Hostname: page-component-848d4c4894-nmvwc Total loading time: 0 Render date: 2024-07-04T07:33:08.531Z Has data issue: false hasContentIssue false
  • English
  • Français

Assessment of genetic variability amongst cultivated populations of Khasi mandarin (Citrus reticulata Blanco) detected by ISSR

Published online by Cambridge University Press:  08 April 2021

Karishma Kashyap ,
Rasika M. Bhagwat  and
Sofia Banu Open the ORCID record for Sofia Banu [Opens in a new window]
Karishma Kashyap
Affiliation:
Department of Bioengineering and Technology, GUIST, Gauhati University, Guwahati781014, India
Rasika M. Bhagwat
Affiliation:
Teri, Western Regional Centre, Mumbai400614, India
Sofia Banu*
Affiliation:
Department of Bioengineering and Technology, GUIST, Gauhati University, Guwahati781014, India
*
*Corresponding author. E-mail: sofiabanu2@gmail.com
Get access Rights & Permissions [Opens in a new window]

Abstract

Khasi mandarin (Citrus reticulata Blanco) is a commercial mandarin variety grown in northeast India and one of the 175 Indian food items included in the global first food atlas. The cultivated plantations of Khasi mandarin grown prominently in the lower Brahmaputra valley of Assam, northeast India, have been genetically eroded. The lack in the efforts for conservation of genetic variability in this mandarin variety prompted diversity analysis of Khasi mandarin germplasm across the region. Thus, the study aimed to investigate genetic diversity and partitioning of the genetic variations within and among 92 populations of Khasi mandarin collected from 10 cultivated sites in Kamrup and Kamrup (M) districts of Assam, India, using Inter-Simple Sequence Repeat (ISSR) markers. The amplification of genomic DNA with 17 ISSR primers yielded 216 scorable DNA amplicons of which 177 (81.94%) were polymorphic. The average polymorphism information content was 0.39 per primer. The total genetic diversity (HT = 0.28 ± 0.03) was close to the diversity within the population (HS = 0.20 ± 0.01). A high mean coefficient of gene differentiation (GST = 0.29) reflected a high level of gene flow (Nm = 1.22), indicating high genetic differentiation among the populations. Analysis of Molecular Variance (AMOVA) showed 78% of intra-population differentiation, 21% among the population and 1% among the districts. The obtained results indicate the existence of a high level of genetic diversity in the cultivated Khasi mandarin populations, indicating the need for preservation of each existing population to revive the dying out orchards in northeast India.

Keywords

AMOVAgene flowgenetic diversityKhasi mandarinpolymorphism
Type
Research Article
Information
Plant Genetic Resources , Volume 19 , Issue 2 , April 2021 , pp. 122 - 132
Copyright
Copyright © The Author(s), 2021. Published by Cambridge University Press on behalf of NIAB

