Source: AGRICULTURAL RESEARCH SERVICE submitted to
STRUCTURAL AND FUNCTIONAL IMPACTS OF COPY NUMBER VARIATIONS ON THE CATTLE GENOME
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
TERMINATED
Funding Source
AFRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
0224623
Grant No.
2011-67015-30183
Project No.
MDR-2010-04524
Proposal No.
2010-04524
Multistate No.
(N/A)
Program Code
A1201
Project Start Date
May 1, 2011
Project End Date
Apr 30, 2016
Grant Year
2011
Project Director
Liu, G.
Recipient Organization
AGRICULTURAL RESEARCH SERVICE
RM 331, BLDG 003, BARC-W
BELTSVILLE,MD 20705-2351
Performing Department
Bovine Functional Genomics Laboratory
Non Technical Summary
Although there have been significant advances in resolving the pattern and nature of single nucleotide polymorphisms (SNPs), similar realizations for larger, more complex forms of genetic variation have just emerged. Several recent publications reveal that copy number variations (CNVs) are common and associated with cattle health and breed formation. Array based platforms, such as array comparative genomic hybridization (aCGH) and SNP arrays, indirectly assay CNVs, do not resolve the structure of the events and are limited to assaying sequence represented in the cattle genome reference sequence. Sequence-based resolution of CNV and the development of high throughput genotyping platforms are required to assess their association with economic traits. An integrated CNV project combining both array and next generation sequencing (NGS) technologies will provide an indispensable resource to explore CNV and will significantly improve annotation of the cattle genome. This project outlines a plan to develop a general integrated framework ? ArraySeq to detect, classify and compare CNVs by jointly using existing NGS, aCGH and SNP genotyping data; we will apply ArraySeq to human and cattle datasets and evaluate its performances through computational comparison and experimental validation; we will then test functional impacts of cattle CNVs by associating them with animal production and health traits. Our project will provide the second generation cattle CNV map (many events at base resolution) - a crucial resource for developing CNV genotyping platforms and a cattle 1000 genomes project. It will also significantly improve the cattle reference genome and its annotation by filling in novel sequence information. Also the proposed ArraySeq can easily re-purposed for other species and other purposes such as functional genomics studies using RNA-seq. Overall, this project will make effective and timely use of the information emerging from the cattle genome and HapMap projects and has great economic potential benefiting all six USDA strategic goals
Animal Health Component
(N/A)
Research Effort Categories
Basic
100%
Applied
(N/A)
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
3043399108040%
3043499108040%
3043999108020%
Knowledge Area
304 - Animal Genome;

Subject Of Investigation
3499 - Dairy cattle, general/other; 3999 - Animal research, general; 3399 - Beef cattle, general/other;

Field Of Science
1080 - Genetics;
Goals / Objectives
An integrated pipeline combining both array and next generation sequencing (NGS) technologies will provide an indispensable resource to explore CNV and will significantly improve annotation of the cattle genome. We will develop an integrated tool (ArraySeq) to detect, classify and compare CNV by jointly using existing next generation sequencing, aCGH and SNP genotyping data; apply ArraySeq to existing human and cattle datasets; evaluate ArraySeq's performance by computational and experimental confirmation; and then rest functional impacts of cattle CNVs on animal production and health.
Project Methods
This project outlines a plan to develop a general integrated framework - ArraySeq to detect, classify and compare CNVs by jointly using existing NGS, aCGH and SNP genotyping data; we will apply ArraySeq to human and cattle datasets and evaluate its performances through computational comparison and experimental validation; we will then test functional impacts of cattle CNVs by associating them with animal production and health traits.

