PLANT SC 7227WT - Plant Genomics

Waite Campus - Semester 1 - 2016

This course involves teaching sessions that may be attended by both Undergraduate and Postgraduate students. Students learn about the tools of genomics and can apply these tools to increase their understanding of plant function. Topics include: Accessing and utilising bioinformatics resources for plant biotechnology; Identification of candidate genes using genetic information (positional cloning), using biochemical and expression analysis (microarray analysis, proteomics, metabolomics); characterization and functional analysis of candidate genes: transformation, mutant populations, knockout systems, heterologous expression systems, protein analysis.

  • General Course Information
    Course Details
    Course Code PLANT SC 7227WT
    Course Plant Genomics
    Coordinating Unit School of Agriculture, Food and Wine
    Term Semester 1
    Level Postgraduate Coursework
    Location/s Waite Campus
    Units 3
    Contact Up to 9 hours per week for 6 weeks
    Available for Study Abroad and Exchange Y
    Assumed Knowledge PLANT SC 7225WT
    Restrictions Available to Biotechnology (Plant Biotechnology) students only
    Course Description This course involves teaching sessions that may be attended by both Undergraduate and Postgraduate students.
    Students learn about the tools of genomics and can apply these tools to increase their understanding of plant function. Topics include: Accessing and utilising bioinformatics resources for plant biotechnology; Identification of candidate genes using genetic information (positional cloning), using biochemical and expression analysis (microarray analysis, proteomics, metabolomics); characterization and functional analysis of candidate genes: transformation, mutant populations, knockout systems, heterologous expression systems, protein analysis.
    Course Staff

    Course Coordinator: Associate Professor Stuart Roy


    Dr Stuart Roy
    Course Co-ordinator
    Plant Genomics Centre, Rm 2.10
    stuart.roy@acpfg.com.au
    08 8313 7159
    Course Timetable

    The full timetable of all activities for this course can be accessed from Course Planner.

  • Learning Outcomes
    Course Learning Outcomes
    Aims:
    The aim of this course is to expose students to the components of plant
    genomics and how they can be used to accelerate the development and production
    of new crop cultivars. Successful students will be able to:

    1.     Identify various ‘omics approaches and their role in understanding plant function

    2.     Understand the differences between forward and reverse genetic approaches and how to make
    judgements about when the different approaches are more appropriate

    3.     Analyse information from plant genomics research and recognise its potential
    applications in crop improvement

    4.     Design and develop experiments to understand and manipulate plant function

    5.     Evaluate the relative merits for particular situations of different genomic and genetic
    approaches for research and its application.

    6.    Communicate effectively using oral and written means for both
    scientific and non-technical audiences

    7.     Cooperate and work effectively as a member of a team to solve
    problems.





    University Graduate Attributes

    This course will provide students with an opportunity to develop the Graduate Attribute(s) specified below:

    University Graduate Attribute Course Learning Outcome(s)
    Deep discipline knowledge
    • informed and infused by cutting edge research, scaffolded throughout their program of studies
    • acquired from personal interaction with research active educators, from year 1
    • accredited or validated against national or international standards (for relevant programs)
    1, 2, 3
    Critical thinking and problem solving
    • steeped in research methods and rigor
    • based on empirical evidence and the scientific approach to knowledge development
    • demonstrated through appropriate and relevant assessment
    4, 5, 7
    Teamwork and communication skills
    • developed from, with, and via the SGDE
    • honed through assessment and practice throughout the program of studies
    • encouraged and valued in all aspects of learning
    6, 7
    Career and leadership readiness
    • technology savvy
    • professional and, where relevant, fully accredited
    • forward thinking and well informed
    • tested and validated by work based experiences
    4, 5
    Intercultural and ethical competency
    • adept at operating in other cultures
    • comfortable with different nationalities and social contexts
    • Able to determine and contribute to desirable social outcomes
    • demonstrated by study abroad or with an understanding of indigenous knowledges
    6, 7
    Self-awareness and emotional intelligence
    • a capacity for self-reflection and a willingness to engage in self-appraisal
    • open to objective and constructive feedback from supervisors and peers
    • able to negotiate difficult social situations, defuse conflict and engage positively in purposeful debate
    7
  • Learning Resources
    Required Resources

    In preparation for this course, students should read the following articles:

    Cockram J., White J., Zuluaga D.L., Smith D., Comadran J., Macaulay M., Luo Z., Kearsey M.J., Werner P., Harrap D., Tapsell C., Liu H., Hedley P.E., Stein N., Schulte D., Steuernagel B., Marshall D.F., Thomas W.T.B., Ramsay L., Mackay I., Balding D.J., Consortium T.A., Waugh R. & O'Sullivan D.M. (2010) Genome-wide association mapping to candidate polymorphism resolution in the unsequenced barley genome. Proceedings of the National Academy of Sciences, 107, 21611-21616.

    Doerge R.W. (2002) Mapping and analysis of quantitative trait loci in experimental populations. Nature Reviews Genetics, 3, 43-52.

    Langridge P. & Fleury D. (2011) Making the most of ‘omics’ for crop breeding. Trends in Biotechnology, 29, 33-40.