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Alansi, S, Tarroum, M, Al-Qurainy, F, Khan, S and Nadeem, M (2016) Use of ISSR markers to assess the genetic diversity in wild medicinal Ziziphus spina-christi (L.) Willd. Collected from different regions of Saudi Arabia. Biotechnology & Biotechnological Equipment 30: 942–947.CrossRefGoogle Scholar
Barkley, NA, Roose, ML, Krueger, RR and Federici, CT (2006) Assessing genetic diversity and population structure in a citrus germplasm collection utilizing simple sequence repeat markers (SSRs). Theoretical Applied Genetics 112: 1519–1531.CrossRefGoogle Scholar
Bernet, GP, Fernandez-Ribacoba, J, Carbonell, EA and Asins, MJ (2010) Comparative genome-wide segregation analysis and map construction using a reciprocal cross design to facilitate citrus germplasm utilization. Molecular Breeding 25: C659–C673.CrossRefGoogle Scholar
Bhagwat, RM, Banu, S, Dholakia, BB, Kadoo, NY, Lagu, MD and Gupta, VS (2014) Evaluation of genetic variability in Symplocos laurina Wall. From two biodiversity hotspots of India. Plant Systematics and Evolution 300: 2239–2247.CrossRefGoogle Scholar
Bhandari, HR, Bhanu, NA, Srivastava, K, Singh, MN and Shreya, HA (2017) Assessment of genetic diversity in crop plants. An overview. Advances in Plants and Agriculture Research 7: 00255.Google Scholar
Bonin, A, Ehrich, D and Manel, S (2007) Statistical analysis of amplified fragment length polymorphism data: a toolbox for molecular ecologists and evolutionists. Molecular Ecology 16: 3737–3758.CrossRefGoogle ScholarPubMed
Campos, ET, Espinosa, MAG, Warburton, ML, Varela, AS and Monter, AV (2005) Characterization of mandarin (Citrus spp.) using morphological and AFLP markers. Interciencia 30: 687–693.Google Scholar
ColettaFilho, HD, Machado, MA, Targon, M and Pompeu, J Jr (2000) The use of random amplified polymorphic DNA to evaluate the genetic variability of Ponkan mandarin (Citrus reticulata Blanco) accessions. Genetics and Molecular Biology 23: 169–172.CrossRefGoogle Scholar
Deshmukh, NA, Patel, RK, Krishnappa, R, Verma, BC, Rymbai, H, Assumi, SR, Lyngdoh, P, Jha, AK and Malhotra, SK (2017) Influence of rootstock age and propagation methods on scion physiology and root morphology of Khasi mandarin (Citrus reticulata). Indian Journal of Agricultural Sciences 87: 203–209.Google Scholar
Deshpande, AU, Apte, GS, Bahulikar, RA, Lagu, MD, Kulkarni, BG, Suresh, HS, Singh, NP, Rao, MKV, Gupta, VS, Pant, A and Ranjekar, PK (2001) Genetic diversity across natural populations of three montane plant species from the Western Ghats, India revealed by inter simple sequence repeats. Molecular Ecology 10: 2397–2408.CrossRefGoogle Scholar
Doyle, JJ and Doyle, JL (1990) Isolation of plant DNA from fresh tissue. Focus 12: 13–15.Google Scholar
Ghosh, SP (1977) Citrus industry of north east India. Punjab Horticultural Journal 17: 13–21.Google Scholar
Govindaraj, M, Vetriventhan, M and Srinivasan, M (2015) Importance of genetic diversity assessment in crop plants and its recent advances: an overview of its analytical perspectives. Genetics Research International 431487: 1–14.CrossRefGoogle Scholar
Grativol, C, Lira-Medeiros, CD, Hemerly, AS and Ferreira, PCG (2011) High efficiency and reliability of inter-simple sequence repeats (ISSR) markers for evaluation of genetic diversity in Brazilian cultivated Jatropha curcas L. accessions. Molecular Biology Report 38: 4245–4256.CrossRefGoogle ScholarPubMed
Hamrick, JL and Godt, MJW (1996) Effects of life history traits on genetic diversity in plant species. Philosophical Transitions of the Royal Society of London, Series B 351: 1291–1298.Google Scholar
