism and Cultivar Identification,” Theoretical and Applied Genetics, Vol. 94, No. 2, 1997, pp. 245-249.
doi:10.1007/s001220050407
[28]
M. R. Thomas and N. S. Scott, “Microsatellite Repeats in Grapevine Reveal DNA Polymorphism When Analysed as Sequence-Tagged Sites (STSs),” Theoretical and Applied Genetics, Vol. 86, 1993, pp. 985-990.
doi:10.1007/BF00211051
[29]
C. He, V. Poysa and K. Yu, “Development and Characterization of Simple Sequence Repeat (SSR) Markers and Their Use in Determining Relationships among Lycopersicon esculentum Cultivars,” Theoretical and Applied Genetics, Vol. 106, 2003, pp. 363-373.
[30]
G. He, R. Meng, M. Newman, G. Gao, R. N. Pittman and C. S. Prakash, “Microsatellites as DNA Markers in Cultivated Peanut (Arachis hypogaea L.),” BMC Plant Biology, Vol. 3, No. 1, 2003, pp. 1-6.
doi:10.1186/1471-2229-3-3
[31]
M. Rossetto, A. Mclauchlan, F. C. L. Harriss, R. J. Henry, P. R. Baverstock, L. S. Lee, T. L. Maguire and K. J. Edwards, “Abundance and Polymorphism of Microsatellite Markers in the Tea Tree (Melaleuca alternifolia, Myrtaceae),” Theoretical and Applied Genetics, Vol. 98, No. 6, 1999, pp. 1091-1098. doi:10.1007/s001220051172
[32]
M. A. Viruel and J. I. Hormaza, “Development, Characterization and Variability Analysis of Microssatellites in Lychee (Litchi chinensis Sonn, Sapindaceae),” Theoretical Applied Genetics, Vol. 108, 2004, pp. 896-902.
doi:10.1007/s00122-003-1497-4
[33]
X. Pang, C. Hu and X. Deng, “Phylogenetic Relationships among Citrus and Its Relatives as Revealed by SSR Markers,” Acta Genetica Sinica, Vol. 30, No. 1, 2003, pp. 81-87.
[34]
P. Koehler-Santos, A. L. Dornelles and L. B. Freitas, “Characterization of Mandarin Citrus Germplasm from Southern Brazil by Morphological and Molecular Analyses,” Pesquisa Agropecuária Brasileira, Vol. 38, No. 7, 2003, pp. 797-806.
doi:10.1590/S0100-204X2003000700003
[35]
C. Ruiz, M. P. Breto and M. J. Asins, “A Quick Methodology to Identify Sexual Seedlings in Citrus Breeding Programs Using SSR Markers,” Euphytica, Vol. 112, No. 1, 2000, pp. 89-94. doi:10.1023/A:1003992719598
[36]
N. A. Barkley, M. L. Roose, R. R. Krueger and C. T. Federici, “Assessing Genetic Diversity and Population Structure in a Citrus Germplasm Collection Utilizing Simple Sequence Repeat Markers (SSRs),” Theoretical and Applied Genetics, Vol. 112, No. 8, 2006, pp. 1519-1531. doi:10.1007/s00122-006-0255-9
[37]
B. Golein, A. Talaie, Z. Zamani and B. Moradi, “Development and Characterization of New Microsatellite Loci from Lemon (Citrus lemon),” International Journal of Agriculture and Biology, Vol. 8, No. 2, 2006, pp. 172-174.
[38]
M., R. Jannati, A. Fotouhi, P. Abad and Z. Salehi, “Genetic Diversity Analysis of Iranian Citrus Varieties Using Micro Satellite (SSR) Based Markers,” Journal of Horticulture and Forestry, Vol. 1, No. 7, 2009, pp. 120-125.
[39]
F. J. Rohlf, “NTSYS-PC Numerical Taxonomy and Multivariate Analysis System,” Version 1.80. Exeter Software, Setauket, New York, 1993.
[40]
M. Nei, “Genetic Distance between Populations,” American Naturalist, Vol. 106, No. 949, 1973, pp. 283-292.
doi:10.1086/282771
[41]
M. Nei and W. H. Li, “Mathematical Models for Studying Genetic Variation in Terms of Restriction Endonucleases,” Proceedings of the National Academy of Sciences, Vol. 76, 1979, pp. 5269-5273.
doi:10.1073/pnas.76.10.5269
[42]
IPGRI, “Descriptors for Cirrus. Revised ed. IPGRI, Rome. Isolated from a Size-Fractionated Genomic Library of Brassica napus L. (rapeseed),” Theoretical and Applied Genetics, Vol. 91, 1999, pp. 206-211.
[43]
A. Ghanbari, N. B. Jelodar and H. Rahiman, “Studying of Genetic Diversity in Satsuma (Citrus unshiu) Mandarin utilizing Microsatellite Markers,” International Journal of Agricultural Research, Vol. 4, 2009, pp. 88-96.
doi:10.3923/ijar.2009.88.96
[44]
Y. Z. Li, Y. J. Cheng, H. L. Yi and X. X. Deng, “Genetic Diversity in Mandarin Landraces and Wild Mandarins from China Based on Nuclear and Chloroplast Simple Sequence Repeat Markers,” Journal of Horticultural Science and Biotechnology, Vol. 81, No. 3, 2006, pp. 371-378.
[45]
P. K. Santos, A. L. C. Dornelles and L. B. Freitas, “Characterization of Mandarin Citrus Germplasm from Southern Brazil by Morphological and Molecular Analyses,” Pesquisa Agropecuária Brasileira, Vol. 38, No. 7, 2003, pp. 797-806.
doi:10.1590/S0100-204X2003000700003
[46]
Q.-Q. Cao, H.-J. Meng, X.-P. Wen, H.-L. Yi and X.-X. Deng, “Genetic Diversity of Male Sterile and Low Fertility Germplasm of Citrus Revealed Using SSR Markers,” Chinese Journal of Agricultural Biotechnology, Vol. 4, No. 2, 2007, pp. 99-104.
doi:10.1017/S1479236207001453
[47]
G. J. Bryan, J. McNicoll, G. Ramsay, R. C. Meyar and W. S. D. Jong, “Polymorphic Simple Sequence Repeatmarker in Chloroplast Genome of Solanaceious Plant,” Theoretical and Applied Genetics, Vol. 99, No. 5, 1999, pp. 859-867. doi:10.1007/s001220051306
[48]
I. Metais, C. Aubry, B. Hamon and R. Jalouzot, “Description and Analysis of Genetic Diversity between Commercial Bean Lines (Phaseolus vulgaris L.),” Theoretical and Applied Genetics, Vol. 101, No. 8, 2000, pp. 1207-1214.
doi:10.1007/s001220051599
