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Course Requirements for the PhD Degree

General Guidelines

Doctoral degree candidates must comply with the Graduate School requirement that the equivalent of at least one continuous academic year of full-time graduate work (9 credits per semester) must be spent in residence at the University of Massachusetts, Amherst.

A student must earn 15 credits in formal course work. This requirement must be satisfied by completing the one-year PB core course curriculum (PB I and PB II) plus additional program-related elective courses such as those listed below. A grade of B- or better must be earned in the PB core courses. In the remaining courses that a student is offering to satisfy degree requirements, a minimum standard for satisfactory work is a 3.0 grade point average. A student who in any two semesters, consecutive or otherwise, has semester averages of below 2.8 is subject to dismissal. The typical academic load for first year PhD students in PB is: First semester: PB I (3 credits); PB related elective course (3 credits); Research rotation (2 credits); Seminar (1 credit). Second semester: PB II (2 credits); PB related elective course (3 credits); Rotation (2 credits); Seminar (1 credit); Journal club (1 credit).

In addition, students need to attend at least one OPD event each fall semester and one in each spring semester. Click here for a list of OPD events.

Program-related courses for the PB Program

PLANTBIO 694A PB II - Topics in Plant Biology Research (Spring)
PLANTBIO 696 Independent Study (Spring Rotation 3)
PLANTBIO 698 Practicum (Fall PhD Rotation 1; Spring PhD Rotation 2)
PLANTBIO 699 Masters Thesis (6-10 Credits Required for MS Students)
PLANTBIO 796 Special Reserach Projects
PLANTBIO 891PB PB I - Topics in Plant Biology Research (Fall)
PLANTBIO 899 PhD Dissertation Credits (Min. 10 Required for PhD Students)
BIOCHEM 642 Advanced General Biochemistry
BIOLOGY 510 Plant Physiology
BIOLOGY 514 Population Genetics
BIOLOGY 559 Cellular and Molecular Biology II
BIOLOGY 580 Developmental Genetics
BIOLOGY 621(421) Plant Ecology
BIOLOGY 675  Plant Cell Biology
BIOLOGY 697 Plant Cell and Molecular Biology
BIOSTATS 610 Power and Sample Size Calculation of the Design of Scientific Studies
FOOD-SCI 797A ST-Genomic Approaches/FoodSci
MOLCLBIO 641 Advanced Cellular Biology
MOLCLBIO 642 Advanced Molecular Biology
STOCKSCH 505 General Plant Pathology
STOCKSCH 523 Plant Stress Physiology
STOCKSCH 525 Mycology
STOCKSCH 535 Diagnostic Plant Pathology
STOCKSCH 572 Nematology
STOCKSCH 575 Environ. Soil Chemistry
STOCKSCH 697PB Phyto/Bioremediation
STOCKSCH 661 Intermediate Biometry

Other courses may be substituted as PB related electives with permission of the Graduate Operations Committee (GOC).

Dissertation Credits

In addition to coursework, Plant Biology PhD Students are required to register for a minimum of 10 Dissertation Credits (Plantbio 899) prior to graduation. 

Journal Clubs

Participation in one journal club is required each semester, not including summer. The exception is the first semester of the first year. Students may enroll in a journal club offered by another department or graduate program. Note that some journal clubs require consent of the instructor to enroll.


Each semester, the Program will sponsor a seminar series. The seminars are held on Thursdays at 4:00 PM and feature a research talk from an invited speaker. The speakers for the Fall series are generally from the Plant Biology Program. The spring series features invited speakers on current issues in Plant Biology research. For the spring series, graduate students will have lunch with the speaker on the day of the seminar to discuss the topic. All students are required to attend the seminars and participate in the discussion sessions and should, therefore, register for 1 credit of BIOLOGY 891A, Section 4 (Seminar Series).

Guidance Committee

The Guidance Committee of entering students (both PhD and MS) will be the Graduate Operations Committee (GOC). The Guidance Committee's role will be to help the student with potential course offerings, potential rotation mentors, and anything else relating to academics. The GOC will be constituted to reflect the balance of disciplinary interests of the Plant Biology Program and will serve as an advisory committee for the student until a Dissertation Committee has been assembled. Each student will meet with their Guidance Committee at least once each semester to review progress. All students should submit an annual PB Graduate Student Progress Report by August 31st for review by the GOC.

