Genetic Variability and Multivariate Analysis of Agro-Morphological Traits in Selected Rice Germplasm (Oryza sativa L.) of India
Abstract
Thirty-six valuable rice germplasm accessions were collected from different regions of West Bengal and evaluated at the experimental farms of The Neotia University, located in the coastal saline zone of West Bengal, India. The mini-core collection is maintained at the university through periodic seed multiplication during the rainy (kharif) season. The accessions were evaluated for twenty-four agro-morphological traits over two consecutive years (2022 and 2023) during the kharif season. The study revealed that two traits—number of tillers (84.488%) and panicles per plant (84.478%)—exhibited the highest heritability, followed by 1000-grain weight (77.627%), days to 50% flowering (74.938%), and panicle length (72.623%). High genotypic coefficient of variation was observed for total yield (42.969%), chaffy grains per panicle (32.656%), leaf area (31.278%), number of tillers per plant (28.621%), 1000-grain weight (27.525%), and filled grains per panicle (27.523%). The highest genetic advance was recorded for total grain number per panicle (68.471%), followed by filled grains per panicle (54.431%). Principal component analysis of the twenty-four traits resulted in eight components with eigenvalues greater than 1. These eight components together accounted for 84.78% of the cumulative variance of the population. The first principal component explained the highest proportion of variance (20.09%), followed by the second (16.67%), third (12.96%), and fourth (10.48%) components. The germplasm bank represents unique traits such as low-input rice, aromatic and non-aromatic fine-grained rice, and micronutrient-rich landraces. This collection, with its diverse and distinctive characteristics, represents a climate-smart gene pool encompassing a broad range of life cycles, enabling adaptation and resilience under unpredictable climatic adversities. The present study successfully identified, integrated, and conserved elite genetic resources that are important for future rice improvement programs.
Keywords:
Agro-Morphological Traits, Food Security, Genetic Advance, Multivariate Analysis, Rice Mini Core Collection
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References
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Govindaraju, I., Das, A. R., Chakraborty, I., Mal, S. S., Sarmah, B., Baruah, V. J., & Mazumder, N. (2025). Investigation of the physicochemical factors affecting the in vitro digestion and glycemic indices of indigenous indica rice cultivars. Scientific Reports, 15(1), 2336. https://doi.org/10.1038/s41598-025-85660-5
Harshitha, P., Jeyaprakash, P., Geetha, K., Selvam, S., & Vanniarajan, C. (2023). Genetic analysis of quality traits in non-aromatic rice varieties for export potential. Electronic Journal of Plant Breeding, 14(3), 1174-1184. https://doi.org/10.37992/2023.1403.139
Salunkhe, H., Kumar, A., Janeja, H. S., Krishna, B., Talekar, N., Mehandi, S., & Pawar, P. (2024) Genetic variability, correlation and path-coefficient analysis for yield and yield attributing traits in aerobic rice (Oryza sativa L.). Electronic Journal of Plant Breeding, 15(1), 226-232. https://doi.org/10.37992/2024.1501.026
Husnah, Y. A., Turhadi, T., Safitri, A., & Fatchiyah, F. (2024). Morphoagronomical Evaluation of Several Indonesian Pigmented Rice (Oryza sativa L.) Accessions from East Java and Central Java, Indonesia. Plant Breeding and Biotechnology, 12, 122-137. https://doi.org/10.9787/PBB.2024.12.122
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Jagadeesh, K., Mahto, C. S., Kumar, N., & Lal, H. C. (2024). Genetic diversity and character association studies for agro-morphological and quality traits of advanced breeding lines in field pea (Pisum sativum L.). Electronic Journal of Plant Breeding, 15(4), 912-920. https://doi.org/10.37992/2024.1504.098
