Geographical differentiation and genetic diversity of Algerian pearl millet assessed with microsatellites
Keywords:
pearl millet, SSR marker, genetic diversity, regional diversity, Algerian landraces
Abstract
Pearl millet, a drought-tolerant cereal, is a crucial role in food security, in arid and semi-arid regions. Despite its global significance, genetic diversity of Algerian pearl millet populations remains underexplored. This study assessed the genetic diversity of 22 pearl millet genotypes from four distinct Saharan agroclimatic zones in Algeria using 24 SSR markers. A total of 87 alleles were detected, with an average of 3.62 alleles per locus and polymorphic information content (PIC) values ranging from 0.043 to 0.815, indicating substantial genetic variability. Analysis of Molecular Variance (AMOVA) revealed greater genetic variance within individuals than among them. Genotypes from Tamanrasset and In Salah exhibited higher diversity than those from Oued Souf and Adrar, with private and rare alleles underscoring the impact of geographic isolation. Cluster analysis and principal coordinates analysis (PCoA) grouped genotypes by geographic origin, identifying five major genetic groups, confirming patterns of gene flow and local adaptation. Populations from Niger and India were highly genetic distant from Algerian landraces making them promising candidates for heterotic hybrid development. These findings provide insights for broadening the genetic base of breeding strategies targeting yield and stress resilience in pearl millet.
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References
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Kirouani, A., Boukhalfoun, L., Ouldkiar, R., & Bouzerzour, H. (2023). Analysis of the effect of GE interaction on the grain yield and its related traits in rainfed Algerian durum wheat (Triticum turgidum L. var. durum) grown in contrasting environments. Revista Facultad Nacional de Agronomia Medellin, 76(2), 10297-10308. https://doi.org/10.15446/rfnam.v76n2.102517
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Mariac, C., Luong, V., Kapran, I., Mamadou, A., Sagnard, F., Deu, M., Chantereau, J., Gerard, B., Ndjeunga, J., Bezançon, G., Pham, J. L., & Vigouroux, Y. (2006). Diversity of wild and cultivated pearl millet accessions (Pennisetum glaucum [L.] R. Br.) in Niger assessed by microsatellite markers. Theoretical and Applied Genetics,114(1), 49-58. https://doi.org/10.1007/s00122-006-0409-9
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Satyavathi, C. T., Ambawat, S., Khandelwal, V., & Srivastava, R. K. (2021). Pearl millet: A climate-resilient nutricereal for mitigating hidden hunger and providing nutritional security. Frontiers in Plant Science, 12, 659938. https://doi.org/10.3389/fpls.2021.659938
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Shinde, H., Dudhate, A., Anand, L., Tsugama, D., Gupta, S. K., Liu, S., & Takano, T. (2020). Small RNA sequencing reveals the role of pearl millet miRNAs and their targets in salinity stress responses. South African Journal of Botany, 132, 395-402. https://doi.org/10.1016/j.sajb.2020.06.011
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Bhardwaj, R., Garg, T., Malik, E. A., Vikal, Y., Sohu, R. S., & Gupta, S. K. (2018). Genetic divergence studies in pearl millet [Pennisetum glaucum L. (R.) Br.] inbred lines. Indian Journal of Genetics and Plant Breeding, 78(3), 382-385. http://oar.icrisat.org/id/eprint/10854
Bougma, L. A., Ouédraogo, M. H., Ouoba, A., Zouré, A. A., Sawadogo, N., & Sawadogo, M. (2021). Genetic differentiation for gene diversity among pearl millet (Pennisetum glaucum (L.) R. Br.) landraces as revealed by SSR markers. International Journal of Agronomy, 2021(1). https://doi.org/10.1155/2021/6160903
Chandra, S., Singh, S. P., Kaswan, V., Chaudhary, S., Singh, A. M., Sankar, M., Meena, G., Choudhary, M., & Chellapilla, T. S. (2020). Morphological and molecular genetic diversity analysis of pearl millet (Pennisetum glaucum) maintainers and restorers. Indian Journal of Agricultural Sciences, 90(11), 2083-2089. https://doi.org/10.56093/ijas.v90i11.108564
