Progress 01/08/14 to 09/30/18
Outputs
Target Audience:Researchers Changes/Problems:Periodic telephone conference calls are held among members of the International Sheep Genomics Consortium who participate on the Sheep Genomes Database project. A significant milestone on this project was completed with the remapping of the 935 sheep genomes to the Rambouillet V1.0 genome sequence. No changes to the original Sheep Genomes Database objectives are anticipated.. Participants in the Ovine FAANG project hold periodic telephone conference calls to discuss progress on the project. Based on progress to date, no changes to original Ovine FAANG project objectives are anticipated. What opportunities for training and professional development has the project provided?Station reports for the NRSP-8 Sheep and Goat Committee members were presented at the NRSP-8 annual meeting in San Diego on January 12, 2019. In addition, NRSP-8 members attended the International Sheep Genomics Consortium (ISGC) meeting on January 14, 2019 where updates on the Ovine FAANG Functional Annotation of the Animal Genome) Project and the Sheep Genome Database were presented. Additional presentations on sheep and goat genomics studies were provided at the IGSC meeting by undergraduate and graduate students and postdoctoral fellows from several international laboratories who had presented posters at the Plant and Animal Genome (PAG) XXVII meeting. How have the results been disseminated to communities of interest?The 2019 annual meeting of the combined NRSP-8 Cattle, Sheep and Goat committees was held on January 12-13 in conjunction with the Plant and Animal Genome (PAG) XXVII meeting. The morning session of the scientific meeting on January 12 was held as a joint session with the NRSP-8 Swine Committee and included an overview of genome assembly tools and improvements, a presentation on adaptability to high altitude, an approach for selection for genomic prediction, and results from studies on DNA methylation, breed of origin effects and haplotypes affecting reproduction. Subsequent sessions of the Cattle/Sheep/Goat combined workshops included 22 presentations covering a wide variety of topics, such as the goat ADAPTmap, international bovine genomics consortia, Angus genomic selection, long noncoding RNAs linked to parasite immune responses of sheep, RNA editing, and microbiomics. Attendance at the sessions included delegates from academia, industry and government from more than 20 countries. Additionally, there were 20 sheep and goat posters presented at the PAG XXVII meeting. What do you plan to do during the next reporting period to accomplish the goals?This is the final report for the 2014-18 NRSP-8 project. A new NRSP-8 project proposal has been submitted and approved for 2018-23.
Impacts
What was accomplished under these goals?
Under the Sheep Genome Database project, all 935 sheep genomes were remapped to the Oar_rambouillet_v1.0 assembly. These alignments and subsequent SNP variants were added to the Sheep Genome Database that is maintained by the European Bioinformatics Institute (EBI) at EMBL (https://www.ebi.ac.uk). The Ovine FAANG project is progressing according to the proposal time-frame. RNA and DNA preparations from approximately 60 sheep tissues have been distributed to each of the project laboratories for analysis using transcriptome and RNA expression techniques. Results will be shared at the upcoming International Society for Animal Genetics (ISAG) conference in July, 2019 in Spain.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Bidwell, C., Waddell, J., Taxis, T. M., Tellam, R., Neary, M. K., & Cockett, N. (2014). New insights into polar overdominance in callipyge sheep. Animal Genetics, 45, 427-438.
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Cheng, H., Xu, X., Hadfield, T., Cockett, N., Charlier, C., Georges, M., & Takeda, H. (2014). Experimental evaluation does not reveal a direct effect of microRNA from the callipyge locus on DLK1 expression. BMC Genomics, 15, 944.
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Fariello, M., Servin, B., Tosser-Klopp, G., Rupp, R., Moreno, C., & Cockett, N. (2014). Selection signatures in worldwide sheep populations. PLoS One, 9, e103813.