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Khoury, C. K., Brush, S., Costich, D. E., Curry, H. A., De Haan, S., Engels, J. M., ... & Thormann, I. (2022). Crop genetic erosion: understanding and responding to loss of crop diversity. New Phytologist, 233(1), 84-118. https://doi.org/10.1111/nph.17733
Kumar, R. H., Sharma, U., Kumar, B., & Verma, P. (2023). Comparative Analysis of Traditional Scented Rice (Oryza sativa L.) Varieties under Organic Cultivation Based on DUS Testing and Yield Assessment. International Journal of Plant & Soil Science, 35(18), 1474-1483. https://doi.org/10.9734/ijpss/2023/v35i183415
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Maiti, A., Hasan, M. K., Sannigrahi, S., Bar, S., Chakraborti, S., Mahto, S. S., ... & Zhang, Q. (2024). Optimal rainfall threshold for monsoon rice production in India varies across space and time. Communications Earth & Environment, 5(1), 302. https://doi.org/10.1038/s43247-024-01414-7
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Mohanty, S. P., Khan, A., Patra, S., Behera, S., Nayak, A. K., Upadhyaya, S., ... & Sah, R. P. (2025). Unraveling the genetic diversity in selected rice cultivars released in the last 60 years using gene-based yield-related markers. Genetic Resources and Crop Evolution, 72(3), 3733-3747. https://doi.org/10.1007/s10722-024-02175-0
Moulick, D., Ghosh, D., Skalicky, M., Gharde, Y., Mazumder, M. K., Choudhury, S., ... & Hossain, A. (2022). Interrelationship among rice grain arsenic, micronutrients content and grain quality attributes: An investigation from genotype× environment perspective. Frontiers in Environmental Science, 10, 857629. https://doi.org/10.3389/fenvs.2022.857629
Mulsanti, I. W., Risliawati, A., & Yunani, N. (2021, December). Agro-morphological characterization based genetic diversity of Indonesian local rice germplasm. In IOP Conference Series: Earth and Environmental Science (Vol. 948, No. 1, p. 012004). IOP Publishing. .https://iopscience.iop.org/article/10.1088/1755-1315/948/1/012004
Ozturk, O., Jarrett, R., & Kravchuk, O. (2024). Order Restricted Randomized Block Designs. Journal of Agricultural, Biological and Environmental Statistics, 29(4), 831-852. https://doi.org/10.1007/s13253-023-00590-x
Prakash, S., Reddy, S. S., Chaudhary, S., Vimal, S., & Kumar, A. (2024). Multivariate analysis in rice (Oryza sativa L.) germplasms for yield attributing traits. Plant Science Today, 11(1), 64-75. https://doi.org/10.14719/pst.2231
Ribeiro-Filho, N., dos Santos Borges, S. R., de Menezes, P. H., de Oliveira, M. R. T., & da Silva, A. P. G. (2024). Red rice (Oryza sativa L.) composition and its water interaction. Food and Humanity, 2, 100299. https://doi.org/10.1016/j.foohum.2024.100299
Sarkar, N. S., Kalaimagal, T., Kavithamani, D., Chandirakala, R., Manonmani, S., Raveendran, M., & Senthil, A. (2024). Assessing genetic relationships, trait associations and diversity patterns in sorghum germplasm through correlation, cluster and principle component analysis. Agricultural Science Digest, 44(3), 445-452. https://doi.org/10.18805/ag.D-5896
Senthilvel, V., Pelhania, G., Moorthy, G., Sukumar, Y., Rajendran, P. A., Krishnaswamy, S. K., ... & Jegadeesan, R. (2025). Stacking of elite indica rice genotype with bacterial blight, blast, and Brown plant hopper resistance genes through marker assisted selection. Physiological and Molecular Plant Pathology, 138, 102730. https://doi.org/10.1016/j.pmpp.2025.102730
Singh, A. K., Lal, K., Singh, V., Tripathy, S., Kumar, A., Singh, N., & Singh, A. (2024). Studies on estimates of heritability and genetic advance for certain quantitative traits in fieldpea (Pisum sativum L. var. arvense). International Journal of Plant & Soil Science, 36(7), 393-398. https://doi.org/10.9734/ijpss/2024/v36i74744