Progress 05/01/11 to 04/30/16

Outputs
Target Audience:Farmers, scientists, livestock industries and policy planners who need improve animal health and production based on genome-enabled animal selection. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Teach and mentor 2 postdoc, 2 technicians, 2 Ph.D. students. 1. Lingyang Xu, Postdoc, contributed to population genetics of CNV 2. El Hay, Postdoc, contributed to Genomic predictions combining CNV and SNP 3. Reuben Anderson, technician, contributed to qPCR, aCGH and NGS 4. Alexander Dimtchev, technician, contributed to qPCR and aCGH 5. Yang Zhou, Ph. D. student, contributed to CNV-based GWAS 6. Botong Shen, Ph. D. student, contributed to CNV call algorithms How have the results been disseminated to communities of interest?1. Invited presentation, Liu, G.E. "Population-genetic properties of differentiated copy number variations in cattle" at China Agriculture University, November 11, 2015, Beijing, China. 2. Invited presentation, Liu, G.E. "Genomic variations and their impacts in the cattle genome" at Proceedings of the 18th National Conference on Animal Genetics and Breeding, November 13-16, 2015, Nanchang, China. 3. Invited presentation, Zhou, Y. et al., "Genome-wide CNV analysis reveals variants associated with growth traits in Bos indicus". Plant & Animal Genome Conference XXIV Proceedings, San Diego, CA, January 9-13, 2016, W155. 4. Invited presentation, Xu, L. et al., "Population-genetic properties of differentiated copy number variation in cattle" at The 26th Annual Beltsville Poster Day. May 20, 2015, Beltsville, MD. 5. Invited presentation, Zhou, Y. et al., "Genome wide CNV analysis reveals variants associated with growth traits in Bos indicus" at the 26th Annual Beltsville Poster Day. May 20, 2015, Beltsville, MD. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? All goals are accomplished. We published the software RAPTR-SV after renaming it from ArraySeq. We evaluated and released it along with other utilities to the public under an open source license (https://github.com/njdbickhart/RAPTR-SV). We published two papers about CNV population genetics based on SNP array and NGS on high profile journals. The sequencing data in BAM format were submitted to SRA and the 1000 Bull Genomes Project. We published two papers on CNVs in Bos indicus. The resultant CNVs was used as additional markers in additional to SNPs for animal selection for production traits.

Publications

  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Li, Y., Carrillo, J.A., Ding, Y., He, Y., Zhao, C., Liu, J., Liu, G.E., Zan, L., Song. J. 2015. Transcriptomic Profiling of Spleen in Grass-Fed and Grain-Fed Angus Cattle. PLoS. One. 10 (9):e0135670.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Wang, L., Xu, L., Liu, X., Zhang, T., Li, N., Hay, E.H.A., Zhang, Y., Yan, H., Zhao, K., Liu, G.E., Zhang, L., Wang, L. 2015. Copy number variation-based genome wide association study reveals additional variants contributing to meat quality in Swine. Sci. Rep. 5:12535.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Xu, L., Hou, Y., Bickhart, D.M., Zhou, Y., Hay, E.H.A., Song, J., Sonstegard, T.S., Van Tassell, C.P., Liu, G.E. 2016. Population-genetic properties of differentiated copy number variations in cattle. Sci. Rep. 6:23161.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Zhou, Y., Utsunomiya, Y.T., Xu, L., Hay, E.H.A., Bickhart, D.M., Carvalheiro, R., Neves, H.H.E., Sonstegard, T.S., Van Tassell, C.P., Garcia, J.F., Liu, G.E. 2016. Genome-wide CNV analysis reveals variants associated with growth traits in Bos indicus. BMC Genomics, 17:419.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Bickhart, D.M., Xu, L., Hutchison, J.L., Cole, J.B., Null, D.J., Schroeder, S.G., Song, J., Garcia, J.F., Van Tassell, C.P., Sonstegard, T.S., Schnabel, R.D., Taylor, J.F., Lewin H.A., Liu, G.E. 2016. Diversity and population-genetic properties of copy number variations and multicopy genes in cattle. DNA Res., 23(3):253-62.