Han, YC, Teng, CZ, Zhong, S, Zhou, MQ, Hu, ZL and Song, YC (2007) Genetic variation and clonal diversity in populations of Nelumbo nucifera (Nelumbonaceae) in central China detected by ISSR markers. Aquatic Botany 86: 69–75.CrossRefGoogle Scholar
Hazarika, TK (2012) Citrus genetic diversity of north-east India, their distribution, ecogeography and ecobiology. Genetic Resources and Crop Evolution 59: 1267–1280.CrossRefGoogle Scholar
Hogbin, PM and Peakall, R (1999) Evaluation of the conservation of genetic research to the management of endangered plant Zieria prostrata. Conservative Biology 13: 514–522.CrossRefGoogle Scholar
Hussain, Z, Khadija, F, Aziz, A, Khan, MN, Salik, MR and Anwar, R (2017) Evaluation of different grafting methods to citrus cultivars. Citrus Research & Technology 38: 1–5.CrossRefGoogle Scholar
Kumar, J and Agarwal, V (2019) Assessment of genetic diversity, population structure and sex identification in dioecious crop, Trichosanthes dioica employing ISSR, SCoT and SRAP markers. Heliyon 5: e01346.CrossRefGoogle ScholarPubMed
Kumar, S, Jena, SN and Nair, NK (2010) ISSR polymorphism in Indian wild orange (Citrus indica Tanaka, Rutaceae) and related wild species in North-east India. Scientia Horticulturae 123: 350–359.CrossRefGoogle Scholar
Lamare, A and Rao, SR (2015) Efficacy of RAPD, ISSR and DAMD markers in assessment of genetic variability and population structure of wild Musa acuminata Colla. Physiology and Molecular Biology of Plants 21: 349–358.CrossRefGoogle ScholarPubMed
Li, M, Zhao, Z and Miao, XJ (2013) Genetic variability of wild apricot (Prunus armeniaca L.) populations in the Ili Valley as revealed by ISSR markers. Genetic Resources and Crop Evolution 60: 2293–2302.CrossRefGoogle Scholar
Malik, SK, Chaudhury, R, Kumar, S, Dhariwal, OP and Bhandari, DC (2012) Mandarins. In: Malik, SK, Chaudhury, R, Kumar, S, Dhariwal, OP and Bhandari, DC (eds) Citrus Genetic Resources in India: Present Status and Management. New Delhi, India: National Bureau of Plant Genetic Resources, pp. 27.Google Scholar
Malik, SK, Kumar, S, Singh, IP, Dhariwal, OP and Chaudhury, R (2013) Socio-economic importance, domestication trends and in situ conservation of wild Citrus species of Northeast India. Genetic Resources and Crop Evolution 60: 1655–1671.CrossRefGoogle Scholar
Marak, CK and Laskar, MA (2010) Analysis of phenetic relationship between Citrus indica Tanaka and a few commercially important Citrus species by ISSR markers. Scientia Horticulturae 124: 345–348.CrossRefGoogle Scholar
Meena, B, Singh, N, Mahar, KS, Sharma, YK and Rana, TS (2019) Molecular analysis of genetic diversity and population genetic structure in Ephedra foliata: an endemic and threatened plant species of arid and semi-arid regions of India. Physiology and Molecular Biology of Plants: An International Journal of Functional Plant Biology 25: 753–764.CrossRefGoogle ScholarPubMed
Miller, MP (1997) Tools for Population Genetic Analysis (TFPGA) 1.3: a Windows program for the analysis of allozyme and molecular population genetic data. Distributed by the author, Northern Arizona University.Google Scholar
Miller, AJ and Gross, BL (2011) From forest to field: perennial fruit crop domestication. American Journal of Botany 98: 1389–1414.CrossRefGoogle ScholarPubMed
Mondal, B and Saha, R (2014) Identification of zygotic and nucellar seedlings of Citrus reticulata and Citrus aurantifolia using RAPD. International Journal of Advance Biotechnological Research 5: 25–30.Google Scholar
