Upland rice production on acid, weathered soils is often constrained by phosphorus (P) deficiency and aluminium toxicity. Farmyard manure application (FYM) can sharply enhance yields and agronomic P fertilizer (TSP) efficiency under such abiotic stresses. We tested the hypothesis that rice genotypes differ in aluminium tolerance and in the extent of using organic P, offering distinct benefits under TSP‐FYM combinations. Multiple field trials were conducted in the uplands of Madagascar, with factorial combinations of six genotypes, amendments of FYM (at a rate of 17–25 kg P ha−1 vs. a zero control) and TSP application (40 kg P ha−1 vs. a zero control), with blanket N&K additions. Rice grain yields reached a maximum of 6 t/ha after three years of TSP + FYM application, with an average of 3.2 t/ha over the years. Grain yields were about 1.2 t/ha for FYM only and about 1.5 t/ha for TSP only while crops failed under zero P input. Genotypic effects on rice yields were much smaller than the large effects of FYM, TSP or its combination. Application of FYM increased soil pH and CaCl2‐extractable P while decreasing CaCl2‐extractable aluminium. An additional liming trial indicated that the beneficial effects of FYM over TSP relate to liming effects. The FYM application lowers aluminium toxicity which overrules potential effects of organic P supply. Hence, genotypic ranking of yields and agronomic efficiency was inconsistent, without superior genotypes under FYM vs. TSP. However, Chomrong Dhan and FOFIFA 172 generally displayed superior yields. Chomrong Dhan is found to be more sensitive to aluminium toxicity whereas FOFIFA 172 is less performant under low P input. Aluminium tolerance should be considered when developing rice genotypes for high P efficiency in weathered soils.

The root phosphorus (P) uptake efficiency (RE), defined as plant P uptake per unit root mass or root area, may contribute to the P efficiency of upland rice grown in acid, P-deficient soils. The identification of root traits conferring RE of rice has been compromised by the lack of attention given to P speciation when evaluating P-mining mechanisms. Here we disentangled the effect of soluble organic P (PO) from that of total soluble P (PT) on the RE in rice seedlings in acid soil. Six rice genotypes were grown for 21 days in Pdeficient substrates, i.e. a sample of an acid mineral soil, an acid peat and a mixture thereof. Each of the three substrates were amended with different P doses, partially limed and incubated, yielding substrates with significant differences in total soluble P (0.004-0.41 mg P/L) and in the percentage of organic P in that pool (PO/PT, 0-57%). Plants showed a large growth response to the P addition. There was a significant genotypic variation in P uptake (0.9-1.5 mg P/plant) and RE (4.4-8.3 mg P/g root mass) under moderate P deficiency but these traits were unaffected by the PO/PT in the soluble fraction of the substrates. Along the same lines, phosphatase activity in the rhizosphere soil was unaffected by genotypes and did not explain the RE among all data (R 2 =0.17, ns). A multiple regression model showed that the RE of rice seedlings was mainly affected by the inherent genotypic effects, the PO/PT and the total soluble P concentration in soil (R 2 =0.73), while the genotype-PO/PT interaction only marginally improved the RE model (R 2 =0.78). This suggests limited genotypic effects due to the better use of organic P. A root elongation test in the acid mineral soil that was either or not limed suggests that the differences in acid soil tolerance may play a larger role in the genotypic performance of RE than organic P utilization potential.