Using Principal Component Analysis to Assess Soil Chemical Properties in the Mwea Irrigation Scheme, Kenya: Implications for Rice Agronomic Management

Daniel M Menge *

International Rice Research Institute, P.O. Box 30709 Nairobi 00100, Kenya and Kenya Agricultural and Livestock Research Organization, P.O. Box 57811, 00200, City Square, Nairobi, Kenya.

Ruth N Musila

Kenya Agricultural and Livestock Research Organization, P.O. Box 57811, 00200, City Square, Nairobi, Kenya.

Sammy Kagito

Kenya Agricultural and Livestock Research Organization, P.O. Box 57811, 00200, City Square, Nairobi, Kenya.

Lourine Bii

Kenya Agricultural and Livestock Research Organization, P.O. Box 57811, 00200, City Square, Nairobi, Kenya and International Maize and Wheat Improvement Center, P.O. Box 1041-00621 Village Market, Nairobi, Kenya.

James Gichuki

Kenya Agricultural and Livestock Research Organization, P.O. Box 57811, 00200, City Square, Nairobi, Kenya.

Emily Gichuhi

Kenya Agricultural and Livestock Research Organization, P.O. Box 57811, 00200, City Square, Nairobi, Kenya.

Caroline A. Kundu

Kenya Agricultural and Livestock Research Organization, P.O. Box 57811, 00200, City Square, Nairobi, Kenya and International Fertilizer Development Centre, P.O. Box 30772-00100, Nairobi, Kenya.

Rosemary Murori

International Rice Research Institute, P.O. Box 30709 Nairobi 00100, Kenya.

Abdelbagi Ismail

International Rice Research Institute, P.O. Box 30709 Nairobi 00100, Kenya.

Ajay Panchbhai

International Rice Research Institute, P.O. Box 30709 Nairobi 00100, Kenya.

*Author to whom correspondence should be addressed.


Sub-Saharan Africa faces significant challenges as a net importer of rice, with self-sufficiency rates plummeting to as low as 14% in countries like Kenya. The Mwea irrigation scheme shoulders the bulk of rice cultivation, contributing over 80% of the country’s production. However, productivity within the scheme has seen a concerning decline, dropping from 5.6 ─ 6.0 t ha-1 to 1.3 ─ 4.6 t ha-1 between 1977 and 2018. This decline could be attributed to site-specific nutritional deficiencies and/or toxicities, rendering generalized agronomic recommendations ineffective in certain areas. To address this problem, our study aimed to assess soil chemical properties variability within the Mwea irrigation scheme, identify clusters with similar nutritional status, and tailor area-specific agronomic recommendations. During May to September 2020, we collected and analyzed four hundred samples from five sections of the scheme for total organic carbon, soil pH, macro and micronutrients, and exchangeable cations. Principal component analysis was conducted on the mean values of the soil chemical properties to identify significant contributors to variation and establish zones with similar patterns. Principal components 1 to 4 collectively explained 72.2% of the total variability. Cluster analysis revealed four distinct clusters, namely MW, TB, KT, and WU. Within cluster MW, soil pH was below the optimum range for rice cultivation, suggesting a need for liming. Potassium deficiency was observed across all clusters, with rice straw incorporation recommended as a long-term solution. Furthermore, zinc deficiency was noted in cluster WU, necessitating zinc fertilizer application. Conversely, iron toxicity was a concern in cluster MW, suggesting the adoption of alternating wetting and drying techniques and cultivating tolerant varieties. By proving tailored recommendations based on localized soil conditions, we aim to bolster rice productivity within the Mwea irrigation scheme and contribute to regional food security efforts.

Keywords: Agronomic management, food security, rice, principal component analysis, soil chemical properties

How to Cite

Menge , D. M., Musila, R. N., Kagito , S., Bii , L., Gichuki , J., Gichuhi , E., Kundu , C. A., Murori , R., Ismail , A., & Panchbhai , A. (2024). Using Principal Component Analysis to Assess Soil Chemical Properties in the Mwea Irrigation Scheme, Kenya: Implications for Rice Agronomic Management. International Journal of Plant & Soil Science, 36(5), 106–126.


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