Progress 05/01/14 to 04/30/15

Outputs
Target Audience:Farmers, scientists, livestock industries and policy planners who need improve animal health and production based on genome-enabled animal selection. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Teach and mentor 1 postdoc, 3 technicians, 3 Ph.D. students. 1. Lingyang Xu, Postdoc, contributed to CNV call algorithms using SNP array 2. Reuben Anderson, technician, contributed to qPCR, aCGH and NGS 3. Alexander Dimtchev, technician, contributed to qPCR and aCGH 4. Jose Adrian Carrillo, Ph. D. student, contributed to CNV call algorithms 5. Yi Ding, Ph. D. student, contributed to CNV call algorithms 6. Botong Shen, Ph. D. student, contributed to CNV call algorithms How have the results been disseminated to communities of interest?1. Invited presentation, Liu, G.E. et al. "Genomic signatures reveal geographic adaption and human selection in cattle" at the 34th Confernece of International Society for Animal Genetics(ISAG), Xi'an, China, July 28 - August 1, 2014. 2. Invited presentation, Bickhart, D.M. et al. "Population sequencing reveals breed and sub-species specific CNVs in cattle" at the 34th Confernece of International Society for Animal Genetics(ISAG), Xi'an, China, July 28 - August 1, 2014. 3. Invited presentation, Liu, G.E. et al. "Structural and functional impacts of copy number variations on the cattle genome" at Inst. of Hydrobiology, Chinese Academy of Sciences, Wuhan, China, August 1, 2014. 4. Invited presentation, Liu, G.E. et al. "Genomic variations and their impacts in the cattle genome" at CapitalBio, Inc., Beijing, China, August 7, 2014. 5. Invited presentation, Liu, G.E. et al. "Whole-genome sequencing reveals the diversity and population-Genetic properties of cattle CNVs" at Plant and Animal Genome Conference, San Diego, CA, January 10-14, 2015. 6. Invited presentation, Bickhart D.M. et al. "Comparison of CNVs in buffalo with other species" at Plant and Animal Genome Conference, San Diego, CA, January 10-14, 2015. 7. Invited presentation, Sonstegard T.S. et al. "Genome changes due to forty years of artificial selection associated with divergent dairy" at Plant and Animal Genome Conference, San Diego, CA, January 10-14, 2015. 8. Invited presentation, Xu L. et al. "Genomic signatures reveal new evidences for selection of important traits in omestic cattle" at Plant and Animal Genome Conference, San Diego, CA, January 10-14, 2015. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? For objectives 1, 2, and 3, we published a journal article about the software RAPTR-SV after renaming it from ArraySeq. We evaluated its capabilities and efficacies using human and cattle data and released it along with other utilities to the public under an open source license (https://github.com/njdbickhart/RAPTR-SV). We submitted a manuscript about CNV population genetics to a high profile journal for publication. The sequencing data in BAM format were submitted to SRA and the 1000 Bull Genomes Project. For objective 4, we performed genome wide association studies (GWAS) between CNVs and viral resistance traits in pig and between CNVs and growth traits in Bos indicus. The resultant CNVs could be used as additional markers for animal selection for traits like production and viral resistance.

Publications

  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Xu L., Zhao F., Ren H., Li L., Lu J., Liu J., Zhang S., Liu G.E., Song J., Zhang L., Wei C., and Du L. 2014. Co-expression analysis of fetal weight-related genes in ovine skeletal muscle during mid and late fetal development stages. Int J Biol Sci. 10(9):1039-50.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Xu L., Cole J.B., Bickhart D.M., Hou Y., Song J., VanRaden P.M., Sonstegard T.S., Van Tassell C.P., and Liu G.E. 2014. Genome wide CNV analysis reveals additional variants associated with milk production traits in Holsteins. BMC Genomics. 15:683.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Xu L., Bickhart D.M., Cole J.B., Schroeder S.G., Song J., Van Tassell C.P., Sonstegard T.S., and Liu G.E. 2015. Genomic signatures reveal new evidences for selection of important traits in domestic cattle. Mol Biol Evol. 32(3):711-25.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Bickhart D.M., Hutchison J.L., Xu L., Schnabel R.D., Taylor J.F., Reecy J.M., Schroeder S., Van Tassell C.P., Sonstegard T.S., and Liu G.E. 2015. RAPTR-SV: a hybrid method for the detection of structural variants. Bioinformatics. 31(13):2084-90.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Hay E.H.A., Choi I., Xu L., Zhou Y., Bickhart D.M., Lunney J.K., and Liu G.E. 2015. Genome wide CNV association of swine responses to porcine reproductive and respiratory syndrome virus infection. The 26th Annual Beltsville Poster Day. p. 34.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Xu L., Hou Y., Zhou Y., Hay E.H.A., Bickhart D.M., Song J., Sonstegard T.S., Van Tassell C.P., and Liu G.E. 2015. Population-genetic properties of differentiated copy number variation in cattle. The 26th Annual Beltsville Poster Day. p. 80.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Zhou Y., Utsunomiya Y.T., Xu L., Hay E.H.A., Bickhart D.M., Sonstegard T.S., Van Tassell C.P., Garcia J.F., and Liu G.E. 2015. Genome wide CNV analysis reveals variants associated with growth traits in Bos indicus. The 26th Annual Beltsville Poster Day. p. 87.