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Thilavech, T., Suantawee, T., Chusak, C., Suklaew, P. O., & Adisakwattana, S. (2025). Black rice (Oryza sativa L.) and its anthocyanins: mechanisms, food applications, and clinical insights for postprandial glycemic and lipid regulation. Food Production, Processing and Nutrition, 7(1), 15. https://doi.org/10.1186/s43014-024-00288-8
Tran, X. H., Tran, T. S., Ho, T., Truong, T. H., Nguyen, D. T., & Nguyen, T. L. (2025). Agro-Morphological Characteristics and Genetic Diversity of Traditional Glutinous Rice Varieties in Quang Ngai Province, Vietnam. International Journal of Environment, Agriculture and Biotechnology, 10(1), 592922. https://dx.doi.org/10.22161/ijeab.101.11
Anumalla, M., Khanna, A., Catolos, M., Ramos, J., Sta. Cruz, M. T., Venkateshwarlu, C., ... & Hussain, W. (2025). Future flooding tolerant rice germplasm: Resilience afforded beyond Sub1A gene. The Plant Genome, 18(2), e70040. https://doi.org/10.1002/tpg2.70040
Anwar, A., Tabassum, J., Ahmad, S., Ashfaq, M., Hussain, A., Ullah, M. A., ... & Javed, M. A. (2025). Screening and assessment of genetic diversity of rice (Oryza sativa L.) germplasm in response to soil salinity stress at germination stage. Agronomy, 15(2), 376. https://doi.org/10.3390/agronomy15020376
Azeez, M. A., Adubi, A. O., & Durodola, F. A. (2018). Landraces and crop genetic improvement. In Rediscovery of Landraces as a Resource for the Future. IntechOpen. https://doi.org/10.5772/intechopen.75944
Bhogal, A. S., Sharma, G., Das, B. K., Das, R., Deka, S. D., Sharma, K. K., & Sarma, D. (2025). Morpho-agronomic variability in photoperiod insensitive aromatic Joha rice mutants under late Sali situation in Assam. Vegetos, 1-13. https://doi.org/10.1007/s42535-025-01236-8
Cai, X., He, W., Qian, Q., & Shang, L. (2025). Genetic resource utilization in wild rice species: Genomes and gene bank. New Crops, 2, 100065. https://doi.org/10.1016/j.ncrops.2025.100065
Chen, T., Pu, N., Ni, M., Xie, H., Zhao, Z., Hu, J., ... & Wang, H. (2025). Development of Fragrant Thermosensitive Genic Male Sterile Line Rice Using CRISPR/Cas9. Agronomy, 15(2), 411. https://doi.org/10.3390/agronomy15020411
Dixit, D., Siddiqui, N., Bollinedi, H., Krishnan, G., Malik, A., Bhowmick, P. K., ... & Singh, A. K. (2022). Assessment of agro-morphological traits, grain physical and physico-chemical properties in the Indian aromatic rice (Oryza sativa) germplasm. Indian Journal of Agricultural Sciences, 92(9), 1157-1161. https://doi.org/10.56093/ijas.v92i9.124304
Duppala, M. K., Srinivas, T., LV, S. R., Suneetha, Y., Sundaram, R. M., Satyanaryana, P. V., ... & Singh, G. (2025). (2025) Marker-assisted backcross breeding for bacterial blight, blast and tolerance to low soil phosphorus in rice (Oryza sativa L.). PREPRINT (Version 1) available at Research Square. https://doi.org/10.21203/rs.3.rs-6286636/v1
Faysal, A. S. M., Ali, L., Azam, M. G., Sarker, U., Ercisli, S., Golokhvast, K. S., & Marc, R. A. (2022). Genetic variability, character association, and path coefficient analysis in transplant Aman rice genotypes. Plants, 11(21), 2952. https://doi.org/10.3390/plants11212952
Fritsche-Neto, R., Ali, J., De Asis, E. J., Allahgholipour, M., & Labroo, M. R. (2024). Improving hybrid rice breeding programs via stochastic simulations: number of parents, number of hybrids, tester update, and genomic prediction of hybrid performance. Theoretical and Applied Genetics, 137(1), 3. https://doi.org/10.1007/s00122-023-04508-6
Ganapati, R. K., Chen, K., Zhao, X., Zheng, T., Zhang, F., Zhai, L., & Xu, J. (2025). Genome-Wide Association Study and Haplotype Analysis Jointly Identify New Candidate Genes for Alkaline Tolerance at Seedling Stage in Rice. Rice Science, 32(4), 537-548. https://doi.org/10.1016/j.rsci.2025.04.006
Govindaraju, I., Das, A. R., Chakraborty, I., Mal, S. S., Sarmah, B., Baruah, V. J., & Mazumder, N. (2025). Investigation of the physicochemical factors affecting the in vitro digestion and glycemic indices of indigenous indica rice cultivars. Scientific Reports, 15(1), 2336. https://doi.org/10.1038/s41598-025-85660-5
