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Plant Biology Ph.D. Policies and Procedures

Research Rotations

Most doctoral students in the Plant Biology Graduate Programs start the program with their graduate advisor already identified and do not “rotate”. However, students who are awarded departmental teaching assistantships, university fellowships or hold other fellowships may choose to rotate. Generally, this involves identifying 2-3 faculty members with whom a student will work with during the fall semester and possibly part of the spring semester. The director of graduate programs (DGP) serves as a temporary advisor to students who choose to rotate.

Rotations give students the opportunity to gain sufficient familiarity with research operations and goals in different faculty laboratories in order to choose and pursue a research topic of high interest. Faculty members can also become familiar with the student. After the final rotation, students must consult with the DGP and choose their graduate advisor. Students enroll in PB 893 during their rotation period. Satisfactory performance in laboratory rotations is required to receive credit for PB 893. Student performance during each rotation is evaluated by the principal investigator of the laboratory. Evaluations include an assessment of laboratory performance, and a written or oral report by the student on their rotation experience.

Students supported by a stipend funded from a faculty member’s grant or targeted resources are not required to participate in the laboratory rotations, but may do so by arrangement with the principal investigators. Students are encouraged to review the faculty research pages and meet with faculty before deciding upon the specific labs in which they will “rotate”.

Doctoral Preliminary Exam Procedures

Doctoral students should complete their preliminary exam requirements before the first day of spring semester classes in their third year in the program. It is advisable that students meet in person with their committee to discuss the preliminary exam. This means students should be holding a committee meeting during the spring semester of their second year or fall semester of their third year to discuss the preliminary exam.

Students have two options for their preliminary exam; which option a student pursues is a joint decision between the student and their committee. The preliminary exams options are as follows:

  • A traditional subject-matter exam – each committee member submits questions for the student to answer in a defined time period. This is followed by an oral exam that may follow the topics of the written exam or range elsewhere.
  • A research proposal – a student proposes a research project to their committee for approval. They then write and submit a research proposal to their committee for evaluation, and ultimately, defend the proposal for the oral part of their preliminary examination. The committee may also ask questions about general plant biology during the oral portion of the exam.

Procedures for a traditional written exam:

Each member of the advisory committee prepares a set of questions for the student to answer and then return to the appropriate faculty member for grading. The student and committee should establish the plan for the exam; i.e., how and to whom the committee members will submit the questions (usually to the advisor, who gives them to the student on the scheduled days for each question set), the specific dates the student will work on each committee member’s questions (this should be written down and approved by all parties), how the student will submit the answers (usually to the advisor, who then returns them to the appropriate committee member), the specific rules for each set of questions (some may be open-book or allow use of web resources, others may not – the specific format and rules for each set of questions is at the discretion of the individual committee member), any variance on the time limit (the norm is 48 hours per set of questions, but the committee may approve longer time limits for any question sets), and a timeline for committee member evaluation of the student’s answers.

Committee members submit their evaluations of the student’s answers to the major advisor, along with whether or not they authorize “permission to proceed” to the oral examination. The committee must be unanimous that the student has permission to proceed. If there is unanimous consent, then the advisor notifies the student and the DGP that the student can proceed with the oral examination as outlined below. If there is not unanimous consent, then the advisor must work with the committee to determine the next steps. The committee may recommend a reexamination, may issue a conditional permission to proceed (the conditions of which must be met before the student can proceed to the oral exam), or the committee may indicate that the student has failed the exam and should no longer participate in the graduate program. Each of these options requires consultation with the DGP, and provision of documentation to the student, DGP and the Graduate School. The DGP will also inform the student of their options regarding appeals and grievances.

If the student has received permission to proceed to the oral exam, they work with their committee (including the Graduate School Representative) to identify a time and date for the oral examination. It is a good idea to establish a tentative oral exam date at the beginning of the examination process, making sure to include sufficient time between the written exam and the proposed oral exam date for the committee to evaluate the student’s answers. Once a date has been confirmed by all committee members, the student prepares and submit the Request to Schedule an Oral Examination to the DGP. Note that the form must be submitted no later than 10 working days prior to the proposed date. If the student is submitting the form close to the 10-day deadline, they should confirm that the DGP will be available to review and submit the form to the Graduate School.

During the oral exam, committee members may question the student on any phase of the graduate course work taken by the student or any subject logically related to an understanding of the subject matter in the major and minor areas of study. Questions are designed to measure the student’s mastery of their field and the adequacy of preparation for research, to test the student’s ability to relate factual knowledge to specific circumstances, to use this knowledge with accuracy and promptness, and to demonstrate a comprehensive understanding of the field of specialization and related areas.

The outcomes of the preliminary oral exams can be an unconditional pass, a conditional pass or a fail. The outcome is formally reported to the Graduate School on an exam report form. Conditional passes require a specific statement of what the student must do in order to pass. This should include dates by which those benchmarks will be accomplished. The report requires that a fail outcome be accompanied by the committee’s judgment of what comes next: either a reexamination (including an estimate of the reexamination date) or termination from the program. The DGP must be involved in discussing options for failed exams. The DGP will also inform the student of their options regarding appeals and grievances.

