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Background Calcareous soils are highly deficient in boron (B) which has become one of the most important deficient micronutrients in Indian soil after zinc (Zn). For various rice-based cropping systems, B-fertilization is essential for increasing crop productivity and the biofortification of the crop, thus suitable soil application protocol for B-fertilization are required for B-deficient soils. Results In a six years-long experiment, different rates of B application viz. 0.5, 1.0, 1.5, and 2.0 kg ha− 1 y− 1 were evaluated to determine the effects of three different modes of B fertilization viz. applied only in the first year, in alternating years, and every year in rice ( Oryza sativa L.) – Indian mustard (Brassica juncea L.) cropping system. It was observed that the application of B at 1.5 kg ha− 1 in every year or 2 kg ha− 1 in alternate years resulted in the highest yield of rice and mustard as well as the system productivity of the rice–mustard cropping system. Application of 2 kg ha− 1 B in the initial year showed the maximum B-uptake by rice, while, application of 1.5–2.0 kg ha− 1 B in every year resulted in the maximum B-uptake by the mustard crop. Conclusion Application of B at 2 kg ha− 1 in alternate years or 1.5 kg ha− 1 in every year was the best B-application protocol under rice–mustard cropping system in B-deficient calcareous soils for ensuring the best system productivity of rice–mustard cropping system and B-availability in soil.

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