Harshitha, P., Jeyaprakash, P., Geetha, K., Selvam, S., & Vanniarajan, C. (2023). Genetic analysis of quality traits in non-aromatic rice varieties for export potential. Electronic Journal of Plant Breeding, 14(3), 1174-1184. https://doi.org/10.37992/2023.1403.139
Salunkhe, H., Kumar, A., Janeja, H. S., Krishna, B., Talekar, N., Mehandi, S., & Pawar, P. (2024) Genetic variability, correlation and path-coefficient analysis for yield and yield attributing traits in aerobic rice (Oryza sativa L.). Electronic Journal of Plant Breeding, 15(1), 226-232. https://doi.org/10.37992/2024.1501.026
Husnah, Y. A., Turhadi, T., Safitri, A., & Fatchiyah, F. (2024). Morphoagronomical Evaluation of Several Indonesian Pigmented Rice (Oryza sativa L.) Accessions from East Java and Central Java, Indonesia. Plant Breeding and Biotechnology, 12, 122-137. https://doi.org/10.9787/PBB.2024.12.122
Izhar, M., & Zakaria, S. (2025, April). Agronomic performance and productivity of improved landraces rice lines under upland cultivation system. In IOP Conference Series: Earth and Environmental Science (Vol. 1476, No. 1, p. 012042). IOP Publishing. https://iopscience.iop.org/article/10.1088/1755-1315/1476/1/012042/meta
Jagadeesh, K., Mahto, C. S., Kumar, N., & Lal, H. C. (2024). Genetic diversity and character association studies for agro-morphological and quality traits of advanced breeding lines in field pea (Pisum sativum L.). Electronic Journal of Plant Breeding, 15(4), 912-920. https://doi.org/10.37992/2024.1504.098
Jin, Y., Liu, T., Hu, J., Sun, K., Xue, L., Bettembourg, M., ... & Sun, C. (2025). Reducing methane emissions by developing low-fumarate high-ethanol eco-friendly rice. Molecular Plant, 18(2), 333-349. https://www.cell.com/molecular-plant/abstract/S1674-2052(25)00029-2
Jing, C. Y., Zhang, F. M., Wang, X. H., Wang, M. X., Zhou, L., Cai, Z., ... & Ge, S. (2023). Multiple domestications of Asian rice. Nature Plants, 9(8), 1221-1235. https://doi.org/10.1038/s41477-023-01476-z
Khoury, C. K., Brush, S., Costich, D. E., Curry, H. A., De Haan, S., Engels, J. M., ... & Thormann, I. (2022). Crop genetic erosion: understanding and responding to loss of crop diversity. New Phytologist, 233(1), 84-118. https://doi.org/10.1111/nph.17733
Kumar, R. H., Sharma, U., Kumar, B., & Verma, P. (2023). Comparative Analysis of Traditional Scented Rice (Oryza sativa L.) Varieties under Organic Cultivation Based on DUS Testing and Yield Assessment. International Journal of Plant & Soil Science, 35(18), 1474-1483. https://doi.org/10.9734/ijpss/2023/v35i183415
Laghari, A. A., Ahmad, A., Memon, S., Musavi, S. A. M., Ali, A., Kumar, A., & Guo, Q. (2025). Genetic diversity in F3 segregating populations of rice (Oryza sativa L.) genotypes under salt stress. Frontiers in Plant Science, 16, 1568859. https://doi.org/10.3389/fpls.2025.1568859
Li, Y., Zhang, W., Li, M., Ling, X., Guo, D., Yang, Y., ... & Wang, J. (2025). Discovery of OsODC as a key enhancer of aroma and development of highly fragrant rice. Plant Communications, 6(1). https://www.cell.com/plant-communications/fulltext/S2590-3462(24)00537-6
Mahajan, S., Gupta, S., & Sharma, M. (2023). India vs China: scenario of rice crop. International Journal of Agricultural & Statistical Sciences, 19(2). http://dx.doi.org/10.59467/IJASS.2023.19.629
Maiti, A., Hasan, M. K., Sannigrahi, S., Bar, S., Chakraborti, S., Mahto, S. S., ... & Zhang, Q. (2024). Optimal rainfall threshold for monsoon rice production in India varies across space and time. Communications Earth & Environment, 5(1), 302. https://doi.org/10.1038/s43247-024-01414-7
Minitab, LLC. (2025). Minitab statistical software (Version 22.1) [Computer software]. https://www.minitab.com/en-us/