Procedures for a research proposal exam:

This option requires more extensive communication with a student’s committee. Again, students are encouraged to meet in person with their committee to discuss the specifics of their preliminary exam. The student needs to determine the expectations of each committee member and make sure that they make every effort to meet those expectations. External committee members and committee members from other departments may not be familiar with the proposal option (their department may only have the traditional preliminary exam option). It is important that the student makes sure these committee members understand the process and our program expectations. It is critical that students take action to make sure they know in advance what each committee member is expecting. This includes such mundane matters as the format of the research proposal. Generally, the committee will expect the student to follow a specific granting agency’s proposal guidelines (i.e., National Science Foundation, US Department of Agriculture, National Institute of Health). Students should confirm with their committee which of these is expected, whether or not all components of a standard grant proposal are to be included (i.e., a budget, current and pending support, facilities statement, etc.), and if proposals must adhere to the strict page limits of the agency or if the committee will impose a higher page limit.

The research proposal exam consist of two parts: the written proposal and an oral defense by the student before the members of their advisory committee.

The Written Preliminary Examination – Research Proposal (Part A)

Students must meet with their committee and receive approval to pursue the research proposal option. That meeting should result in an agreed-upon written understanding of the format to be followed (which research-granting agency format will be used and which components of the proposal should be included) and the establishment of a schedule for the various steps of the process. There should be an extensive discussion of possible proposal topics, but final approval of the topic for a research proposal follows the process outlined below.

Students will choose a novel research topic for their proposal, distinct from their research if that research is part of funded or other ongoing research in the lab. However, the topic may include experimental approaches that are familiar to the student. Alternatively, the topic may be directly related to a student’s research if their advisory committee unanimously agrees that it is not part of funded or other ongoing research in the lab.

Students should start this process several months before they plan to write the proposal and should read papers in their area of interest. Once they have an idea for a general topic of importance in plant research, students develop a hypothesis and contact their committee members individually to get feedback on their hypothesis. This preliminary step helps to avoid spending a lot of time on something that a committee member thinks is too related to a student’s research. The advisor and committee will have suggestions relevant to a student’s particular area of research, and if students take the time to do this advance preparation, it will help them work efficiently through the proposal writing.

The next step is to write a one page abstract that is submitted to a student’s advisor for feedback. After revising the abstract based on the advisors feedback, students should submit the abstract to the rest of the committee, requesting feedback and approval of the abstract as the subject of the research proposal. This is a critical step: interacting with committee members about the topic and scope of the proposal early on will help to ensure that the proposal is something that can be defended in the oral examination. Students will find their committee members to be invaluable in pointing out major problems with the research approach; perhaps it is not hypothesis-driven, perhaps it is overly ambitious, perhaps there are pitfalls to the techniques of which the student is not aware, perhaps the student has made assumptions that will not pan out. It is up to the student to take all of the comments from their committee members into consideration and then either write the original proposal, modify the original aims or present a new abstract to their committee.

The goal of this process is to give students advance warning that a faculty member thinks they might have problems defending the proposed work. Our goal is to guide your independence, but to save you from a wasted effort. In many ways, this preliminary exercise is one of the most valuable aspects of the preliminary exam.

Once the abstract has been approved (or at least vetted as being appropriate in scope and subject), then the student may proceed with writing their proposal. At this point, students are entirely on their own, as this is, after all, an examination. Students will have four weeks to write their proposal. Once it is completed, students submit it to their major advisor, who will then convey it to the committee members. The committee members evaluate the proposal, and send their feedback and evaluation to the major advisor, who will then inform the student of the outcome.

The possible outcomes are:

  • Pass: the student has satisfactorily completed the written examination and has permission to schedule their oral exam
  • Conditional Pass: the committee provides the student with a written set of expectations of what must be accomplished and by what date in order for them to earn a pass on their preliminary exam. The DGP should be involved in this process.
  • Fail: the advisory committee will either recommend a reexamination (with a proposed deadline by which that should occur) or that the student no longer participate in the graduate program. The DGP must be involved and will inform the student of their options regarding appeal and grievance.

The Oral Preliminary Examination – Defense of the Proposal (Part B)

Once a student is given permission to proceed to the oral examination, they should consult with their committee (including the Graduate School Representative) to identify a time, date and place for the oral exam. Then, students must complete a Request to Schedule a Doctoral Oral Examination form and send it to their advisor, who will forward it to the DGP indicating that the committee has unanimously granted permission for the student to proceed to the oral exam.

Students should determine their committee’s expectations for the oral exam in the initial planning meeting for their preliminary exam. If not, then students should discuss this with their major advisor and contact their committee members to make sure they understand the expectations of all committee members.

A typical exam starts with the student giving a brief (20-30 minute) presentation of their research proposal. Students will then respond to questions from their advisory committee. The questions will focus on the research proposal, but may include any question relevant to it or to the expected proficiency in plant biology.

Immediately following the examination, the advisory committee will decide its outcome, which can be one of the following:

  • Unconditional pass
  • Conditional pass – The committee must indicate what conditions the student must satisfy to earn an unconditional pass and the date by which that must occur on the exam report form.
  • Fail – The committee must indicate whether they recommend a reexamination (and the date by which that should occur) or that the student be separated from the program on the exam form. The DGP must be consulted regarding this decision and will inform the student of their options regarding appeal or grievance.


Once the student has passed both the written and oral portions of the preliminary examination, they will have achieved candidacy status.