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Heaton, M., Leymaster, K., Kalbfleisch, T., Kijas, J., Clarke, S., McEwan, J., & Cockett, N. (2014). SNPs for parentage testing and traceability in globally diverse breeds of sheep. PLoS One, 9, e94851.
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Jiang, Y., Xie, M., Chen, W., Talbot, R., Maddox, J., Faraut, T., Wu, C., Muzny, D., Li, Y., Zhang, W., & Cockett, N. (2014). The sheep genome illuminates biology of the rumen and lipid metabolism. 344, 1168-1173
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Li, J., Greenwood, P., Cockett, N., Hadfield, T., Vuocolo, T., Bryne, K., White, J., Tellam, R., & Schirra, H. (2014). Impacts of the callipyge mutation on ovine plasma metabolites and muscle fibre type. PLOS One, 9, e99726.
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Progress 10/01/16 to 09/30/17
Outputs
Target Audience:Researchers Changes/Problems:No changes to the Sheep Genomes Database project. No changes to original FAANG project objectives. What opportunities for training and professional development has the project provided?Station reports for the NRSP8 Sheep and Goat Committee members were presented at the NRSP8 annual meeting in San Diego on January 13, 2018. In addition, NRSP8 members attended the International Sheep Genomics Consortium (ISGC) meeting on January 15, 2018 where plans for future development of tools and resources for the sheep genome were prioritized. Progress on the Ovine FAANG Functional Annotation of the Animal Genome) Project and the Sheep Genome Database were presented. How have the results been disseminated to communities of interest?An NRSP8 Sheep Coordinator report was provided at the Plant and Animal Genome meeting in San Diego on January 13, 2018. H. Daetwyler (La Trobe U. Australia) presented the Sheep Genome Database update during the January 15, 2018 ISGC meeting. B. Murdock (U. of Idaho) also provided an update on the Ovine FAANG Project at the ISGC meeting. What do you plan to do during the next reporting period to accomplish the goals?For the Sheep Genome Database project, Run 3 will align all Run 2 sequences and any new sheep genomes to the Oar_rambouillet_v1.0 assembly. These alignments will be added to the Sheep Genome Database and will be available at the end of 2018. Periodic phone calls and face-to-face meetings at ISGC and PAG conferences have been used to discuss progress on the Ovine FAANG project. RNA preparations from approximately 100 sheep tissues will be completed by USDA/ARS U.S. MARC and then distributed to project members for analysis. Results will be shared at an upcoming FAANG conference held in Adelaide, Australia.
Impacts
What was accomplished under these goals?
The Sheep Genomes Database contains whole genome sequences from 935 sheep from 21 countries and 69 breeds. Over 50 million SNPs and indels have been identified with high confidence using two variant-calling platforms. Variants are available as raw (unfiltered) or filtered data following application of a comprehensive QC protocol and information about the variants can be found through dbSNP. In the Ovine FAANG project, RNA sequences was generated by K. Worley (BCM-HGSC) from 20 samples for miRNA sequence, 9 samples for mRNA sequence and 5 samples for long-read mRNA sequence. B. Murdoch (U. of Idaho) is using cap analysis of gene expression (CAGE) to identify active promoters and confirm transcription start sites, and ATAC-seq will be used by S. White and M. Mousel (U. of Washington) to assess chromatin accessibility.