Progress 05/01/13 to 04/30/14

Outputs
Target Audience: Farmers, scientists, livestock industries and policy planners who need improve animal health and production based on genome-enabled animal selection. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Teach and mentor 1 postdoc, 3 technicians, 2 Ph.D. students. 1. Lingyang Xu, Postdoc, contributed to CNV call algorithms using SNP array 2. Elliott Mattson, technician, contributed to RNA-Seq algorithms using NGS 3. Reuben Anderson, technician, contributed to qPCR, aCGH and NGS 4. Alexander Dimtchev, technician, contributed to qPCR and aCGH 5. Jose Adrian Carrillo, Ph. D. student, contributed to CNV call algorithms 6. Yi Ding, M.S. student, contributed to CNV call algorithms How have the results been disseminated to communities of interest? 1. Invited presentation, Liu, G.E. et al. “Structural and functional impacts of cattle copy number variations” at the 5th International Symposium on Animal Functional Genomics (ISAFG 2013), Guarujá, Sao Paolo, Brazil, September 9-11, 2013. 2. Invited presentation, Bickhart, D.M. et al. "The use of population-scale sequencing to identify CNVs impacting productive traits in different cattle breeds" at Plant and Animal Genome Conference, San Diego, CA, January 11-15, 2014. 3. Invited presentation, Xu, L. et al. "A genome-wide survey reveals a deletion polymorphism associated with resistance to gastrointestinal nematodes in Angus cattle" at Plant and Animal Genome Conference, San Diego, CA, January 11-15, 2014. 4. Invited presentation, Liu, G. et al. "Population sequencing reveals breed and sub-species specific CNVs in cattle" at the 15th annual Advances in Genome Biology and Technology (AGBT) meeting, Marco Island, FL, February 12-15, 2014. 5. Invited presentation, Liu, G. et al. "Population sequencing reveals breed and sub-species specific CNVs in cattle" The Biology Of Genomes, Cold Spring Harbor, NY, May 6-10, 2014. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? For objectives 1, 2, and 3, we have identified 1991 CNV regions (CNVRs) using population-scale sequencing data generated from 74 cattle of 8 breeds (Holstein, Angus, Jersey, Limousin, Romagnola, Brahman, Gir and Nelore). A total of 3.6% (102.0 Mb) of the cattle genome is predicted to be copy number variable, representing a substantial increase over the previous estimates (~2%). We validated this sequence-based CNV call set using qPCR and aCGH achieving a high validation rate. Hundreds of CNVs were found to be either breed specific or differentially variable across breeds, such as RICTOR in dairy breeds and PNPLA3 in the beef breeds. Population genetics analyses based on CNVs revealed the population structures of these taurine and indicine breeds. At the same time, we optimized software pipeline to analyze NGS data. The software package is currently in a pre-alpha state posted at https://github.com/njdbickhart/CoSVarD for user feedbacks. We expect to publish a journal article detailing the capabilities and efficacy of the software before release to the public under an open-source license. For objective 4, we performed genome wide association studies (GWAS) between CNVs and parasite resistance traits in Angus cattle and between CNVs and milk traits in Holsteins. In Angus parasite resistance GWAS, we identified one associated deletion CNV on chr7 near immune-related genes such as ZNF496 and NLRP3. In Holstein milk production GWAS, we proved that while 75% trait-associated CNVs can be tagged by neighboring SNPs, the left 25% associated CNVs were not captured by neighboring SNPs. The resultant CNVs could be used as additional markers for animal selection for traits like production, parasite resistance, fertility and feed efficiency.

