ANSC 6390 – QTL and Markers

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ANSC 6390 – QTL and Markers

Final exam
Received on 02/04/2025
Due on 16/04/2025
Using a linkage disequilibrium analysis, a researcher has mapped QTL affecting the capacity of does (female goats) to skip the dry period between lactations on chromosome 20, between 33,000K bp and 36,000K bp. Then, the researcher identified three additional polymorphisms (SNPs) in this region and decided to look at the possible association of these three SNPs with the capacity of does to skip the dry period. The researcher hired you as a research assistant and your task is to run the association analyses of these SNPs with the trait of interest. You received four files:

1. gen.txt: a space delimited file containing identification of 249 genotyped does and the corresponding unphased genotypes for each of the 3 SNPs.

2. ped.txt: a space delimited file containing animal identification, Sire identification and Dam identification (i.e., the available pedigree related to the genotyped does). A 0 (zero) in this file means a missing parent.

3. phen.txt: a space delimited file containing doe identification, birth year of the doe, days in milk of the doe prior to parturition, and the days dry phenotype (0 for normal days dry (> 15 days) and 1 for no days dry).
4. snp_info.txt: a file containing the SNP information, including chromosome number, position in bp, and its alleles.

You must carry out association analyses for the 3 SNPs with the days dry phenotype and applying proper genetic model(s). Even though the days dry phenotype is discrete, assume it as a continuous variable (i.e. you do not need to fit a threshold model), just a regular linear model.

Once you are satisfied with your analyses, you must write down the work done as a short paper to be sent to the World Congress of Genetics Applied to Livestock Production (WCGALP), including Abstract, Introduction, Material and Methods, Results and Discussion, Conclusions and References. The short paper should have a maximum of 3-4 pages in total and be typed using font 12 and single spaced lines (Be creative to fill any information not provided). For an example of a short paper click on this link (https://asas.org/docs/default-source/wcgalp-proceedings-oral/291_paper_9158_manuscript_1018_0.pdf?sfvrsn=2).

The least you must present in the results and the least you must discuss in the paper is:
- Estimated minor allele frequency for each SNP.
- Test for HW equilibrium for each SNP.
- Level of linkage disequilibrium among the SNPs.
- Estimated SNP effects on the trait, corresponding tests of significance and genetic interpretation of the results, given the genetic model(s) used in the analyses.
- Estimated proportion of the genetic variance explained by the SNPs.2
- Any functional candidate gene(s) based on the region of the SNPs and their effects on the trait.
Hind: Got to https://www.ncbi.nlm.nih.gov/gdv?org=capra-hircus&group=bovidae and select chromosome 20, then type the region to be displayed on the left side of the page (chr20: 33.0M- 36.0M). Look at the genes within this region and find any possible functional candidate gene(s). If appropriate, refine the region based on the association results.
- Assumptions and limitations of your analyses.

If you perform any editing of the data, you must report it in your short paper.

You must attach to your short paper copies of the parameter files for ASREML, SAS, or other software you have used to run your analyses.

Your payment (grade) will be proportional to the correctness of the analyses, results and interpretation, and the effort put into the analyses and into the final report (short paper). Be careful with details, as it would be required in a paper.

Getting the files needed:

You can download the files for this final exam directly from the course website.

Good luck!

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