    Roy S.J., Huang W., Wang X.J., Evrard A., Schmöckel S.M., Zafar Z.U. & Tester M. (2013) A novel protein kinase involved in Na+ exclusion revealed from positional cloning. Plant Cell & Environment, 36, 553-568

    Shavrukov Y., Bovill J., Afzal I., Hayes J., Roy S., Tester M. & Collins N. (2013) HVP10 encoding V-PPase is a prime candidate for the barley HvNax3 sodium exclusion gene: evidence from fine mapping and expression analysis. Planta, 1-12.

    Shavrukov Y., Gupta N., Miyazaki J., Baho M., Chalmers K., Tester M., Langridge P. & Collins N. (2010) HvNax3—a locus controlling shoot sodium exclusion derived from wild barley (Hordeum vulgare ssp. spontaneum). Functional & Integrative Genomics, 10, 277-291.

    Shendure J. & Ji H. (2008) Next-generation DNA sequencing. Nature Biotechnology, 26, 1135-1145.

    Zhu C., Gore M., Buckler E.S. & Yu J. (2008) Status and prospects of association mapping in plants. The Plant Genome, 1, 5-20.


    Recommended Resources
    • Acquaah G (2007) Principles of plant genetics and breeding, Blackwell Publishing, Malden. 
    • Buchanan B, Gruissem W, Jones R (2000) Biochemistry and molecular biology of plants. Rockville,Md.: American Society of Plant Physiologists. 
    • Glick B (2003) Molecular biotechnology: principles and applications of recombinant DNA 
    • Kole, C., Michler, C.H., Abbott, A.G & Hall, T.C. (eds.) 2010, Transgenic Crop Plants, Volume 1: Principles and Development, Springer-Verlag, Berlin.
    • Kole, C., Michler, C.H., Abbott, A.G & Hall, T.C. (eds.) 2010, Transgenic Crop Plants, Volume 2: Utiliization and Biosafety, Springer-Verlag, Berlin.
    • Taiz L, Zeiger E (2010) Plant physiology. Sunderland, Mass: Sinauer Associates
    • Trigiano RN, Gray DJ (2005) Plant development and biotechnology
    Writing guide: The following booklet provides a useful guide on written communication in science:
    • Cargill, M. & Bellotti, M. 2004, Written Communication in the Agricultural and Natural Resource Sciences, The University of Adelaide, Adelaide. http://www.agwine.adelaide.edu.au/students/external/carwripg1.pdf
    Online Learning

    Teaching materials and course documentation will be posted on the MyUni website (http://myuni.adelaide.edu.au/)
  • Learning & Teaching Activities
    Learning & Teaching Modes
    The course will include a series of lectures which will be complimented by practical sessions and problem-based group learning solutions. Students are encouraged to attend the weekly Australian Centre for Plant Functional Genomics seminars (Thursdays at 4pm) which will cover a range of topics and applications of the ‘omics technologies used in Plant Genomics. The seminars are given by national and international experts in the field of Plant Genomics.
    Workload

    The information below is provided as a guide to assist students in engaging appropriately with the course requirements.

    A student enrolled in a 3 unit course, such as this, should expect to spend, on average 12 hours per week on the studies required. This includes both the formal contact time required to the course (e.g., lectures and practicals), as well as non-contact time (e.g., reading and revision).
    Learning Activities Summary
    The course is taught over seven weeks in May and June, with a one week break in the middle.

    Lectures:
    Students will learn what is a genome and the different technologies that have been used and are now being used to sequence plant genomes, including Next Generation and Third Generation sequencing technologies. The course will cover how to use molecular markers, genetic maps and plant phenotyping to perform both bi-parental Quantitative Trait Loci mapping and Genome-Wide Association Studies to identify regions of DNA important for influencing a desired phenotype.

    Practicals:
    Students will put into many of the techniques they have learnt about in lectures to use molecular markers to identify crops which are salt tolerance.

    Group exercises:
    A key step in scientific writing is having your manuscripts undergo peer review. To understand what this process involves students will be given a manuscript that they will review for submission to a mock journal. The students will assess the quality of the research in the manuscript, how the document is written and whether the conclusions made in the paper are justified and will write a reviewers report to the journal suggesting whether the manuscript should be accepted, under go revision or rejected.
    Specific Course Requirements

    Practical session code of conduct

    Practicals will be held in the teaching laboratories below the Charles Hawker Centre 

    All students must follow these rules in practical exercises

    1. No eating, drinking, application of makeup, etc. in laboratories; no water bottles or items of food or drink may be visible in laboratories

    2. Closed shoes must be worn at all times in all practical exercises, wherever they are held.

    3. Lab coats and other personal protective equipment must be worn at all times in laboratories or other areas whenever students are instructed to wear them; these should be removed when leaving the laboratory.

