Genetic Diversity and Structure of Natural, Planted and Selected Populations of Tree Bean (Parkia timoriana (DC.) Merr.) in North East India
DOI:
https://doi.org/10.36808/if/2022/v148i12/166054Keywords:
Domestication, Microsatellite, Farmer selections, Shannon Diversity index, Indigenous fruit treesAbstract
Planted populations of indigenous fruit trees (IFTs) in the tropics may be the link towards efficient utilization and conservation of its genetic resources, but little is known of the genetic diversity they harbor. Tree bean (Parkia timoriana) is an economically important IFT that is cultivated and planted on and off farm in tropical regions of Northeast India. Using 3-microsatellite markers, we compared the genetic variation and structure of five-planted populations and a farmer-selected with three natural populations within northeast India. Pooled planted and selected populations showed marginal reduction in genetic diversity values compared to natural populations. Individually, cultivated populations from Manipur had higher Shannon diversity index (I=1.30 and 1.32) compared to wild populations (I= 1.30, 1.08 and 1.12). The farmer selected population displayed appreciable levels of diversity (Na= 5.33 and I=1.12). Structure analysis revealed high degree of admixture in natural and two planted populations and PCA depicted close congruence with the geographical distribution of populations. The present study reveals that famer driven selection process has not resulted to any major reduction in genetic diversity. There is ample diversity with natural as well as planted populations of the species, which shall be crucial components for trait improvement in tree breeding programs.
References
Angelsen, A., Jagger, P., Babigumira, R., Belcher, B., Hogarth, N.J., Bauch, S., Börner, J., Smith-Hall, C. and Wunde, S. (2014). Environmental income and rural livelihoods: a global-comparative analysis. World Development, 64 (1):12–28.
Awodoyin, R.O., Olubode, O.S., Ogbu, J.U., Balogun, R.B., Nwawuisi, J.U. and Orji, K.O. (2015). Indigenous fruit trees of tropical Africa: status, opportunity for development and biodiversity management. Agricultural sciences, 6 (01):31–41.
Changtragoon, S. (1997). Impact of disturbance on genetic diversity of Cycas siamensis in Thailand. In : Wrap-up Workshop of the CIFOR-IPGRI Impact of Disturbance Project, Bangalore, India. 18-22 August 1997.
Doyle, J.J. and Doyle, J.L. (1987). A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin, 19 (1):11¬–15.
Earl, D.A. and VonHoldt, B.M. (2012). STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation genetics resources, 4 (2):359–361.
El Mousadik, A. and Petit, R.J. (1996). High level of genetic differentiation for allelic richness among populations of the argan tree [Argania spinosa (L.) Skeels] endemic to Morocco. Theoretical and Applied Genetics, 92 (7):832–839.
Evanno, G., Regnaut, S. and Goudet, J. (2005). Detecting the number of clusters of individuals using the software structure: A simulation study. Molecular Ecology, 14 (8):2611–2620.
Excoffier, L. and Lischer, H.E.L. (2010). Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources, 10 (3):564–567.
Fisher, R. (1930). The genetical theory of natural selection. Oxford: Oxford University Press, London, UK.
Gacheri, N., Wanjala, B., Jamnadass, R. and Muchugi, A. (2016). Analysis of the impact of domestication of Warburgia ugandensis (Sprague) on its genetic diversity based on amplified fragment length polymorphism. African Journal of Biotechnology, 15 (31):1673–1680.
Glaubitz, J.C. (2004). CONVERT: a user friendly program to reformat diploid genotypic data for commonly used population genetic software packages. Molecular Ecology Notes, 4 (2): 309–310.
Hamrick, J.L. and Godt, M.J.W. (1996). Effects of life history traits on genetic diversity in plant species. Transactions of the Royal Society of London, Series B; 351 (1345):1291–1298.
Harfouche, A., Meilan, R., Kirst, M., Morgante, M., Boerjan, W., Sabatti, M. and Scarascia Mugnozza, G. (2012). Accelerating the domestication of forest trees in a changing world. Trends in Plant Science, 17 (2):64–72.
Hartl, D.L. and Clark, A.G. (1997). Principles of Population Genetics, 3rd edn. Sinauer Associates, Sunderland.
Hoban, S., Paz-Vinas, I., Aitken, S., Bertola, L., Breed, M.F., Bruford, M., Funk, W.C., Grueber, C., Heuertz, M., Hohenlohe, P., Hunter, M., Jaffé, R., Fernandes, M., Mergeay, J., Moharrek, F., O'Brien, D., Segelbacher, G., Vernesi, C., Waits, L. and Laikre, L. (2020). Effective population size remains a suitable, pragmatic indicator of genetic diversity for all species, including forest trees. Biological Conservation, 253.