Publications

  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Xu, L., Hou, Y., Bickhart, D.M., Song, J., Liu, G.E. 2014. Comparative analysis of CNV calling algorithms: literature survey and a case study using bovine high-density SNP data. Microarrays 2(3), 171-185.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Xu, L., Hou, Y., Bickhart, D.M., Song, J., Van Tassell, C.P., Sonstegard, T.S., Liu, G.E. 2014. A genome-wide survey reveals a deletion polymorphism associated with resistance to gastrointestinal nematodes in Angus cattle. Funct Integr Genomics. [Epub ahead of print]. DOI: 10.1007/s10142-014-0371-6.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Bickhart, D.M., Liu, G.E. 2014. The challenges and importance of structural variation detection in livestock. Front Genet. 5:37. DOI: 10.3389/fgene.2014.00037.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Liu G.E., Xu, L., and Huang, K.S. Recent Advances in Studying of Copy Number Variation and Gene Expression. Gene Expression to Genetical Genomics 2014:7 1-5. DOI:10.4137/GGG.S14286.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Porto-Neto, L.R., Sonstegard, T.S., Liu, G.E., Bickhart, D.M., Da Silva, M.V., Machado, M.A., Utsunomiya, Y.T., Garcia, J.F., Gondro, C., Van Tassell, C.P. 2013. Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping. BMC Genomics. 14:876. DOI: 10.1186/1471-2164-14-876.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: P�rez O'Brien, A.M., Utsunomiya, Y.T., M�sz�ros, G., Bickhart, D.M., Liu, G.E., Van Tassell, C.P., Sonstegard, T.S., Da Silva, M.V., Garcia, J.F., S�lkner, J. 2014. Assessing signatures of selection through variation in linkage disequilibrium between taurine and indicine cattle. Genet Sel Evol. 46:19. DOI: 10.1186/1297-9686-46-19.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Zhao, C., Zan, L., Wang, Y., Updike, M.S., Liu, G.E., Bequette, B.J., Baldwin, R.L., Song, J. Functional proteomic and interactome analysis of proteins associated with beef tenderness in angus cattle. Livestock Science. 161(2014):201-209. DOI: 10.1016/j.livsci.2013.11.030.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Liu, G.E., Bickhart, D.M. 2013. Structural and functional impacts of copy number variations on the cattle genome. The 5th International Symposium on Animal Functional Genomics Meeting Abstract. p. 3.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Liu, G.E., Xu, L., Cole, J.B., Hou, Y. Bickhart, D.M., Van Raden, P.M., Sonstegard, T.S., Van Tassell, C.P. 2013. A genome-wide association study between copy number variation and milk production traits in a Holstein population. The University of Maryland/Beltsville ARS 3rd Annual Symposium.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Xu, L., Hou, Y., Bickhart, D.M., Song, J., Van Tassell, C.P., Sonstegard, T.S., Liu, G.E. 2013. A genome-wide survey reveals a deletion polymorphism associated with resistance to gastrointestinal nematodes in Angus cattle. The University of Maryland/Beltsville ARS 3rd Annual Symposium.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Liu, G.E., Bickhart, D.M., Xu, L., Hutchison, J.L., Y., Sonstegard, T.S., Van Tassell, C.P., Schroeder, S.G., Garcia, J.F., Taylor, J.F., Schnabel, R.D., Lewin, H.A. 2014. Population sequencing reveals breed and sub-species specific CNVs in cattle. Advances in Genome Biology & Technology Conference Meeting Abstract. p. 58.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Xu, L., Cole, J.B., Bickhart, D.M., Hou, Y., Song, J., Van Raden, P.M., Sonstegard, T.S., Van Tassell, C.P., Liu, G.E. 2014. Genome wide CNV analysis reveals additional variants associated with milk production traits in Holsteins. BARC Poster Day. p. 67, abstract 54.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Bickhart, D.M., Xu, L., Hutchison, J.L., Y., Sonstegard, T.S., Van Tassell, C.P., Schroeder, S.G., Garcia, J.F., Taylor, J.F., Schnabel, R.D., Lewin, H.A., Liu, G.E. 2014. Population sequencing reveals breed and sub-species specific CNVs in cattle. Conference on the Biology of Genomes, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY. p199.