Mohanty, S. P., Khan, A., Patra, S., Behera, S., Nayak, A. K., Upadhyaya, S., ... & Sah, R. P. (2025). Unraveling the genetic diversity in selected rice cultivars released in the last 60 years using gene-based yield-related markers. Genetic Resources and Crop Evolution, 72(3), 3733-3747. https://doi.org/10.1007/s10722-024-02175-0
Moulick, D., Ghosh, D., Skalicky, M., Gharde, Y., Mazumder, M. K., Choudhury, S., ... & Hossain, A. (2022). Interrelationship among rice grain arsenic, micronutrients content and grain quality attributes: An investigation from genotype× environment perspective. Frontiers in Environmental Science, 10, 857629. https://doi.org/10.3389/fenvs.2022.857629
Mulsanti, I. W., Risliawati, A., & Yunani, N. (2021, December). Agro-morphological characterization based genetic diversity of Indonesian local rice germplasm. In IOP Conference Series: Earth and Environmental Science (Vol. 948, No. 1, p. 012004). IOP Publishing. .https://iopscience.iop.org/article/10.1088/1755-1315/948/1/012004
Ozturk, O., Jarrett, R., & Kravchuk, O. (2024). Order Restricted Randomized Block Designs. Journal of Agricultural, Biological and Environmental Statistics, 29(4), 831-852. https://doi.org/10.1007/s13253-023-00590-x
Prakash, S., Reddy, S. S., Chaudhary, S., Vimal, S., & Kumar, A. (2024). Multivariate analysis in rice (Oryza sativa L.) germplasms for yield attributing traits. Plant Science Today, 11(1), 64-75. https://doi.org/10.14719/pst.2231
Ribeiro-Filho, N., dos Santos Borges, S. R., de Menezes, P. H., de Oliveira, M. R. T., & da Silva, A. P. G. (2024). Red rice (Oryza sativa L.) composition and its water interaction. Food and Humanity, 2, 100299. https://doi.org/10.1016/j.foohum.2024.100299
Sarkar, N. S., Kalaimagal, T., Kavithamani, D., Chandirakala, R., Manonmani, S., Raveendran, M., & Senthil, A. (2024). Assessing genetic relationships, trait associations and diversity patterns in sorghum germplasm through correlation, cluster and principle component analysis. Agricultural Science Digest, 44(3), 445-452. https://doi.org/10.18805/ag.D-5896
Senthilvel, V., Pelhania, G., Moorthy, G., Sukumar, Y., Rajendran, P. A., Krishnaswamy, S. K., ... & Jegadeesan, R. (2025). Stacking of elite indica rice genotype with bacterial blight, blast, and Brown plant hopper resistance genes through marker assisted selection. Physiological and Molecular Plant Pathology, 138, 102730. https://doi.org/10.1016/j.pmpp.2025.102730
Singh, A. K., Lal, K., Singh, V., Tripathy, S., Kumar, A., Singh, N., & Singh, A. (2024). Studies on estimates of heritability and genetic advance for certain quantitative traits in fieldpea (Pisum sativum L. var. arvense). International Journal of Plant & Soil Science, 36(7), 393-398. https://doi.org/10.9734/ijpss/2024/v36i74744
SPSS Inc. (2009). PASW Statistics for Windows (Version 18.0) [Computer software]. https://www.ibm.com/spss
Thilavech, T., Suantawee, T., Chusak, C., Suklaew, P. O., & Adisakwattana, S. (2025). Black rice (Oryza sativa L.) and its anthocyanins: mechanisms, food applications, and clinical insights for postprandial glycemic and lipid regulation. Food Production, Processing and Nutrition, 7(1), 15. https://doi.org/10.1186/s43014-024-00288-8
Tran, X. H., Tran, T. S., Ho, T., Truong, T. H., Nguyen, D. T., & Nguyen, T. L. (2025). Agro-Morphological Characteristics and Genetic Diversity of Traditional Glutinous Rice Varieties in Quang Ngai Province, Vietnam. International Journal of Environment, Agriculture and Biotechnology, 10(1), 592922. https://dx.doi.org/10.22161/ijeab.101.11
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Saha, B., Chand, S., Purkaystha, S., Mandal, T., & Mondal, B. (2026). Genetic Variability and Multivariate Analysis of Agro-Morphological Traits in Selected Rice Germplasm (Oryza sativa L.) of India. International Journal of Advancement in Life Sciences Research, 9(1), 171-182. https://doi.org/https://doi.org/10.31632/ijalsr.2026.v09i01.013
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