Hollingsworth, P., Dawson, I., Goodall-Copestake, W. P., Richardson, J. E., Weber, J. C., Sotelo Montes, C. and Pennington, R. T. (2005). Do farmers reduce genetic diversity when they domesticate tropical trees? A case study from Amazonia. Molecular Ecology, 14 (2):497–501.
Jamnadass, R., Lowe, A. and Dawson, I. (2009). Molecular Markers and the Management of Tropical Trees: the Case of Indigenous Fruits. Tropical Plant Biology, 2 (1):1–12.
Kelly, B.A., Hardy, O.J. and Bouvet, J.M. (2004). Temporal and spatial genetic structure in Vitellaria paradoxa (shea tree) in an agroforestry system in southern Mali. Molecular Ecology, 13 (5):1231–1240.
Kindt, R. and Lengkeek, A.G. (1999). Tree diversity on farm-use it or lose it. In: agricultural biodiversity conservation. Intermediate Technology Development Group East Africa, Nairobi, Kenya. 27-29 January 1999.
Kopelman, N.M., Mayzel, J., Jakobsson, M., Rosenberg, N.A. and Mayrose, I. (2015). Clumpak: a program for identifying clustering modes and packaging population structure inferences across K. Molecular Ecology Resources, 15 (5):1179–1191.
Lassen, K.M., Kjær, E.D., Ouédraogo, M. and Nielsen L.R. (2014). Microsatellite primers for Parkia biglobosa (Fabaceae: Mimosoideae) reveal that a single plant sires all seeds per pod. Applications in plant sciences, 6 (2).
Leakey, R.R.B., Tchoundjeu, Z., Smith, R.I., Munro, R.C., Fondoun, J.M., Kengue, J., Anegbeh, P.O., Atangana, A.R., Waruhiu, A.N., Assah, E., Usoro, C. and Ukafor, V. (2004). Evidence that subsistence farmers have domesticated indigenous fruits (Dacryodes edulis and Irvingia gabonensis) in Cameroon and Nigeria. Agroforestry Systems, 60 (2):101–111.
Leakey, R.R.B., Tchoundjeu, Z., Schreckenberg, K., Simons, A.J., Shackleton, S., Mander, M., Wynberg, R., Shackleton, C. and Sullivan, C. (2007). Trees and markets for agroforestry tree products: targeting poverty reduction and enhanced livelihoods. In: World agroforestry into the future (D. Garrity, A. Okono, M. Parrott and S. Parrott, Eds.), World Agroforestry Centre, pp. 11–22.
Leberg, P.L. (2002). Estimating allelic richness: effects of sample size and bottlenecks. Molecular Ecology, 11 (11):2445–2449.
Lee, C.T., Wickneswari, R., Mahani, M. and Zakri, A.H. (2002). Maintenance of genetic diversity in Parkia speciosa in logged-over forests. Journal of Tropical Forest Science, 14 (2):163–178.
Lee, C.T., Wickneswari, R., Mahani, M.C. and Zakri, A.H. (2002). Effect of selective logging on the genetic diversity of Scaphium macropodum. Biological Conservation, 104 (1):107–118.
Lengkeek, A., Muchugi, A., Agufa, C., Ahenda, J. and Dawson, I. (2006). Comparing genetic diversity in agroforestry systems with natural forest: A case study of the important timber tree Vitex fischeri in central Kenya. Agroforestry Systems, 67 (3):293–300.
Longvah, T. and Deosthale, Y.G. (1998). Nutrient composition and food potential of Parkia roxburghii, a less known tree legume from northeast India. Food Chemistry, 62 (4):477–481.
Lowe, A., Boshier, D., Ward, M., Bacles, C.F. and Navarro, C. (2005). Genetic resource impacts of habitat loss and degradation; reconciling empirical evidence and predicted theory for neotropical trees. Heredity, 95 (4):255–273.
Luettmann, K., Michalczyk, I.M., Mengel, C., Ziegenhagen, B., Heymann, E.W., Pinedo Saboya, P.P. and Bialozyt, R. (2010). Characterisation of nuclear microsatellite loci in the Neotropical tree Parkia panurensis (Fabaceae). American journal of Botany, 97 (5):34–36.