    4. Bags, coats, etc. that are brought into a lab must be placed under the bench to avoid causing obstructions.

    5. All containers used during a practical session must be labelled, including water and other common non-toxic substances

    6. Report all accidents, both personal and/or involving experimental materials, to the person in charge

    7. Playing around in a laboratory and any other work areas is dangerous; participants in improper behaviour will be asked to leave

    8. Students must dispose of materials as directed

    9. Students must wash their hands upon departing the labs and other work areas

    10. Students must clean and tidy their bench and/or work area before departure; benches and/or work areas will be inspected at the end of each practical session. Place discarded cultures and infections material in the containers provided. Never discard cultures in any other place, especially not into the sinks

  • Assessment

    The University's policy on Assessment for Coursework Programs is based on the following four principles:

    1. Assessment must encourage and reinforce learning.
    2. Assessment must enable robust and fair judgements about student performance.
    3. Assessment practices must be fair and equitable to students and give them the opportunity to demonstrate what they have learned.
    4. Assessment must maintain academic standards.

    Assessment Summary
    Assessment Task Percentage of total assessment of grade Learning Outcomes being assessed
    Final Exam 40% 4, 5, 6, 7
    Peer-review scientific paper 30% 1,3,5, 6
    Short answer questions to practicals and practical report 30% 1,2,3,4,5
    Assessment Related Requirements

    The Plant Biotechnology programs are delivered through face-to-face class sessions in which student interactions with the lecturer and fellow students are expected and encouraged. It is assumed that students will attend all scheduled classes. If you are absent, it is your responsibility to catch up on information discussed in class; do not expect the lecturer to repeat part of a class session to cover your absence. 

    If you have not attended at least 80% of the class sessions, you will forego your right, on academic grounds, to any additional assessment opportunities. The course coordinator will monitor attendance. Whether it is assessed or not, it is important that you attend classes and contribute to discussions. Make sure that you complete any required preparatory work to be able to contribute effectively to class discussions and gain the most out of your education

    Assessment Detail

    Practical report: During the course of the practicals you will be asked to answer twelve questions relating to what you learned during that day in the practical the practical. Questions will be based your knowledge of various aspects of the techniques you used and the advantages and disadvantages of the type of experiment performed. After the very last practical you will be asked to write a short practical report  describing both your findings and the findings of the group.

    Poster project: Students will begin the poster project in Foundations in Plant Biotechnology

    Exam: The final examination will be a three hour short answer written examination, with questions designed to assess your understanding of the concepts covered in the course

    Submission

    Submission of assessments:

    Practical assessment:
    submission of answers to the practical questions will be through the MyUni site. Short questions will appear online after each practical for answering. The final practical report will also be submitted online through the MuUni site. Feedback from the lecturer will be at classes and through the MyUni site. All submissions must use the course cover-sheets provided in the course



    Late submission of assessments:

    If an extension is not applied for, or not granted then a penalty for late submission will apply. A penalty of 10% of the value of the assignment for each calendar day that is late (i.e. weekends count as 2 days), up to a maximum of 50% of the available marks will be applied. This means that an assignment that is 5 days or more late without an approved extension can only receive a maximum of 50% of the mark.

     
    Course Grading

    Grades for your performance in this course will be awarded in accordance with the following scheme:

    M10 (Coursework Mark Scheme)
    Grade Mark Description
    FNS   Fail No Submission
    F 1-49 Fail
    P 50-64 Pass
    C 65-74 Credit
    D 75-84 Distinction
    HD 85-100 High Distinction
    CN   Continuing
    NFE   No Formal Examination
    RP   Result Pending

    Further details of the grades/results can be obtained from Examinations.

    Grade Descriptors are available which provide a general guide to the standard of work that is expected at each grade level. More information at Assessment for Coursework Programs.

    Final results for this course will be made available through Access Adelaide.

  • Student Feedback

    The University places a high priority on approaches to learning and teaching that enhance the student experience. Feedback is sought from students in a variety of ways including on-going engagement with staff, the use of online discussion boards and the use of Student Experience of Learning and Teaching (SELT) surveys as well as GOS surveys and Program reviews.

    SELTs are an important source of information to inform individual teaching practice, decisions about teaching duties, and course and program curriculum design. They enable the University to assess how effectively its learning environments and teaching practices facilitate student engagement and learning outcomes. Under the current SELT Policy (http://www.adelaide.edu.au/policies/101/) course SELTs are mandated and must be conducted at the conclusion of each term/semester/trimester for every course offering. Feedback on issues raised through course SELT surveys is made available to enrolled students through various resources (e.g. MyUni). In addition aggregated course SELT data is available.

  • Student Support
  • Policies & Guidelines
  • Fraud Awareness

    Students are reminded that in order to maintain the academic integrity of all programs and courses, the university has a zero-tolerance approach to students offering money or significant value goods or services to any staff member who is involved in their teaching or assessment. Students offering lecturers or tutors or professional staff anything more than a small token of appreciation is totally unacceptable, in any circumstances. Staff members are obliged to report all such incidents to their supervisor/manager, who will refer them for action under the university's student’s disciplinary procedures.

The University of Adelaide is committed to regular reviews of the courses and programs it offers to students. The University of Adelaide therefore reserves the right to discontinue or vary programs and courses without notice. Please read the important information contained in the disclaimer.