Laboratory Rotations for Non-Targeted PhD Students

Entering PB (PhD) students (unless targeted) will do three research rotations. The student is expected to join a lab by their first summer. At the conclusion of the third laboratory rotation, the student will select a laboratory in which to complete their dissertation research and obtain approval from the PB faculty member to work in their laboratory.

The purpose of the laboratory rotations is to attain research experience, and to learn first-hand about working with potential advisors and their laboratories. Expectations regarding time commitment (hours per week) and expected activities/accomplishments during the rotation will be decided jointly by the faculty member and student. The faculty member and student will complete a Rotations/Practicum Agreement Form which will provide the following information: 1) objectives and planned activities; and 2) evaluation criteria. The student will submit the completed Practicum Agreement Form to the Graduate Program Director. The Graduate Program Director may request changes in the Practicum Agreement Form if the objectives and/or expectations are not clear. The three rotations must occur in different laboratories. Students should register for two credits of PLANTBIO 698 (Practicum) for the first two rotations and PLANTBIO 696 (Independent study) for the third rotation.

Rotation schedule for 2023-24:

  • Rotation 1: September 18–December 1
  • Rotation 2: December 4–February 23
  • Rotation 3: February 26–May 10

Rotation expectations:

  • Student experiments should be designed to provide insight into the scientific approaches and experimental techniques used in the lab, with the realization that production of clean and controlled data, as opposed to extensive data, is an appropriate goal.
  • Students should leave the rotation lab understanding the research carried out in that lab.
  • During the rotation, students are expected to consider the rotation lab as home base, which means that other than classes and TA responsibilities students should be in lab during working hours.
  • There should be ample interaction between the student and the PI.
  • Students should leave the rotation lab with a good sense of the lab environment.

In addition to helping to match students and PIs rotations are meant to:

  • Increase the network of faculty and students with whom students interact and will be able to potentially collaborate with in the future.
  • Increase the diversity of experimental approaches available to students in their research.
  • Expand the student’s conceptual framework for approaching problems in science. Provides students the opportunity to explore a completely different field from their research interest.

Students may quickly find a lab that they would like to join. Therefore, if after two rotations, a student has identified a PI and lab, then the student can perform the third rotation in that lab. However, students who have been accepted into a lab after two rotations may still, in discussions with their PI, decide to perform a third rotation to gain additional diverse experience and increase their network of contacts within the program.

Targeted PhD Students

If a student has been in correspondence with an individual faculty member prior to submission of an application for admission and if the student has had substantial prior research experience the student can be targeted to the faculty member's laboratory and is required to complete only one outside rotation.  Typically, a targeted student will have a MS degree or the equivalent. Students who intend to join the laboratory of a specific PB program faculty member, either due to having accepted scholarship/fellowship funds for a defined project, or through agreement with a PB faculty member on entering the program, MUST still complete one rotation outside their intended PI's laboratory. This can be done during any of the rotation periods. The student is encouraged to choose a laboratory in consultation with their intended PI in order to maximize learning and networking opportunities.  The student may also choose to do a second rotation outside their PI's laboratory in consultation with the PI. A faculty member targeting a student is expected to demonstrate ablity to provide funding for at least two semesters and will be responsible for further funding, during the time that the student remains in their laboratory. All targeted students must be admitted by the Admissions Committee using criteria identical to those used for other students.

Teaching Requirement

All PhD students, whether targeted or not, are required to complete two semesters of teaching while supported by a teaching assistantship (TA). The timing of the teaching requirement for targeted students will be determined by the availability of PB Teaching Assistantships.

Preliminary PhD Comprehensive Examination

PB First-year core courses

All first year students (MS and PhD) will enroll in PB Core I (currently PLANTBIO 891PB) in the fall and PhD students will enroll in PB Core II in the spring. PB Core I is a three-credit-hour course, in which students have lectures from various faculty members of PB. Each faculty presents material for one week of the course and each sets the students an exam question. The faculty member will lecture in depth on a topic in plant biology. In a semester, students will hear from many but not all PB faculty. In PB Core II, a two-credit-hour course, students will learn how to write a grant proposal. Based on an abstract from a funded proposal, students will write a proposal implicit in the abstract. This course also includes discussion on ethical conduct in scientific research. For PB Core I, the course coordinator establishes the lecturing roster and collects the grades. For PB Core II, the coordinator runs the class itself.

