Assertion: As a result of intensive irrigation, the traditional crops sown in Rajasthan- gram, bajra and jowar have been replaced by wheat, cotton, groundnut and rice.
Reasoning: This has also caused waterlogging and soil salinity, and thus, in the long run, it hampers the sustainability of agriculture.

Both Assertion (A) and reasoning (R) are correct, but R is not the correct explanation of A.

The correct answer is Option 2: Both Assertion (A) and reasoning (R) are correct, but R is not the correct explanation of A.

Assertion: As a result of intensive irrigation, the traditional crops sown in Rajasthan- gram, bajra and jowar have been replaced by wheat, cotton, groundnut and rice. This is correct. 
Reasoning: This has also caused waterlogging and soil salinity, and thus, in the long run, it hampers the sustainability of agriculture.  This is correct. 

Does R explains A? No.  The shift to these crops was caused by the availability of canal water. While both statements are true and related to the same geographical context, the reasoning describes the environmental impact of the shift, not the cause of the shift itself.

NCERT: The traditional crops sown in the area, gram, bajra and jowar have been replaced by wheat, cotton, groundnut and rice. This is the result of intensive irrigation. This intensive irrigation, no doubt, initially has led to a tremendous increase in agricultural and livestock productivity. This has also caused waterlogging and soil salinity, and thus, in the long run, it hampers the sustainability of agriculture.