Choudhary, M., Hossain, F., Muthusamy, V., Thirunavukkarasu, N., Saha, S., Pandey, N., Jha, S. K., & Gupta, H. S. (2016). Microsatellite marker-based genetic diversity analyses of novel maize inbreds possessing rare allele of β-carotene hydroxylase (crtRB1) for their utilization in β-carotene enrichment. Journal of Plant Biochemistry and Biotechnology, 25(1), 12-20. https://doi.org/10.1007/s13562-015-0300-3
Deevi, C. K., Swamikannu, N., Pingali, P. R., & Gumma, M. K. (2024). Current Trends and Future Prospects in Global Production, Utilization, and Trade of Pearl Millet. In V. A. Tonapi., N. Thirunavukkarasu., S. Gupta., P. I. Gangashetty., & O. Yadav (Eds.), Pearl Millet in the 21st Century. Springer Nature, Singapore. https://doi.org/10.1007/978-981-99-5890-0
Lemgharbi, M., Belhadi, B., Souilah, R., Djabali, D., & Nadjemi, B. (2023). Biodiversity of pearl millet (Pennisetum glaucum [L.] R. Br.) in southern Algeria (Tidikelt region). Biodiversity Journal, 14(3), 491-504. https://doi.org/10.31396/Biodiv.Jour.2023.14.3.491.504
Evanno, G., Regnaut, S., & Goudet, J. (2005). Detecting the number of clusters using the software STRUCTURE: a simulation study. Molecular Ecology, 14(8), 2611-2620. https://doi.org/10.1111/j.1365-294X.2005.02553.x
Fulton, T. M., Chunwongse, J., & Tanksley, S.D. (1995). Microprep protocol for extraction of DNA from tomato and other herbaceous plants. Plant Molecular Biology Reporter, 13(3), 207-209. https://doi.org/10.1007/BF02670897
Govindaraj, M., Rai, K. N., Kanatti, A., Upadhyaya, H. D., Shivade, H., & Rao, A. S. (2020). Exploring the genetic variability and diversity of pearl millet core-collection germplasm for grain nutritional traits improvement. Scientific Reports, 10, 21177. https://doi.org/10.1038/s41598-020-77818-0
Gunguniya, D. F., Kumar, S., Patel, M. P., Sakure, A. A., Patel, R., Kumar, D., & Khandelwal, V. (2023). Morpho-biochemical characterization and molecular marker based genetic diversity of pearl millet (Pennisetum glaucum (L.) R. Br.). PeerJ, 11, e15403. https://doi.org/10.7717/peerj.15403
Gupta, S. K., Nepolean, T., Shaikh, C. G., Rai, K., Hash, C. T., Das, R. R., & Rathore, A. (2018). Phenotypic and molecular diversity-based prediction of heterosis in pearl millet (Pennisetum glaucum L. (R.) Br.). The Crop Journal, 6(3), 271-281. https://doi.org/10.1016/j.cj.2017.09.008
Kirouani, A., Boukhalfoun, L., Ouldkiar, R., & Bouzerzour, H. (2023). Analysis of the effect of GE interaction on the grain yield and its related traits in rainfed Algerian durum wheat (Triticum turgidum L. var. durum) grown in contrasting environments. Revista Facultad Nacional de Agronomia Medellin, 76(2), 10297-10308. https://doi.org/10.15446/rfnam.v76n2.102517
Kirouani, A., Henkrar, F., Udupa, S. M., Boukhalfoun, L., & Bouzerzour, H. (2018). Genetic diversity in Algerian durum wheat varieties (Triticum turgidum L. var. durum) using microsatellite markers. Bioscience Journal, 34(6), 1575-1583. https://doi.org/10.14393/BJ-v34n6a2018-42332
Kuang, Z., Xiao, C., Ilyas, M. K., Ibrar, D., Khan, S., Guo, L., Wang, W., Wang, B., Huang, H., Li, Y., Li, Y., Zheng, J., Saleem, S., Tahir, A., Ghafoor, A., & Chen, H. (2022). Use of SSR Markers for the Exploration of Genetic Diversity and DNA Finger-Printing in Early-Maturing Upland Cotton (Gossypium hirsutum L.) for Future Breeding Program. Agronomy, 12(7), 1513. https://doi.org/10.3390/agronomy12071513
Kumar, S., Hash, C. T., Singh, G., Basava, R. K., & Srivastava, R. K. (2020). Identification of polymorphic SSR markers in elite genotypes of pearl millet and diversity analysis. Ecological Genetics and Genomics, 14, 100051. https://doi.org/10.1016/j.egg.2019.100051
Liu, K., & Muse, S. V. (2005). PowerMaker: An integrated analysis environment for genetic maker analysis. Bioinformatics, 21(9), 2128-2129. https://doi.org/10.1093/bioinformatics/bti282
Makwana, K., Tiwari, S., Tripathi, M. K., Sharma, A. K., Pandya, R. K., & Singh, A. K. (2021). Morphological characterization and DNA finger printing of pearl millet (Pennisetum Glaucum (L.) germplasms. Range Management and Agroforestry, 42(2), 205-221.