A student passing both PB Core I and PB Core II (with a grade of B- or better) will be considered to have passed part one of their comprehensive exam. A student failing PB Core I will be given a chance to retake the exam during spring semester, presumably in the form of a typical oral comprehensive exam, as arranged by the Graduate Program Director (GPD). A student failing PB Core II will be given a chance to retake the exam during the summer, presumably in the form of a proposal writing exercise, as arranged by the GPD. Students that fail the second examinations will be dismissed from the Ph.D. program, and the matter will be presented to the Graduate Operations Committee to determine options available to the student.

Defense of original research proposal

1. General Comments

By February of the second semester of the second year, the PhD student will convene their Dissertation Committee. Their mentor will serve in an advisory capacity to the rest of the committee (see below for more information about this committee). The Dissertation Committee will administer part two of the comprehensive exam. This exam will be a defense of an original research proposal relating to the student’s planned dissertation project. The student will write up a proposed set of experiments, including methods, potential outcomes, an introduction where the questions at stake are asked, a discussion where potential results are interpreted and potential impact on the field predicted, and a comprehensive bibliography. The student will give copies of the proposal to committee members no less than two weeks before the exam and during the exam will present the proposal orally and handle questions. In both written and oral portions, the student will be expected to demonstrate mastery of the relevant literature and concepts. The exam should take place before the end of the spring semester.

The defense is designed to test the competence of the doctoral candidate in skills not evaluated by previous examinations. The skills to be tested include:

- the ability to become expert in a limited area of the current research literature, - to conceive an original research project,
- to apply newly learned tools to the investigation,
- to envision the possible results of planned experiments,

- to set criteria by which the data and results will be assessed,
- and to establish reasonable priorities among possible approaches to the problem.

2. Detailed Guidelines

The cover page of the proposal should contain the title, the student's name, the date, and the statement: "A research proposal submitted to the Plant Biology Graduate Program, University of Massachusetts, Amherst, in partial fulfillment of the requirements for the Preliminary Comprehensive Examination."

The proposal should be a maximum of 12 pages single-spaced and include
(a) an abstract/summary, which should be no more than 500 words. (not part of 12 pages)

The abstract should include the research question, the rationale for the study, the hypothesis, the specific aims and the methods to be used. Descriptions of the method may include the design, procedures, the sample and any instruments that will be used. The summary is the first thing a reviewer sees – it should engage them and make them want to read the whole proposal.

(b) an Introduction/Background section, which should be about 2-3 pages, including figures (These are suggested page limits).

The main purpose of the introduction is to provide the necessary background or context for your research problem. You need to have in mind the biological problem that you wish to address.  In your introduction you provide a review of the literature that describes what is known about this area and make sure to state what isn’t known-this should include your biological problem.  You can also include any preliminary data in this section.

The introduction is NOT just a typical review article of the field. It should directly lead to the experiments you plan. That is, be sure to point out where information is missing, and you are encouraged to say something like “experiments in Aim 1 address this gap”. When the reader is done with the introduction they should be convinced that there are important questions to be addressed and have some idea that YOU are addressing them.

(c) a Specific Aims section, which should be 1 page maximum. This is really the essence of your proposal. It should include two or three sentences that state the over all goal and the experimental system. Then each aim/objective should be stated and a brief description of the approach and expected outcome.

(d) an Experimental Design section, which should be about 5-6 pages, including figures. This is the heart of your proposal. You need to detail the rationale for each specific aim and experimental approach. You must convince your committee that the experiments that you propose will allow you to address your hypotheses and contribute to your main goal. Starting each aim with the rationale, also allows you to provide more specific background details closer to where they are needed than burying them back in the Introduction.

In this section, you need to detail how you will accomplish each specific aim. You need to convey that you understand how each experimental method is carried out, how the results are analyzed, and what you expect the outcomes to be for each experiment. Discuss what you would do if the results are inconclusive and the caveats associated with experiments you are proposing. Your committee expects that you have thought of more than one way to accomplish each aim if possible. Thus, it is important to suggest alternative approaches to support your experimental results. In each aim, you should include either a specific section on “Pitfalls & alternative approaches”, or include this information when discussing the potential outcomes of the experiments.

(e) a Timeline section, which should not take up more than a quarter of a page. Indicate what you expect to accomplish for each 3-6 month period, by specific aim or “subaim”.

(e) a References Cited section, which is not included in the 12 page limit. This section should provide complete list of citations (all authors, year, title, journal, volume, first and last page) for all cited references.

Each member of the Exam Committee will receive a copy of the proposal from the candidate, at least 14 calendar days prior to the date of the examination. Members of the Committee have up until 5 calendar days before the scheduled examination to move for rejection of the proposal as submitted. To do so, the committee members will contact the student’s mentor who, in consultation with all committee members, will decide what steps are necessary in order to proceed with the examination.