Publications
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Progress 10/01/15 to 09/30/16
Outputs
Target Audience:Target Audience Researchers Changes/Problems:Changes/Problems Periodic monthly phone calls by the Ovine FAANG Project members were useful in developing the project goals, objectives and proposed outcomes. A grant proposal was submitted to NIFA/AFRI in August, 2016 and funding was approved in November, 2016. What opportunities for training and professional development has the project provided?Opportunities Station reports for the NRSP8 Sheep and Goat Committee members were presented at the NRSP8 annual meeting in San Diego on January 14 and 15, 2017. In addition, NRSP8 members attended the International Sheep Genomics Consortium (ISGC) meeting on January 16, 2017 where plans for future development of tools and resources for the sheep genome were prioritized. The successful funding of the Ovine FAANG Functional Annotation of the Animal Genome) Project was announced. How have the results been disseminated to communities of interest?Dissemination An NRSP8 Sheep Coordinator report and a report for activities conducted at Utah State University were provided at the Plant and Animal Genome meeting in San Diego on January 15, 2017. What do you plan to do during the next reporting period to accomplish the goals?Plan of Work Aliquots of tissue samples collected from Benz 2616 will be distributed to team members in Spring, 2017. All transcriptome and regulatory data generated in the Ovine FAANG Project will directly connect to the de novo reference genome sequence generated from Benz 2616 at Baylor College of Medicine (BCM).
Impacts
What was accomplished under these goals?
Accomplishments A new ovine genomics project has been organized based on guidelines designed by FAANG. Investigators from several US institutions (USDA/ARS MARC, Washington State University, Utah State University, University of Idaho, BCM-HGSC and Virginia Tech), CSIRO (Australia), Roslin Institute (UK) and AgResearch (New Zealand) were involved in the design of the project. The Ovine FAANG Project has been awarded a 2016 NIFA/AFRI grant (B. Murdoch PD) and will contribute to the core activities of FAANG by providing transcriptome data and detailed annotation of genes and regulatory features in the sheep. An important milestone for the Ovine FAANG Project occurred in April 2016, when members of ISGC research group as well as personnel from the Department of Animal, Dairy and Veterinary Sciences at Utah State University collected 100 tissues from Benz 2616. Tissue samples were either snap frozen in liquid nitrogen and can be used for assays such as RNA-seq and ChIP-seq, or slowly frozen or processed into DNA that can be used in chromatin accessibility assays. Additionally, formalin fixed paraffin embedded (FFPE) tissues were processed for histological examination from approximately sixty locations representative of all major body systems. All transcriptome and regulatory data generated in the Ovine FAANG Project will directly connect to the de novo reference genome sequence generated from Benz 2616.
Publications
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Progress 10/01/14 to 09/30/15
Outputs
Target Audience:Target Audience Researchers, sheep producers Changes/Problems:Changes/Problems Bi-monthly phone calls by the sheep FAANG project members have been useful in discussing issues with tissue collection and sample preservation. What opportunities for training and professional development has the project provided?Opportunities Station reports for the NRSP8 Sheep and Goat Committee members were presented at the NRSP8 annual meeting in San Diego on January 9 and 10, 2015. In addition, NRSP8 members attended the International Sheep Genomics Consortium (ISGC) meeting on January 11, 2015 where plans for future development of the sheep genome assembly were prioritized. The development of a sheep FAANG (Functional Annotation of the Animal Genome) project was also discussed. How have the results been disseminated to communities of interest?Dissemination An NRSP8 Sheep Coordinator report and a report for activities conducted at Utah State University were provided at the Plant and Animal Genome meeting in San Diego on January 10, 2015. What do you plan to do during the next reporting period to accomplish the goals?Plan of Work Tissues from two Rambouillet ewes will be collected and processed in January for the FAANG project. Tissue samples will be distributed to those researchers interested in contributing functional and regulatory analyses to the FAANG dataset.
Impacts
What was accomplished under these goals?
Accomplishments NRSP-8 funds have supported development of a resequencing database of sheep whole genome sequences with extensive annotation of variants. Sequences have been obtained for more than 450 animals and aligned to the ovine Texel reference sequence (Oar v3.1) as well as a new ovine reference sequence generated from a Rambouillet animal donated by USDA, ARS MARC. Analysis of 250 of the sequences have revealed over 80 million genetic variants that can be used for genetically mapping traits. Data in the database will be publicly available on the Sheep Genome website in February, 2016.