Munankarmi, NN, Rana, N, Bhattarai, T, Shrestha, RL, Joshi, BK, Baral, B and Shrestha, S (2018) Characterization of the genetic diversity of acid lime (Citrus aurantifolia (Christm.) Swingle) cultivars of eastern Nepal using inter-simple sequence repeat markers. Plants 7: 46.CrossRefGoogle ScholarPubMed
Nei, M (1972) Genetic distance between populations. The American Naturalist 106: 283–292.CrossRefGoogle Scholar
Nei, M (1973) Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences 70: 3321–3323.CrossRefGoogle ScholarPubMed
Nei, M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89: 583–590.CrossRefGoogle ScholarPubMed
Nei, M (1987) Genetic distance and molecular phylogeny. In: Ryman, N and Utter, F (eds) Population Genetics and Fishery Management. Seattle: University of Washington Press, pp. 193–223.Google Scholar
Nilkanta, H, Amom, T, Tikendra, L, Rahaman, H and Nongdam, P (2017) ISSR marker based population genetic study of Melocanna baccifera (Roxb.) Kurz: a commercially important bamboo of Manipur, North-East India. Scientifica 2: 1–19.CrossRefGoogle Scholar
Nybom, H (2004) Comparison of different nuclear DNA markers for estimating intraspecific genetic diversity in plants. Molecular Ecology 13: 1143–1155.CrossRefGoogle ScholarPubMed
Nybom, H and Bartish, IV (2000) Effects of life history traits and sampling strategies on genetic diversity estimates obtained with RAPD markers in plants. Perspectives in Plant Ecology, Evolution and Systematics 3: 93–114.CrossRefGoogle Scholar
Oueslati, A, Salhi-Hannachi, A, Luro, F, Vignes, H, Mournet, P and Ollitrault, P (2017) Genotyping by sequencing reveals the interspecific C. maxima/C. reticulata admixture along the genomes of modern citrus varieties of mandarins, tangors, tangelos, orangelos and grapefruits. PLoS ONE 12: e0185618.CrossRefGoogle Scholar
Pal, D, Malik, SK, Kumar, S, Choudhary, R, Sharma, KC and Chaudhury, R (2013) Genetic variability and relationship studies of mandarin (Citrus reticulata Blanco) using morphological and molecular markers. Agricultural Research 2: 236–245.CrossRefGoogle Scholar
Patel, RK, Babu, KD, Singh, A, Yadav, DS and De, LC (2010) Soft wood grafting in mandarin (C. reticulata Blanco): a novel vegetative propagation technique. International Journal of Fruit Science 10: 54–64.CrossRefGoogle Scholar
Peakall, R and Smouse, PE (2006) GENALEX 6: genetic analysis in Excel: population genetic software for teaching and research. Molecular Ecology Notes 6: 288–295.CrossRefGoogle Scholar
Pons, E, Navarro, A, Ollitrault, P and Pena, L (2011) Pollen competition as a reproductive isolation barrier represses transgene flow between compatible and co-flowering citrus genotypes. PLoS One 6: e25810.CrossRefGoogle ScholarPubMed
Rajwade, AV, Arora, RS, Kadoo, NY, Harsulkar, AM, Ghorpade, PB and Gupta, VS (2010) Relatedness of Indian flax genotypes (Linum usitatissimum L.): an inter-simple sequence repeat (ISSR) primer assay. Molecular Biotechnology 45: 161–170.CrossRefGoogle ScholarPubMed
Shahsavar, AR, Izadpanah, K, Tafazoli, E and Tabatabaei, BE (2007) Characterization of Citrus germplasm including unknown variants by Inter-Simple Sequence Repeat (ISSR) markers. Scientia Horticulturae 112: 310–314.CrossRefGoogle Scholar
Sharafi, AA, Abkenar, AA, Sharafi, A and Masaeli, M (2016) Genetic variation assessment of acid lime accessions collected from south of Iran using SSR and ISSR molecular markers. Physiology and Molecular Biology of Plants 22: 87–95.CrossRefGoogle ScholarPubMed
Sharafi, AA, Abkenar, AA and Sharafi, A (2017) Molecular genetic diversity assessment of Citrus species grown in Iran revealed by SSR, ISSR and CAPS molecular markers. Journal of Scientific Research 2: 22–27.Google Scholar
