PB607 –Electronic Resources for the Biological Sciences – Weekly Assignment #1
This assignment is due Wednesday, September 9, 1998 at the beginning of class. We want to know both your answer and how you arrived at it. If you perform searches please provide your exact query. For example:
Ex. Can you find any references on metabolic pathways and bioinformatics?
Ans. PubMed search: bioinformatics metabolic pathways
9 citations (then list or print the page)
If you would like to include URLs or screen shots, that’s OK! Anything that helps us understand how you arrived at your answer is to your benefit!
You are interested in finding information about rice accessions with high tolerance to salt.
Answer: Search PubMed . Could search on indica AND salt tolerance, find 2 hits, both relating to rice.
Same search in Agricola turns up 12 hits, some (but not all) of which are related to rice.
If you search on rice AND salt tolerance, you get more hits, several of which mention the varieties used, but do not say whether they were of the indica subspecies.
Answer: Several "resistant" indica varieties are mentioned across this set of references, including (repeatedly) Pokkali. Other mentions include Nona Bokra, Buhra Rata, Panwell.
3. Are there any sequenced genes or proteins related to these articles? ( 1pt.)
Answer: From your PubMed query, display nucleotide and protein links. If you’re using just the 2 hits from the indica AND salt tolerance search, there are no nucleotide hits and 3 protein hits.
One of you thought to do nucleotide/protein searches using Pokkali and found additional nucleotide and protein hits – way to go Antonio!
4. You are interested in using this variety in your breeding program. You want an accession that is not susceptible to lodging and has a medium grain length. Which accession(s) (if any) would you choose? (4 pts.)
Answer: Using GRIN, do an accession search for Pokkali, get 6 hits (one of which is a Quarantine record). Examine each record for Observation data, looking at lodging and grain length. Accession P40019 has the lowest lodging score (although it still exhibits some lodging) of the medium-grained accessions..
Some of you even checked whether seed was available for this accession (unfortunately it was not) – good job.
Answer: Definition: GERMINATION AND SEEDLING GROWTH IN A SALINE SOLUTION. (# LIVE
SEEDLINGS/ # GERMINATED) X (# LIVE + # DEAD SEEDLINGS/# GERM). [0 =SENSITIVE, 10 = TOLERANT].
6. What range of scores is most prominent? (1 pt.)
Answer: The range 0.00-0.62 is most common
Range Number of Accessions
0.00 - 0.62 12062
0.62 - 1.23 1307
1.23 - 1.85 409
1.85 - 2.46 156
2.46 - 3.08 86
3.08 - 3.70 29
3.70 - 4.31 11
4.31 - 4.93 6
4.93 - 5.54 3
5.54 – 6.16 1
7. Does the range of scores for salt distribution appear normally distributed? ( 1 pt.)
Answer: No, it is highly skewed toward salt sensitivity.
8. What is the plant introduction number and cultivar name of the accession with the highest recorded salt tolerance? (2 pts.)
Answer: .PI 464588 GEUMGANGBYEO
9. What is this accession’s pedigree? (1 pt.)
Answer: Suweon 232 / IR 24
10. What is this accession’s salt tolerance score? (1 pt.)
Answer: 5.60
11. Are there any other beneficial traits recorded for this accession? (2 pt.)
Answer: Lodging is quite low (0-10% lodged)
12. From which parent do you think the salt tolerance came from and why? Does there appear to be within-variety variation for salt tolerance in this parent? Please explain and include accession numbers. (4 pts.)
Answer: No data is available for Suweon 232, but if you look up IR24, there are 9 accessions.
4 have 0.0 salt tolerance
1 have 0.31
1 has 2.25 (PI442966)
Several have no salt tolerance scores.
There does indeed appear to be within-variety variation in IR24 for salt tolerance. Since we have no data on Suweon 232, looking only at IR24, accession PI442966 would be the most likely candidate, since it is the only one with remotely high salt tolerance.
It is possible that the other parent, Suweon 232 contributes strongly to the salt tolerance shown in Guemganbyeo. Alternatively, both parents could have relatively low tolerance and what we are seeing in
Guemganbyeo is transgressive segregation.
It is also interesting to note that the pedigree information was inconsistent for the above mentioned accessions of IR24. The curators of GRIN cannot verify this information, and must rely on what the submitter provides. This can be a point of confusion for the user.
Answer: Look at the observed distribution for salt tolerance, check out the 3 in the next highest category.
They are:
PI 279132 GU ZE
PI 399813 IR 1702-74-3-2
PI 439048 BHARATHY
No pedigree is given for PI279132 or PI439048, but PI399813 does have IR24 as a parent.
(If you look up the 6 in the next lowest category, none of them have IR24 as a parent).
Note: this question was supposed to refer to IR24, but incorrectly pointed you back to question 8, which was Guemganbyeo. Many of you did an advanced search on the Pedigree field using Guemganbyeo, which produced no hits. This would have been the correct way to approach this, and you got full credit if you did this.