Manning, K., Pelling, R., Higham, T., Schwenniger, J.-L., & Fuller, D. Q. (2011). 4500-year-old domesticated pearl millet (Pennisetum glaucum) from the Tilemsi Valley, Mali: New insights into an alternative cereal domestication pathway. Journal of Archaeological Science, 38(2), 312-322. https://doi.org/10.1016/j.jas.2010.09.007
Mariac, C., Luong, V., Kapran, I., Mamadou, A., Sagnard, F., Deu, M., Chantereau, J., Gerard, B., Ndjeunga, J., Bezançon, G., Pham, J. L., & Vigouroux, Y. (2006). Diversity of wild and cultivated pearl millet accessions (Pennisetum glaucum [L.] R. Br.) in Niger assessed by microsatellite markers. Theoretical and Applied Genetics,114(1), 49-58. https://doi.org/10.1007/s00122-006-0409-9
Nepolean, T., Gupta, S.K., Dwivedi, S. L., Bhattacharjee, R., Rai, K. N., & Hash, C. T. (2012). Genetic diversity in maintainer and restorer lines of pearl millet. Crop Science, 52(6), 2555-2563. https://doi.org/10.2135/cropsci2011.11.0597
Oumar, I., Mariac, C., Pham, J.-L., & Vigouroux, Y. (2008). Phylogeny and origin of pearl millet (Pennisetum glaucum [L.] R. Br.) as revealed by microsatellite loci. Theoretical and Applied Genetics, 117, 489-497. https://doi.org/10.1007/s00122-008-0793-4
Peakall, R., & 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. https://doi.org/10.1093/bioinformatics/bts460
Ramya, A. R., Ahamed, M. L., Satyavathi, C. T., Rathore, A., Katiyar, P., Bhasker Raj, A. G., Kumar, S., Gupta, R., Mahendrakar, M. D., Yadav, R. S., & Srivastava, R. K. (2018). Towards defining heterotic gene pools in pearl millet [Pennisetum glaucum (L.) R. Br.]. Frontiers in Plant Science, 8, 1-11. https://doi.org/10.3389/fpls.2017.01934
Rani, R., Khandelwal, V., Jhunjhadia, S., Ambawat, S., Bhanwariya, S., Singh, A., & Kumar, V. (2024). Quantifying genetic diversity based on morphological and molecular analysis in pearl millet [Pennisetum glaucum (L.) R. Br.] inbred lines. Annals of Arid Zone, 63(3), 105-110. https://epubs.icar.org.in/index.php/AAZ/article/view/151562
Rhoné, B., Defrance, D., Berthouly-Salazar, C., Mariac, C., Cubry, P., Couderc, M., Dequincey, A., Assoumane, A., Kane, N. A., Sultan, B., Barnaud, A., & Vigouroux, Y. (2020). Pearl millet genomic vulnerability to climate change in West Africa highlights the need for regional collaboration. Nature Communications, 11, 5274. https://doi.org/10.1038/s41467-020-19066-4
Sangwan, S., Yashveer, S., Kumar, R., Hemender, Sharma, S., & Redhu, N. (2019). Multi trait analysis reveals substantial diversity in pearl millet [Pennisetum glaucum (L.) R. Br.] inbred lines. Journal of Experimental Biology and Agricultural Sciences, 7(4), 358-375. https://doi.org/10.18006/2019.7(4).358.375
Satyavathi, C. T., Ambawat, S., Khandelwal, V., & Srivastava, R. K. (2021). Pearl millet: A climate-resilient nutricereal for mitigating hidden hunger and providing nutritional security. Frontiers in Plant Science, 12, 659938. https://doi.org/10.3389/fpls.2021.659938
Sawadogo, N., Nanema, R. K., Bationo/Kando, P., Traore, R. E., Nebie, B., Tiama, D., Sawadogo, M., & Zongo, J. D. (2015). Évaluation de la diversité génétique des sorghos à grains sucrés (Sorghum bicolor (L.) Moench) du Nord du Burkina Faso. Journal of Applied Biosciences, 84(1), 7654. https://doi.org/10.4314/jab.v84i1.3
Serba, D. D., & Yadav, R. S. (2016). Genomic tools in pearl millet breeding for drought tolerance: Status and prospects. Frontiers in Plant Science, 7, 1724. https://doi.org/10.3389/fpls.2016.01724
Shinde, H., Dudhate, A., Anand, L., Tsugama, D., Gupta, S. K., Liu, S., & Takano, T. (2020). Small RNA sequencing reveals the role of pearl millet miRNAs and their targets in salinity stress responses. South African Journal of Botany, 132, 395-402. https://doi.org/10.1016/j.sajb.2020.06.011
Singh, A. K., Rana, M. K., Singh, S., Kumar, S., Durgesh, K., & Arya, L. (2013). Assessment of genetic diversity among pearl millet [Pennisetum glaucum (L.) R Br.] cultivars using SSR markers. Range Management and Agroforestry, 34(1), 77-81. https://publications.rmsi.in/index.php/rma/article/view/459/426
Singh, S., & Gupta, S. K. (2019). Formation of heterotic pools and understanding relationship between molecular divergence and heterosis in pearl millet [Pennisetum glaucum (L.) R. Br.]. PLoS ONE, 14(5), e0207463. https://doi.org/10.1371/JOURNAL.PONE.0207463
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Published
2025-12-08
How to Cite
Kirouani, A., Babay, E., Ouldkiar, R., Belhadi, B., Souilah, R., Boukhalfoun, L., Djabali, D., & Nadjemi, B. (2025). Geographical differentiation and genetic diversity of Algerian pearl millet assessed with microsatellites. Revista De La Facultad De Agronomía De La Universidad Del Zulia, 42(4), e254256. Retrieved from https://produccioncientifica.luz.edu.ve/index.php/agronomia/article/view/44866
Issue
Section
Crop Production
Copyright (c) 2025 Abderrezzak Kirouani, Elyes Babay, Redha Ouldkiar, Badreddine Belhad, Rachid Souilah, Leila Boukhalfoun, Djaafar Djabali, Boubekeur Nadjemi
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