Publications
- Type:
Other
Status:
Published
Year Published:
2015
Citation:
Refereed Journal Articles
Fisher, P. J., Hayhoe, C. R., Lown, J. M. (2015). Gender Differences in Saving Behaviors among Low- to Moderate-Income Households. Financial Services Review, 24(1), 1-13. www.drsm.org/FSR_journal/Financial_Services_Review_home.
- Type:
Other
Status:
Published
Year Published:
2015
Citation:
Refereed Journal Articles
Lown, J. M., Kim, J., Gutter, M. S., Hunt, A. T. (2015). Self Efficacy and Savings Among Middle and Low Income Households. Journal of Family and Economic Issues, 36(4), 491-502. link.springer.com/article/10.1007%2Fs10834-014-9419-y#page-1
- Type:
Other
Status:
Published
Year Published:
2015
Citation:
Refereed Journal Articles
Xu, X., Ectors, F., Davis, E. E., Cockett, N., Charlier, C., Georges, M., Takeda, H. (2015). Ectopic expression of retrotransposon-derived PEG11 and DLK1 underlie the callipyge muscular hypertrophy. PLOS One, 10, e0140594.
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Progress 01/08/14 to 09/30/14
Outputs
Target Audience: Target Audience Researchers Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? Opportunities The NRSP8 Sheep Committee met during the Plant and animal Genome meeting in San Diego on January 11 and 12 2014. Station reports from all NRSP8 committee members and the Sheep Coordinator were presented on January 12 2014. The International Sheep Genomics Consortium (ISGC) meeting was held on January 13, 2014 in conjunction with the PAG meeting in San Diego. Updates on sheep genomics resources were provided and new directions for the ISGC efforts were discussed. The Sheep Genomics Workshop was held in Lincoln, NE on November 13 and 14, 2014. The workshop was conducted to facilitate discussions on the challenges that limit the application of genomic information in the U.S. sheep industry. Participants of the workshop developed a strategy that will result in improved genomic information and tools available to sheep producers. Another equally goal of the workshop was the development of collaborative efforts among the workshop participants for the successful implementation of the strategy. How have the results been disseminated to communities of interest? Dissemination An NRSP8 Sheep Coordinator report was provided at the Plant and Animal Genome meeting in San Diego on January 11, 2014. What do you plan to do during the next reporting period to accomplish the goals? Plan of Work Blood samples from industry relevant sheep as well as those sheep carrying interesting mutations will be collected. Whole genome sequence (WGS) data will be determined for the animals and submitted to the Sheep Genomes Database for analysis.
Impacts
What was accomplished under these goals?
Accomplishments The Ovine Reference Genome Sequence Database version 3.1 (Oar V3.1) is publicly available through the website (http://www.livestockgenomics.csiro.au/sheep/oar3.1.php). The reference genome contains 2.95 Gbp sequence. Gaps between contigs are being covered using PacBio at the BCM-HGSC. The ovine reference sequence paper published in Science (June, 2014) with 74 authors from 8 countries and 26 institutions. Brian Dalrymple and Jiang Yu (CSIRO, Australia) are the lead authors. Highlights of differences between the genome structure of sheep, cattle and goats are included in the paper. The analysis of about a terabite of data on the transcriptome is also included. Variation of alleles, allelic imbalance and copy number variation were included in the paper. Biological stories included digestive tract enzymes, evolution of the rumen, lipid metabolism and evolution of wool.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Griesdorn, T. S., Lown, J. M., DeVaney, S. A., Cho, S. H., Evans, D. A. (2014). Association between behavioral life-cycle constructs and financial risk tolerance of low-to-moderate-income households. Journal of Financial Counseling and Planning, 24(1), 27-39. www.afcpe.org/publications/
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Lown, J. M., Kim, J., Gutter, M. S., Hunt, A. T. (2014). Self Efficacy and Savings Among Middle and Low Income Households. Journal of Family and Economic Issues. link.springer.com/article/10.1007%2Fs10834-014-9419-y#page-1
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