Singh, N, Choudhury, DR, Singh, AK, Kumar, S, Srinivasan, K, Tyagi, RK, Singh, NK and Singh, R (2013) Comparison of SSR and SNP markers in estimation of genetic diversity and population structure of Indian rice varieties. PLoS ONE 8: e84136.CrossRefGoogle ScholarPubMed
Singh, AK, MeeteiNg, T, Singh, BK and Mandal, N (2016) Khasi mandarin: its importance, problems and prospects of cultivation in North-eastern Himalayan region. International Journal of Agriculture, Environment and Biotechnology 9: 573–592.CrossRefGoogle Scholar
Singh, SK, Chhajer, S, Pathak, R, Bhatt, RK and Kalia, RK (2017) Genetic diversity of Indian jujube cultivars using SCoT, ISSR, and rDNA markers. Tree Genetics & Genomes 13: 1–12.CrossRefGoogle Scholar
Slatkin, M (1985) Rare alleles as indicators of gene flow. Evolution 39: 53–65.CrossRefGoogle ScholarPubMed
Slatkin, M (1987) Gene flow and the geographic structure of natural populations. Science (New York, N.Y.) 236: 787–792.CrossRefGoogle ScholarPubMed
Smith, JSC, Chin, ECL, Shu, H, Smith, OS, Wall, SJ, Senior, ML, Mitchell, SE, Kresovich, S and Ziegle, J (1997) An evaluation of the utility of SSR loci as molecular markers in maize (Zea mays L.) comparisons with data from RFLPs and pedigree. Theoretical and Applied Genetics 95: 163–173.CrossRefGoogle Scholar
Tatikonda, L, Wani, SP, Kannan, S, Beerelli, N, Sreedevi, TK, Hoisington, DA, Devi, P and Varshney, RK (2009) AFLP-based molecular characterization of an elite germplasm collection of Jatropha curcas L., a biofuel plant. Plant Science 176: 505–513.CrossRefGoogle ScholarPubMed
Uchoi, A, Malik, SK, Choudhary, R, Kumar, S, Pal, D, Rohini, MR and Chaudhury, R (2017) Molecular markers in assessing genetic variation of Indian citron (Citrus medica L.) cultivars collected from different parts of India. Indian Journal of Biotechnology 16: 346–356.Google Scholar
Uzun, A, Gulsen, O, Yesiloglu, T, Akakacar, Y and Tuzcu, O (2010) Distinguishing grapefruit and pummelo accessions using ISSR markers. Czech Journal of Genetics and Plant Breeding 46: 170–177.CrossRefGoogle Scholar
Verma, S and Rana, TS (2011) Genetic diversity within and among the wild populations of Murraya koenigii L. Spreng., as revealed by ISSR analysis. Biochemical Systematics and Ecology 39: 139–144.CrossRefGoogle Scholar
Wang, X, Xing, S, Xiao-jing Liu, LS and Kong, Q (2015) Genetic diversity of Styrax obassia Sieb. Et Zucc. Based on AFLP markers. Biochemical Systematics and Ecology 61: 28–34.CrossRefGoogle Scholar
Yan, W, Li, J, Zheng, D, Friedman, C and Wang, H (2019) Analysis of genetic population structure and diversity in Mallotus oblongifolius using ISSR and SRAP markers. Peer Journal 7: 71–73.CrossRefGoogle ScholarPubMed
Yap, IV and Nelson, RJ (1996) Winboot: a program for performing bootstrap analysis of binary data to determine the confidence limits of UPGMA-based dendrograms. IRRI Discussion Paper, Series, vol 14, IRRI, Manila.Google Scholar
Yeh, FC, Yang, RC and Boyle, T (2000). POPGENE version 1.32: Microsoft Windows-based freeware for population genetic analysis. Centre for International Forestry Research, University of Alberta, Edmonton, Alberta, Canada.Google Scholar
Yu, Y, Chen, C, Huang, M, Yu, Q, Du, D, Mattia, MR and Gmitter, FG (2018) Genetic diversity and population structure analysis of citrus germplasm with single nucleotide polymorphism markers. Journal of the American Society for Horticultural Science 143: 399–408.CrossRefGoogle Scholar
Supplementary material: File

Kashyap et al. supplementary material

Kashyap et al. supplementary material

Download Kashyap et al. supplementary material(File)
File 93.2 KB