Phenotypic Variation of Cocos nucifera L. Stems and Its Implications for Population Genetics in Pesisir Barat Lampung
Abstract
Coconut (Cocos nucifera L.) plays a vital role in coastal ecosystems and local economies, yet its population diversity may be shaped by historical cultivation practices. This study evaluated stem phenotypic variation and its implications for population genetics in coconut populations of Pesisir Barat, Lampung. A total of 92 individual trees were sampled using stratified purposive sampling across representative coastal sites. Three stem morphometric traits were measured following IPGRI (1995) descriptors, namely stem circumference at 1.5 m above ground (CS), stem circumference at 20 cm above the base (CB), and the height of the 11th internode from the ground surface (HS). Data were analyzed using descriptive statistics, coefficients of variation (CV), and Principal Component Analysis (PCA). Results showed relatively limited phenotypic variation, with CS exhibiting the lowest variability (CV 9.87%), while CB and HS showed moderate variability (CV 15.35% and 16.75%, respectively). PCA revealed close clustering of individuals, with the first two principal components explaining 91.0% of the total phenotypic variation, indicating limited phenotypic differentiation within the population. The observed phenotypic homogeneity may partly reflect the historical legacy of the PRPTE program, which distributed relatively uniform planting material during 1982–1984. Although inferences regarding genetic diversity remain preliminary, the findings suggest constrained population-level differentiation and highlight the importance of integrating morphometric and molecular approaches to support germplasm management, breeding strategies, and long-term sustainability of C. nucifera in coastal ecosystems.
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Afful, N. T., Annor, C., Nyadanu, D., Akromah, R., & Amoatey, H. M. (2024). Genetic variation, heritability and genetic advance of eggplant accessions (Solanum spp.). Bulgarian Journal of Agricultural Science, 30(1), 67–74. https://www.scopus.com/inward/record.uri?eid=2-s2.0-85188238304&partnerID=40&md5=752510a33d9c3ca0ab4c2a0653b53d3d
Andersson, L., & Purugganan, M. (2022). Molecular genetic variation of animals and plants under domestication. Proceedings of the National Academy of Sciences of the United States of America, 119(30). https://doi.org/10.1073/pnas.2122150119
Arumugam, T., & Hatta, M. A. M. (2022). Improving Coconut Using Modern Breeding Technologies: Challenges and Opportunities. In Plants (Vol. 11, Number 24). MDPI. https://doi.org/10.3390/plants11243414
Badan Pusat Statistik. (2024). Luas Perkebunan Kelapa di Kabupaten Pesisir Barat Tahun 2023. Badan Pusat Statistik Provinsi Lampung.
Bruggisser, M., Hollaus, M., Otepka, J., & Pfeifer, N. (2020). Influence of ULS acquisition characteristics on tree stem parameter estimation. ISPRS Journal of Photogrammetry and Remote Sensing, 168, 28–40. https://doi.org/https://doi.org/10.1016/j.isprsjprs.2020.08.002
Cao, Z., Li, J., Lei, H., Yan, M., Wang, Q., Ji, R., Zhang, S., Min, X., Sun, Z., & Wei, Z. (2025). PCA-Driven Multivariate Trait Integration in Alfalfa Breeding: A Selection Model for High-Yield and Stable Progenies. Plants, 14(18). https://doi.org/10.3390/plants14182906
Civan, P., Rincent, R., Danguy-Des-Deserts, A., Elsen, J.-M., & Bouchet, S. (2024). Population Genomics Along with Quantitative Genetics Provides a More Efficient Valorization of Crop Plant Genetic Diversity in Breeding and Pre-breeding Programs. In O. P. Rajora (Ed.), Population Genomics: Crop Plants (pp. 225–288). Springer International Publishing. https://doi.org/10.1007/13836_2021_97
Davis, C. D., Epps, C. W., Flitcroft, R. L., & Banks, M. A. (2018). Refining and defining riverscape genetics: How rivers influence population genetic structure. WIREs Water, 5(2), e1269. https://doi.org/https://doi.org/10.1002/wat2.1269
De Battisti, D. (2021). The resilience of coastal ecosystems: A functional trait-based perspective. Journal of Ecology, 109(9), 3133–3146. https://doi.org/https://doi.org/10.1111/1365-2745.13641
Elsani, W., Niati, W., Wulan Ayu, I., Maryam Oklima, A., Kusumawardani, W., & Dwi Lestari, N. (2023). Identifikasi Spesies Tumbuhan Penyusun Ekosistem Pesisir Pantai Dusun Patedong, Desa Sebotok, Pulau Moyo, Sumbawa. Jurnal Agroteknologi, 3(2), 55–65.
