Cereal Genomics Workshop

Cold Spring Harbor Lab

Gramene Exercise 2 – Comparisons

9/15/05

1. Imagine you are a plant breeder interested in working with drought tolerance. What term will you search for?

General Gramene:
Do a general search for “drought” from the top of the Gramene home page.

2a- What types of information in Gramene are associated with “drought”?

2b – Why is this general search important?

3a - How many standard vocabulary (ontology) terms are associated with “drought” in the database?

3b - What ontologies are they associated with?

3c - How many contain drought in the term name?

3d - Why did some terms show up but did not contain drought in the term name, and what does this mean for you?

4a - How many ontology terms are there for “drought tolerance”?

4b - Why is there more than one?

4c - What are some synonyms for “drought tolerance”?

Click on the TO Accession ID’s for drought tolerance.

5a - What do you find?

5b - What is a parent term?

5c - What is a child term?

5d - What are sibling terms?

5e - Why do you think we point this out to you?

6. What sibling or parent terms for drought tolerance may also give information on drought?

7a - How many associations are there for the term accession for the trait ontology(TO) term “drought tolerance”?

7b - If any, what type are they and what species are they associated with.

8a – What are the Accession ID’s for the QTL associated with Oryza Sativa?

8b - What is the evidence code associated with them?

8c - What does the evidence code mean?

9a - If you click on a rice QTL Accession ID from this page, what module do you go to?

9b - Where is the QTL with TO:0000276 found on the rice genome?

9c - Can you identify where each QTL resides

9d - How many studies are associated with each QTL?

10 -

If you had already done all your background research, and were simply interested in finding the QTL for drought tolerance in rice, where would you begin?

Cereal Genomics Workshop

Cold Spring Harbor Lab

Gramene Exercise 2 – Comparisons

9/15/05

1 – You are a sorghum breeder, working with drought tolerance. There isn’t a lot of information for sorghum, so you decide to compare sorghum with rice, a species with much more information. Where do you start?

Select the CMap link from the Gramene Home Page, then explore map information available from Gramene.

2a - How many different Map types does Gramene currently have?

2b - How many species?

2c – How many features?

2d – How many map sets?

Go to the Matrix, which shows correspondences between a pair of maps. Select sorghum from the species menu and search for maps.

3a - How many sorghum maps are there?

3b - What type(s) are they?

3c – Examine the maps with correlations to these sorghum maps. Which rice map has the highest number of correspondences to sorghum? Hint, Correspondences are represented by the first number in the square.)

Select the box in the matrix with the highest number of correspondences to rice.

4 - For each sorghum chromosome determine what rice chromosome has the highest number of correspondences with it.

There is a known sorghum QTL for drought tolerance located at the bottom of Chromosome C.

5 a- Is there a known rice QTL to drought tolerance in rice in the syntenic position on Chromosome C?

5b If so what is the accession ID for the QTL?