Lyngdoh, N., Ravikanth, G., Kumar, M. and Pandey, A.K. (2016). Parkia timoriana based agroforestry systems in the North-East India. Environment Ecology, 34 (4A):1950–1952.
Meirmans, P.G. (2020). genodive version 3.0: Easy-to-use software for the analysis of genetic data of diploids and polyploids. Molecular Ecology Resources, 20 (4):1126–1131.
Neale, D. B. (2007). Genomics to tree breeding and forest health. Current Opinion in Genetics and Development, 17 (6):539–544.
Ofori, D.A., Gyau, A., Dawson, I.K., Asaah, E., Tchoundjeu, Z. and Jamnadass, R. (2014). Developing more productive African agroforestry systems and improving food and nutritional security through tree domestication. Current Opinion in Environmental Sustainability, 6:123–127.
Peakall, R. and Smouse, P.E. (2012). GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics, 28 (19):2537–2539.
Popoola, J., Agbolade, J., Ajiboye, A., Akinola, O., Lewu, F., Kioko, J. and Omonhinmin, C. (2020). Assessment of genetic diversity of African Locust Bean (Parkia biglobosa Jacq.) landraces using microsatellite markers. Journal of Critical Reviews, 7 (11):3196–3205.
Pritchard, J.K., Stephens, M. and Donnelly, P. (2000). Inference of population structure using multi locus genotype data. Genetics, 155 (2):945–959.
Reusch, T., Ehlers, A., Hämmerli, A. and Worm, B. (2005). Ecosystem recovery after climatic extremes enhanced by genetic diversity. Proceedings of the National Academy of Sciences, 102 (8):2826–2831.
Roy, S.S., Kumar, S., Sharma, S.K., Devi, A.R., Singh, N.A. and Ngachan, S.V. (2016). Tree bean (Parkia roxburghii): A potential multipurpose tree legume of Northeast India. National Symposium on Vegetable Legumes for Soil and Human Healthy, Indian Institute of Vegetable Research, Varanasi, India. 12-14 February 2016.
Salam, J.S., Singh, P.K., Dutta, B. K. and Sahoo, U.K. (2009). Chemical composition and nutritive indices in Parkia roxburghii G. Don, a leguminous plant of India. Indian Journal of Agricultural Biochemistry, 22 (2):87–93.
Simons, A.J. and Leakey, R.R.B. (2004). Tree domestication in tropical agroforestry. In: New Vistas in Agroforestry: Advances in Agroforestry (P.K.R. Nair, M.R. Rao. and L.E. Buck, Eds.), Springer, pp. 167–181.
Simons, A.J., Jaenicke, H., Tchoundjeu, Z., Dawson, I., Kindt, R., Oginosako, Z., Lengkeek, A. and De Grande, A. (2000). The future of trees is on farm: tree domestication in Africa. In: Forests and Society: The Role of Research, XXI IUFRO World Congress, Kuala Lumpur, Malaysia. pp. 752–760.
Stadlmayr, B., Charrondiere, U.R., Eisenwagen, S., Jamnadass, R. and Kehlenbeck, K. (2013). Nutrient composition of selected indigenous fruits from sub- Saharan Africa. Journal of the Science of Food and Agriculture, 93 (11):2627–2636.
Thangjam, R. (2014). Inter-Simple Sequence Repeat (ISSR) Marker Analysis in Parkia timoriana (DC.) Merr. Populations from Northeast India. Applied Biochemistry and Biotechnology, 172 (4):1727–1734.
Thejangulie, A., Rupankar, B., Letngam, T., Makdoh, B., Nirmal, Mungmuana Kumar, A.B., Rajendran, S. and Muniappan, A. (2017). Traditional uses, phytochemistry and biological activities of Parkia timoriana (DC.) Merr., an underutilised multipurpose tree bean: a review. Genetic Resources and Crop Evolution, 65 (2):679–692.
Van Oijen, D. (2002). Will the spirit of nGai survive A tree survey on ethnobotany, conservation potential and biomass on 35 farms in Meru, Kenya. Report Practical period, W.U.R., Wageningen, The Netherlands.
Wickneswari, R., Lee, C.T., Norwati, M. and Boyle, T.J.B. (2000). Impact of logging on genetic diversity in humid tropical forests. In: Forest Genetics and Sustainability; Forest Sciences (C. Matyas, Eds.), Springer, pp. 171–181.
Downloads
Downloads
Additional Files
Published
How to Cite
Issue
Section
License
Unless otherwise stated, copyright or similar rights in all materials presented on the site, including graphical images, are owned by Indian Forester.