Feng, Z., Cheng, Z., Ren, L., Liu, B., Zhang, C., Zhao, D., Sun, H., Feng, H., Long, H., & Xu, B. (2024). Real-time monitoring of maize phenology with the VI-RGS composite index using time-series UAV remote sensing images and meteorological data. Computers and Electronics in Agriculture, 224. https://doi.org/10.1016/j.compag.2024.109212
Gonul, A. S., Candemir, C., & Thompson, P. (2025). Subtyping schizophrenia via machine learning by using structural neuroimaging. Translational Psychiatry, 15(1), 472. https://doi.org/10.1038/s41398-025-03704-w
Gouveia, M. H., Borda, V., Leal, T. P., Moreira, R. G., Bergen, A. W., Kehdy, F. S. G., Alvim, I., Aquino, M. M., Araujo, G. S., Araujo, N. M., Furlan, V., Liboredo, R., Machado, M., Magalhaes, W. C. S., Michelin, L. A., Rodrigues, M. R., Rodrigues-Soares, F., Sant Anna, H. P., Santolalla, M. L., … Tarazona-Santos, E. (2020). Origins, Admixture Dynamics, and Homogenization of the African Gene Pool in the Americas. Molecular Biology and Evolution, 37(6), 1647–1656. https://doi.org/10.1093/molbev/msaa033
Henrietta, H. M. (2025). Exploring Innovations in Plant Breeding and Biotechnological Approaches for the Sustainable Cultivation of Coconut (Cocos nucifera L.). In K. F. M. Salem, J. M. Al-Khayri, & S. M. Jain (Eds.), Breeding and Biotechnology of Leaf, Fruit, and Seed Fiber Crops (pp. 623–657). Springer Nature Switzerland. https://doi.org/10.1007/978-3-032-00407-9_15
Hori, K., Okunishi, T., Nakamura, K., Iijima, K., Hagimoto, M., Hayakawa, K., Shu, K., Ikka, T., Yamashita, H., & Yamasaki, M. (2022). Genetic Background Negates Improvements in Rice Flour Characteristics and Food Processing Properties Caused by a Mutant Allele of the PDIL1-1 Seed Storage Protein Gene. Rice, 15(1). https://doi.org/10.1186/s12284-022-00560-w
IPGRI. (1995). Descriptors for coconut (Cocos nucifera L.). International Plant Genetic Resources Institute.
Kano-Nakata, M., Mitsuya, S., Inukai, Y., Suralta, R., Niones, J., Kawai, T., & Yamauchi, A. (2024). Root Plasticity for Adaptation and Productivity of Crop Plants Grown Under Various Water Stresses (pp. 37–63). Springer Nature. https://doi.org/10.1007/978-981-99-9112-9_3
Khoury, C. K., Brush, S., Costich, D. E., Curry, H. A., de Haan, S., Engels, J. M. M., Guarino, L., Hoban, S., Mercer, K. L., Miller, A. J., Nabhan, G. P., Perales, H. R., Richards, C., Riggins, C., & Thormann, I. (2022). Crop genetic erosion: understanding and responding to loss of crop diversity. In New Phytologist (Vol. 233, Number 1, pp. 84–118). John Wiley and Sons Inc. https://doi.org/10.1111/nph.17733
Kumar, R., Munshi, A., Behera, T. K., Jat, G. S., Choudhary, H., Talukdar, A., Dash, P., & Singh, D. (2022). Association mapping, trait variation, interaction and population structure analysis in cucumber (Cucumis sativus L.). Genetic Resources and Crop Evolution, 69(5), 1901–1917. https://doi.org/10.1007/s10722-022-01352-3
Lambers, H., & Oliveira, R. S. (2019). Growth and Allocation. In H. Lambers & R. S. Oliveira (Eds.), Plant Physiological Ecology (pp. 385–449). Springer International Publishing. https://doi.org/10.1007/978-3-030-29639-1_10
Langstroff, A., Heuermann, M. C., Stahl, A., & Junker, A. (2022). Opportunities and limits of controlled-environment plant phenotyping for climate response traits. Theoretical and Applied Genetics, 135(1). https://doi.org/10.1007/s00122-021-03892-1
Li, M., Liu, Z., Jiang, N., Laws, B., Tiskevich, C., Moose, S. P., & Topp, C. N. (2023). Topological data analysis expands the genotype to phenotype map for 3D maize root system architecture. Frontiers in Plant Science, 14. https://doi.org/10.3389/fpls.2023.1260005
Liu, Z., Hikosaka, K., Li, F., Zhu, L., & Jin, G. (2021). Plant size, environmental factors and functional traits jointly shape the stem radius growth rate in an evergreen coniferous species across ontogenetic stages. Journal of Plant Ecology, 14(2), 257–269. https://doi.org/10.1093/jpe/rtaa093
Ma, Z. (Sam), Li, L., & Zhang, Y. P. (2020). Defining Individual-Level Genetic Diversity and Similarity Profiles. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-62362-8
Mable, B. K. (2019). Conservation of adaptive potential and functional diversity: integrating old and new approaches. Conservation Genetics, 20(1), 89–100. https://doi.org/10.1007/s10592-018-1129-9
Madić, M., Knežević, D., Paunović, A., & Đurović, D. (2016). Plant height and internode length as components of lodging resistance in barley. In Original research paper Acta Agriculturae Serbica: XXI.
