| Summary: | Calcareous soils are highly deficient in boron (B) due to having high levels of free CaCO<sub>3</sub> and low organic matter. This has become one of the most important deficient micronutrients in Indian soil after zinc (Zn). For various rice (<i>Oryza sativa</i> L.)-based cropping systems, B fertilization is essential for increasing crop productivity and the biofortification of the crop, thus a suitable soil application protocol for B fertilization is required for B-deficient soils. In a six-year experiment, different rates of B application, namely, 0.5, 1.0, 1.5, and 2.0 kg ha<sup>−1</sup> y<sup>−1</sup>, were evaluated to determine the effects of three different modes of B fertilization, i.e., applied only in the first year, applied in alternating years, and applied every year, in a rice (<i>Oryza sativa</i> L.)–Indian mustard (<i>Brassica juncea</i> L.) cropping system. It was observed that the application of B at 1.5 kg ha<sup>−1</sup> every year or 2 kg ha<sup>−1</sup> in alternate years resulted in the highest yield of rice and mustard, as well as the maximum system productivity of the rice–mustard cropping system. Application of 2 kg ha<sup>−1</sup> of B in the initial year showed the maximum B uptake by rice, while application of 1.5–2.0 kg ha<sup>−1</sup> of B every year resulted in the maximum B uptake by the mustard crop. Application of B at 2 kg ha<sup>−1</sup> in alternate years or 1.5 kg ha<sup>−1</sup> every year was the best B-application protocol in B-deficient calcareous soils for ensuring the highest productivity of the rice–mustard cropping system and B availability in the soil.
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