The candidate will defend their research proposal before the Exam Committee. In general, the candidate will be expected to open the examination with a formal presentation of approximately 30 minutes duration, outlining the salient points of the proposal. During the defense, the student must show that the experimental approach proposed is scientifically valid and that the techniques to be employed will yield useful and interpretable information. The remainder of the examination will be devoted to the discussion of questions posed by individual committee members. At the conclusion of the examination the student will leave the room. The student should remain available to the committee as it deliberates and votes.

An evaluation of the candidate's performance will result in a "Pass", "Conditional Pass", or "Fail". Immediately following the examination, the Chair of the Exam Committee will communicate all comments and concerns to the candidate, and will also transmit, in writing, the results of the Examination and all recommendations of the Committee (“Pass”, “Conditional Pass”, or “Fail”) to the GPD.

A “Conditional Pass” will be accompanied by specific stipulations to the student for further work. Students who are judged to have failed the examination will receive one additional opportunity to take the examination. The second examination must be passed within six months of the first examination. Students who fail the second examination will be dismissed from the PhD program.

Immediately following the examination, the Chair of the Exam Committee will communicate all comments and concerns to the candidate, and will also transmit, in writing, the results of the Examination and all recommendations of the Committee (“Pass”, “Conditional Pass”, or “Fail”) to the GPD.


Dissertation Committee

Students must assemble a Dissertation Committee prior to their defense of their research proposal in the fourth semester of study. The committee will consist of the Research Advisor, who will serve as the chair for the committee, plus three additional members. One of the additional members must be a faculty member from a department that is different than the chair's department. A committee member who is not a member of the UMass Graduate Faculty can be chosen with approval of the PB GOC. The names of the committee members must be submitted to the PB office and subsequently approved by the Graduate Operations Committee and the Graduate School. It is the responsibility of the Dissertation Committee to monitor the student's research and progress toward the Ph.D. degree. The Dissertation Committee shall meet with the student at least once per year to discuss the course of the research and will file a brief report with the GPD as appropriate. It is the responsibility of the student to arrange these annual meetings.

Dissertation Prospectus

A student is required to present a Dissertation Prospectus to their Dissertation Committee and receive approval of its contents by the end of the sixth semester of study. The prospectus must be submitted to the Graduate School at least seven months prior to the date of the Final Doctoral Oral Examination. It must be accompanied by a cover sheet signed by each member of the Dissertation Committee. A copy of the prospectus must be placed in the student’s file in the PB office.

Final Doctoral Oral Examination (Dissertation Defense)

The format of the Ph.D. dissertation document is set by the Graduate School (Refer to the Graduate School website for the: Checklist for Final Doctoral Oral Examinations, and Doctoral Degree Requirements). It is the responsibility of the student to learn about and follow the rules governing the dissertation format, please refer to the Graduate School's "Guidelines for Master's Thesis and Doctoral Dissertations." The student must deliver their completed dissertation to the Dissertation Committee no later than four weeks before the Final Oral Examination. The time and place of the Final Oral Examination must be publicly announced by the Graduate School; information as to the time and place of the examination must, therefore, be submitted to the Graduate School by the Graduate Program Director at least four weeks prior to the examination.

The Final Oral Examination will consist of two parts. The student will first present an open seminar on their research results. The seminar will be followed by questioning by the Dissertation Committee. The seminar and the questioning by the committee can take place on the same day or on different days. The student will then submit the Doctoral Degree Eligibility form to the Graduate Program Director for submission to the Graduate School (see Documents: Graduate School).

Evaluation Of Research

To be successful at research, a student must perform well in a number of areas.

Beginning with the first rotation, a student’s performance will be assessed each semester as described in Rotations/Practicum Agreement Form (contact IDGP office for most up to date form). The evaluation will be placed in the student’s file in the PB office; a copy will be sent to the student.

Students with “Poor” evaluations for two consecutive semesters will lose their stipends (TA or RA) and be terminated from the Program.

Period Of Study

It is expected that students will complete the PhD degree in four to five years. Funding (TA/RA) will be guaranteed for up to five years contingent upon satisfactory progress towards the PhD degree. Funding beyond five years may be provided based on approval by the Dissertation Committee and the PB Director.

Statute Of Limitations

The Graduate School has established a six-year Statute of Limitations for the PhD degree.

Logo showing green leaves around the words Plant Biology above the UMass Amherst wordmark