Morales, H. E., Faria, R., Johannesson, K., Larsson, T., Panova, M., Westram, A. M., & Butlin, R. K. (2026). Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast. Science Advances, 5(12), eaav9963. https://doi.org/10.1126/sciadv.aav9963
O’Hara, K. E., Zozaya, S. M., Hahn, E. E., Holleley, C. E., & Moritz, C. (2026). Repeated Independent Formation of Triploid Lineages Contributes to Clonal Diversity in Heteronotia binoei Parthenogens. Molecular Ecology, 35(2), e70240. https://doi.org/10.1111/mec.70240
Pangestu, D. A., Sutjahjo, S. H., & Ritonga, A. W. (2023). Genetic and morphological diversity of various corn lines for the determination of waxy corn (Zea mays var. ceratina) parents. Biodiversitas, 24(10), 5643–5652. https://doi.org/10.13057/biodiv/d241046
Parvizi, E., Fraser, C. I., & Waters, J. M. (2022a). Genetic impacts of physical disturbance processes in coastal marine ecosystems. Journal of Biogeography, 49(10), 1877–1890. https://doi.org/https://doi.org/10.1111/jbi.14464
Parvizi, E., Fraser, C. I., & Waters, J. M. (2022b). Genetic impacts of physical disturbance processes in coastal marine ecosystems. Journal of Biogeography, 49(10), 1877–1890. https://doi.org/https://doi.org/10.1111/jbi.14464
Pecetti, L., Annicchiarico, P., Crosta, M., Notario, T., Ferrari, B., & Nazzicari, N. (2023). White Lupin Drought Tolerance: Genetic Variation, Trait Genetic Architecture, and Genome-Enabled Prediction. International Journal of Molecular Sciences, 24(3). https://doi.org/10.3390/ijms24032351
Pillay, M. (2024). The Genetic Homogeneity of Uganda’s East African Highland Bananas (Mutika/Lujugira) Does Not Match the Extensive Morphological Variation Identified in this Subgroup. International Journal of Plant Biology, 15(2), 267–280. https://doi.org/10.3390/ijpb15020023
Rajesh, M. K., Gangurde, S. S., Pandey, M. K., Niral, V., Sudha, R., Jerard, B. A., Kadke, G. N., Sabana, A. A., Muralikrishna, K. S., & Samsudeen, K. (2021). Insights on Genetic Diversity, Population Structure, and Linkage Disequilibrium in Globally Diverse Coconut Accessions Using Genotyping-by-Sequencing. OMICS A Journal of Integrative Biology, 25(12), 796–809. https://doi.org/10.1089/omi.2021.0159
Scherdel, P., Dunkel, L., van Dommelen, P., Goulet, O., Salaün, J.-F., Brauner, R., Heude, B., & Chalumeau, M. (2016). Growth monitoring as an early detection tool: a systematic review. The Lancet Diabetes & Endocrinology, 4(5), 447–456. https://doi.org/10.1016/S2213-8587(15)00392-7
Singh, S., Dhatt, K. K., & Kumar, P. (2023). Exploring genetic diversity of Dahlia (Dahlia variabilis Desf.) germplasm using multivariate statistics. Journal of Horticultural Sciences, 18(1), 67–76. https://doi.org/10.24154/jhs.v18i1.2149
Swarup, S., Cargill, E. J., Crosby, K., Flagel, L., Kniskern, J., & Glenn, K. C. (2021). Genetic diversity is indispensable for plant breeding to improve crops. Crop Science, 61(2), 839–852. https://doi.org/https://doi.org/10.1002/csc2.20377
Thakur, N. R., Ingle, K. P., Sargar, P. R., Baraskar, S. S., Kasanaboina, K., Awio, B., Pranati, J., & Abdi, G. (2024). Sustainable Utilization of Wild Germplasm Resources. In J. M. Al-Khayri, S. M. Jain, & S. Penna (Eds.), Sustainable Utilization and Conservation of Plant Genetic Diversity (pp. 551–590). Springer Nature Singapore. https://doi.org/10.1007/978-981-99-5245-8_16
Thurman, L. L., Stein, B. A., Beever, E. A., Foden, W., Geange, S. R., Green, N., Gross, J. E., Lawrence, D. J., LeDee, O., Olden, J. D., Thompson, L. M., & Young, B. E. (2020). Persist in place or shift in space? Evaluating the adaptive capacity of species to climate change. Frontiers in Ecology and the Environment, 18(9), 520–528. https://doi.org/https://doi.org/10.1002/fee.2253
