Progress 06/01/20 to 05/31/21
Outputs Target Audience:
Nothing Reported
Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Most conferences were either moved to online or cancelled due to COVID19. How have the results been disseminated to communities of interest?
Nothing Reported
What do you plan to do during the next reporting period to accomplish the goals?Objectives 1-4 are scheduled to be completed in year 2 of the project.
Impacts What was accomplished under these goals?
All of this work was significantly delayed due to the COVID19 pandemic initially due to campus closure/restrictions and later due to reagent acuisition delays. 1) Transcriptome profile 107 hypothalamus, 107 small intestine and 150 liver tissues from animals selected to have extreme residual feed intake phenotypes. We identified all of the samples needed for this project and they were retrieved from our freezer system. Testing of RNA extraction procedures was done in 2020. Production RNA extractions were initiated in January 2021 with the first 100 samples completed data generation on 4/14/2021. The remaining 250 RNA extractions were completed in May 2021 and submitted for data generation. 4) Impute SNP chip genotypes on 11,000 animals with measurements of feed efficiency to 850k and whole genome sequence to enable GWAS for feed efficiency related traits. Significant progress was made on building an imputation pipeline to efficiently impute SNP-chip genotypes. We began exploring different approaches to increase imputation accuracy both at SNP-chip and sequence level imputation.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Bickhart DM, McClure JC, Schnabel RD, Rosen BD, Medrano JF, Smith TPL. Advances in sequencing technology herald a new frontier in cattle genomics and genome-enabled selection. 2020. Journal of Dairy Science 103:6, 5278-5290. https://doi.org/10.3168/jds.2019-17693
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Triant DA, Le Tourneau JJ, Unni DR, Diesh CM, Shamimuzzaman M, Walsh AT, Gardiner J, Goldkamp A, Li Y, Nguyen H, Roberts C, Zhao Z, Alexander LJ, Decker JE, Schnabel RD, Schroeder SG, Sonstegard TS, Taylor JF, Rivera RM, Hagen DE, Elsik CG. Using Online Tools at the Bovine Genome Database to Manually Annotate Genes in the New Reference Genome. Anim Genet. 2020;51(5):675-682. https://doi.org/10.1111/age.12962
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Silva DBS, Fonseca LFS, Pinheiro DG, Magalh�es AFB, Muniz MMM, Ferro JA, Baldi F, Chardulo LAL, Schnabel RD, Taylor JF, Albuquerque LG. Spliced genes in muscle from Nelore Cattle and their association with carcass and meat quality. 2020. Sci Rep 10, 14701.
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Wang X, Ju Z, Jiang Q, Zhong J, Liu C, Wang J, Hoff JL, Schnabel RD, Zhao H, Gao Y, Liu W, Wang L, Gao Y, Yang C, Hou M, Huang N, Regitano LCA, Porto-Neto LR, Decker JE, Taylor JF, Huang J. Introgression, admixture, and selection facilitate genetic adaptation to high-altitude environments in cattle. 2021. Genomics. https://doi.org/10.1016/j.ygeno.2021.03.023
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