The correct answer is 1 and 3 only.

The National Biodiversity Authority (NBA) is a statutory body established under the Biological Diversity Act, 2002 to regulate access to biological resources and associated knowledge for commercial or research purposes. Its primary role is to protect India`s biodiversity and the traditional knowledge associated with it.

The ways in which NBA helps in protecting Indian agriculture are:

NBA checks the biopiracy and protects the indigenous and traditional genetic resources. It ensures that the use of biological resources and associated knowledge is fair and equitable, and that the benefits arising from such use are shared fairly with the local communities and stakeholders who have conserved and nurtured them.

The statement "NBA directly monitors and supervises the scientific research on genetic modification of crop plants" is incorrect. NBA does not directly monitor and supervise the scientific research on genetic modification of crop plants. This is the role of other regulatory bodies such as the Genetic Engineering Appraisal Committee (GEAC).

Application for Intellectual Property Rights related to genetic/biological resources cannot be made without the approval of NBA. This is correct. NBA has the power to grant or refuse approval for the grant of Intellectual Property Rights (IPRs) related to biological resources and associated knowledge. This helps to prevent biopiracy and ensure that the benefits arising from the use of such resources are shared equitably.

Therefore, the correct answer is "1 and 3 only".