In its three-year agenda document, the government think- tank also outlined various measures like MSP reform and better marketing infrastructure to be adopted for doubling of farmers' income.
"Genetically modified (GM) seeds have emerged as a powerful new technology promising high productivity, improved quality and lower use of fertilisers, weedicides and pesticides in the last one to two decades," Niti Aayog said.
Indian farmers have adopted the GM seeds by growing BT cotton, the only crop allowed for commercial cultivation.
On the minimum support price (MSP) system, Niti Aayog said the MSP has distorted cropping patterns, with excessive focus on the cultivation of wheat, rice and sugarcane in the procurement states and neglect of other crops such as pulses, oilseed and coarse grains.
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The MSP has led to depletion of water resources, soil degradation and deterioration in water quality in some states, especially in the north-western region. It has discriminated against eastern states where procurement at the MSP is minimal or non-existent.
While MSP should be continued for need-based procurement, Niti Aayog said that under the deficiency payments system, a subsidy would be provided on other targeted crop if rates fall below an MSP-linked threshold.
"This approach would not require procurement and thereby preventing the accumulation of unwanted stocks. More importantly, it would spread price incentives to producers in all the regions and all the crops considered important for providing price support," the document said.
Each farmer would have to register crop and acreage sown with the nearest APMC mandi.
"This system would keep the quantum of the subsidy in some check and also meet the restrictions on the subsidy imposed by the World Trade Organization (WTO). The system can initially be piloted in one or two crops in a few districts," it said.