The marking scheme for Paper II of UPSC Botany Optional Subject is as follows:

1. Section A: Microbiology
- This section consists of 8 questions, out of which the candidate needs to attempt 5.
- Each question carries 60 marks, totaling to 300 marks.
- The answers should be comprehensive, well-structured, and should demonstrate a deep understanding of the subject.
- Key points, diagrams, and examples should be included wherever necessary to support the answers.

2. Section B: Cryptogams, Phanerogams, and Plant Anatomy
- This section consists of 8 questions, out of which the candidate needs to attempt 5.
- Each question carries 60 marks, totaling to 300 marks.
- The answers should be descriptive and should cover all the relevant aspects of the topic.
- Diagrams, labeled structures, and flowcharts can be used to enhance the clarity and understanding of the answers.
- Key terms and concepts should be appropriately defined and explained.

3. Section C: Plant Physiology and Biochemistry
- This section consists of 8 questions, out of which the candidate needs to attempt 5.
- Each question carries 60 marks, totaling to 300 marks.
- The answers should demonstrate a strong understanding of the physiological and biochemical processes in plants.
- Relevant examples, experimental findings, and diagrams should be included to support the answers.
- The candidate should provide a logical and coherent explanation of the concepts and theories.

4. Section D: Genetics, Plant Breeding, and Biotechnology
- This section consists of 8 questions, out of which the candidate needs to attempt 5.
- Each question carries 60 marks, totaling to 300 marks.
- The answers should cover the principles of genetics, plant breeding techniques, and biotechnological applications in plants.
- The candidate should provide clear explanations, supported by examples and diagrams.
- The answers should demonstrate a critical understanding of the subject and the ability to apply the knowledge to solve problems.

5. Section E: Ecology and Plant Geography
- This section consists of 8 questions, out of which the candidate needs to attempt 5.
- Each question carries 60 marks, totaling to 300 marks.
- The answers should demonstrate a comprehensive understanding of ecological concepts, plant distribution patterns, and their adaptations.
- The candidate should provide relevant examples, diagrams, and case studies to support the answers.
- The answers should reflect an analytical and critical approach towards ecological issues.

In conclusion, the marking scheme for Paper II of UPSC Botany Optional Subject emphasizes comprehensive and well-structured answers that demonstrate a deep understanding of the subject. It is important to include relevant examples, diagrams, and experimental findings to support the answers and enhance clarity. Critical thinking, analytical skills, and the ability to apply the knowledge to solve problems are key components of scoring well in this paper.