PLANT SC 7227WT - Plant Genomics

Waite Campus - Semester 1 - 2014

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 20 hours per week for 3 weeks
    Assumed Knowledge PLANT SC 7225WT
    Restrictions Available to GradCertPHB, GradDipPHB, MHB 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


    Dr Chad Habel
    CLPD
    Level 2 West, Schulz Building
    North Terrace Campus
    Tel: +61 8 8303 3019
    chad.habel@adelaide.edu.au
    Course Timetable

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

  • Learning Outcomes
    Course Learning Outcomes
    1 Identify various 'omics approaches and their role in understangin plant function
    2 Understand the differences between forward and reverse genetic approaches and how to make jugements when the different approaches are more appropriate
    3 Analyse information from plant genomics research and recognise its potential 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
    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)
    Knowledge and understanding of the content and techniques of a chosen discipline at advanced levels that are internationally recognised. 1, 2
    The ability to locate, analyse, evaluate and synthesise information from a wide variety of sources in a planned and timely manner. 2, 3, 4
    An ability to apply effective, creative and innovative solutions, both independently and cooperatively, to current and future problems. 2, 3, 4, 5
    Skills of a high order in interpersonal understanding, teamwork and communication. 4
    A proficiency in the appropriate use of contemporary technologies. 1, 2, 3, 4, 5
    A commitment to continuous learning and the capacity to maintain intellectual curiosity throughout life. 1
    A commitment to the highest standards of professional endeavour and the ability to take a leadership role in the community. 4, 5
    An awareness of ethical, social and cultural issues within a global context and their importance in the exercise of professional skills and responsibilities. 1, 2, 3, 4, 5
  • Learning Resources
    Required Resources
    In preparation for this course, students should read the following articles:
    • Langridge P. & Fleury D. (2011) Making the most of ‘omics’ for crop breeding. Trends in Biotechnology, 29, 33-40.
    • Rivandi, J. Miyazaki J., Hrmoca M., Pallotta M., Teser M., Collins N.C., (2011) A SOS3 homologue maps to HvNAX4, a barley locus controlling an environmentally sensitive Na+ exclusion trait. Journal of Experimental Botany, 62, 1201-1216
    • Roy S.J., Tucker E.J. & Tester M. (2011) Genetic analysis of abiotic stress tolerance in crops. Current Opinion in Plant Biology, 14, 232-239.
    • Roessner U. & Bowne J. (2009) What is metabolomics all about? BioTechniques, 46, 363-365.
    • 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
    • Schilling RK, Marschner P, Shavrukov Y, Berger B, Tester M, Roy SJ, Plett DC (2013) Expression of the Arabidopsis vacuolar H+-pyrophosphatase gene (AVP1) improves the shoot biomass of transgenic barley and increases grain yield in a saline field Plant Biotechnology Journal DOI: 10.111/pbi.12145
    • Shavrukov Y, Bovill J, Afzal I, Hayes JE, Roy SJ, Tester M, Collins NC (2013) HVP10 encoding V-PPase is a prime candidate for the barley HvNax3 sodium exclusion gene: evidence from fine mapping and expression analysis. Planta 237, 1111-1122
    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
    Week Lecture/Practical/Class exercise Topic
    Week1
    Practical 1
    Monday 12th May 9.30am-1pm
    Determining allelic diversity of salinity tolerance genes in barley (part 1)
    Stuart Roy
    Class exercise
    Monday 12th May 2-4pm
    Lecture 1
    Tuesday 13th May 9.30-10.30am
    Introduction to plant genomics
    Stuart Roy
    Lecture 2
    Tuesday 13th May 10.30-11.30am
    Forward and reverse genetics
    Stuart Roy
    Class exercise
    Wednesday 14th May 9-11am
    Practical 2
    Wednesday 14th May 1-5pm
    Determining allelic diversity of salinity tolerance genes in barley (part 2)
    Stuart Roy
    Lecture 3
    Thursday 15th May 9.30-11.30am
    Plant phenotyping and QTL mapping
    Stuart Roy
    ACPFG seminar
    Class exercise
    Friday 16th May 9-11am
    Lecture 4
    Friday 16th May 1-3pm
    Transcriptomics
    Ute Baumann
    Week 2
    Practical 3
    Monday 19th May 9.30am-1pm
    Determining allelic diversity of salinity tolerance genes in barley (part 3)
    Stuart Roy
    Class exercise
    Monday 19th May 2-4pm
    Class exercise
    Tuesday 20th May 9-11am
    Lecture 5
    Wednesday 21st May 9.30-11.30am
    Metabolomics
    Ute Roessner
    Practical 4
    Wednesday 21st May 1-5pm
    Determining allelic diversity of salinity tolerance genes in barley(part 4)
    Lecture 6
    Thursday 22nd May 9.30-11.30am
    Generation of transgenic plants
    Darren Plett
    ACPFG seminar
    4-5pm
    Class exercise
    Friday 23rd May 1-3pm
    Lecture 7
    Friday 23rd May 1-3pm
    Characterisation and functional analysis of transgenic plants
    Andrew Jacobs
    Week 3
    Practical 5
    Monday 26th May 9.30am-1pm
    Determining allelic diversity of salinity tolerance genes in barley (part 5)
    Stuart Roy
    Class exercise
    Monday 26th May 2-4pm
    Lecture 8
    Tuesday 27th May 9.30-11.30am
    Case study 1: Positional cloning and characterisation of a novel protein kinase for plant salinity tolernace
    Stuart Roy
    Class exercise
    Wednesday 28th May 9-11am
    Practical 6
    Wednesday 28th May 1-3pm
    Revision
    Lecture 9
    Thursday 29th May 9.30-11.30am
    Case study 2: Expression of the Arabidopsis vacuolar H+ pyrophosphatase gene (AVP1) improves the shoot biomass of transgenic barley and increases grain yield in a saline field
    Stuart Roy
    ACPFG seminar
    Lecture 10
    Friday 30th May 1-3pm
    Revision
    Exam
    Tuesday 3rd June
    9.30am-12.30pm

    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% 1,2,3,5
    Poster project 30% 1,3,5
    Short answer questions to practicals and practical report 30% 2,3,4
    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.