Uddin, S., Jaskani, M. J., Deng, Z., Maqbool, R., Abbas Naqvi, S. A., Parajuli, S., Sharif, N., Saleem, A. R., Ledon, S., & Ikram, S. (2024). Phenotypic and Molecular-Markers-Based Assessment of Jamun (Syzygium cumini) Genotypes from Pakistan. Horticulturae, 10(8). https://doi.org/10.3390/horticulturae10080879
Wang, C., Gong, H., Feng, M., & Tian, C. (2023). Phenotypic Variation in Leaf, Fruit and Seed Traits in Natural Populations of Eucommia ulmoides, a Relict Chinese Endemic Tree. Forests, 14(3). https://doi.org/10.3390/f14030462
Yadav, N. K., Patel, A. B., Singh, S. K., Mehta, N. K., Anand, V., Lal, J., Dekari, D., & Devi, N. C. (2024). Climate change effects on aquaculture production and its sustainable management through climate-resilient adaptation strategies: a review. Environmental Science and Pollution Research, 31(22), 31731–31751. https://doi.org/10.1007/s11356-024-33397-5
Yazgi, A., & Degirmencioglu, A. (2007). Optimisation of the seed spacing uniformity performance of a vacuum-type precision seeder using response surface methodology. Biosystems Engineering, 97(3), 347–356. https://doi.org/https://doi.org/10.1016/j.biosystemseng.2007.03.013
Zainol, F. A., Arumugam, N., Daud, W. N. W., Suhaimi, N. A. M., Ishola, B. D., Ishak, A. Z., & Afthanorhan, A. (2023). Coconut Value Chain Analysis: A Systematic Review. Agriculture, 13(7), 1379. https://doi.org/10.3390/agriculture13071379
Zapico, F. L., Dizon, J. T., Borromeo, T. H., McNally, K. L., Fernando, E. S., & Hernandez, J. E. (2020). Genetic erosion in traditional rice agro-ecosystems in Southern Philippines: drivers and consequences. Plant Genetic Resources: Characterization and Utilization, 18(1), 1–10. https://doi.org/DOI: 10.1017/S1479262119000406
Zeltinš, P., Matisons, R., Gailis, A., Jansons, J., Katrevičs, J., & Jansons, Ā. (2018). Genetic parameters of growth traits and stem quality of silver birch in a low-density clonal plantation. Forests, 9(2). https://doi.org/10.3390/f9020052
Zhang, J., He, Y., Liu, J., Fan, J., Shang, J., & Yan, X. (2024). Integrating spectral data and phylogeographic patterns to study plant genetic variation: a review. In Grass Research (Vol. 4). Maximum Academic Press. https://doi.org/10.48130/grares-0024-0009
Zhang, Q., Holyoak, M., Chen, C., Liu, Z., Liu, J., Che, X., Dong, A., Yang, C., & Zou, F. (2020). Trait-mediated filtering drives contrasting patterns of species richness and functional diversity across montane bird assemblages. Journal of Biogeography, 47(1), 301–312. https://doi.org/https://doi.org/10.1111/jbi.13738
Zhang, R., Cao, H., Sun, C., & Martin, J. J. J. (2021). Characterization of Morphological and Fruit Quality Traits of Coconut (Cocos nucifera L.) Germplasm. HortScience, 56(8), 961–969. https://doi.org/10.21273/HORTSCI15887-21
Zhang, R., Shan, F., Wang, C., Yan, C., Dong, S., Xu, Y., Gong, Z., & Ma, C. (2020). Internode elongation pattern, internode diameter and hormone changes in soybean (Glycine max) under different shading conditions. Crop and Pasture Science, 71(7), 679–688. https://doi.org/10.1071/CP20071
Zhao, Y., Wang, H. J., Yang, B., Li, P. B., Kuerban, Z., Wang, H., Feng, G., & Hu, X. (2026). Multivariate trait profiling and genetic diversity in a global foxtail millet germplasm panel. Plant Biology. https://doi.org/10.1111/plb.70183
Zimmerman, S. J., Aldridge, C. L., & Oyler-McCance, S. J. (2020). An empirical comparison of population genetic analyses using microsatellite and SNP data for a species of conservation concern. BMC Genomics, 21(1), 382. https://doi.org/10.1186/s12864-020-06783-9
DOI: http://dx.doi.org/10.21043/jobe.v9i1.37200
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