Progress 05/01/12 to 04/30/13

Outputs
Target Audience: Farmers, scientists, livestock industries and policy planners who need improve animal health and production based on genome-enabled animal selection. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Teach and mentor 2 postdoc, 2 technicians, 2 Ph.D. students and 2 Master students. 1. Lingyang Xu, Postdoc, contributed to CNV call algorithms using SNP array 2. Derek Bickhart, Postdoc, contributed to CNV call algorithms using NGS 3. Reuben Anderson, technician, contributed to qPCR, aCGH and NGS 4. Alexander Dimtchev, technician, contributed to qPCR and aCGH 5. Fei Tian, Ph. D. student, contributed to CNV call algorithms 6. Jose Adrian Carrillo, Ph. D. student, contributed to CNV call algorithms 7. Fei Zan, M.S. student, contributed to CNV call algorithms 8. Yi Ding, M.S. student, contributed to CNV call algorithms How have the results been disseminated to communities of interest? 1. Invited presentation, Liu, G. et al. “Mapping cattle copy number variation by population-scale genome sequencing” at ISAG Domestic Animal Sequencing Workshop (Chairs: James Reecy, Dave Burt), Cairns, Australia, July 16, 2012. 2. Invited presentation, Hou, Y. et al. “Fine mapping of copy number variations on two cattle genome assemblies using high density SNP array” at ISAG Comparative & Functional Genomics Workshop (Chair: Klaus Wimmers), Cairns, Australia, July 19, 2012. 3. Invited presentation, Liu, G. et al “Use of CNVs in understanding genetic basis of RFI” at ISAG Animal Selection, Genetics & Genomics Network (ASGGN) Satellite Meeting (Chair: Hutton Oddy and John McEwen), Cairns, Australia, July 21, 2012 4. Invited presentation, Liu, G. et al. “Mapping cattle copy number variations in the buffalo genome” at Plant and Animal Genome Conference, San Diego, CA on January 12-16, 2013. 5. Invited presentation as senior corresponding author, Bickhart, D.M. et al. “Combined arms: a full spectrum approach to structural variant discovery in livestock populations” at Plant and Animal Genome Conference, San Diego, CA on January 12-16, 2013. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? For objectives 1, 2, and 3, we performed the first comprehensive discovery of CNV using next-generation sequencing from 100 individuals. We identified thousands of CNV regions, many of which had not been reported previously. We validated this sequence-based CNV call set using three independent molecular techniques achieving a high validation rate. At the same time, we developed software pipeline to analyze NGS data. The software package is currently in a pre-alpha state. After extensive testing, we expect to publish a journal article detailing the capabilities and efficacy of the software before release to the public under an open-source license. We are finishing ArraySeq to combine both array and next-generation sequencing (NGS) data for CNV discovery. These will provide the second-generation cattle CNV map. It also will significantly improve annotation of the cattle genome. For objective 4, over 30,000 Bovine50K SNP data were collected and processed by the program PennCNV and Golden Helix SVS. We are testing functional impacts of cattle CNV by associating them with animal production and health traits.

Publications

  • Type: Journal Articles Status: Published Year Published: 2012 Citation: Hou, Y., Bickhart, D.M., Chung, H., Hutchison, J.L., Norman, H.D., Connor, E.E., Liu, G. 2012. Analysis of copy number variations in Holstein cows identify potential mechanisms contributing to differences in residual feed intake. Functional and Integrative Genomics. 12(4):717-723.
  • Type: Journal Articles Status: Published Year Published: 2012 Citation: Zhao, C., Fei, T., Yu, Y., Luo, J., Mitra, A., Zhan, F., Hou, Y., Liu, G., Zan, L., Updike, M., Song, J. 2012. Functional Genomic Analysis of Variation on Beef Tenderness Induced by Acute Stress in Angus Cattle. Comparative and Functional Genomics. DOI: 10.1155/2012/756284.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Bickhart, D.M., Liu, G. 2013. Identification of candidate transcription factor binding sites in the cattle genome. Genomics, Proteomics and Bioinformatics. 11(3):195198.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Shin, J., Li, R.W., Goa, Y., Bickhart, D.M., Liu, G., Li, W., Wu, S., Li, C. 2013. Butyrate induced IGF2 activation correlated with distinct chromatin landscapes due to histone modification. Gene Regul Syst Bio. 7:5770.
  • Type: Journal Articles Status: Published Year Published: 2012 Citation: Zhao, C., Tian, F., Yu, Y., Liu, G., Zan, L., Updike, M., Song, J. 2012. miRNA-dysregulation associated with tenderness variation induced by acute stress in angus cattle. J Anim Sci Biotechnol. 3:12.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Mcclure, M.C., Kim, E., Bickhart, D.M., Null, D.J., Cooper, T.A., Cole, J.B., Wiggans, G.R., Marsan, P.A., Colli, L., Santus, E., Liu, G., Schroeder, S.G., Matukumalli, L., Van Tassell, C.P., Sonstegard, T.S. 2013. Fine mapping for Weaver Syndrome in the Brown Swiss breed with the identification of possible casual mutations across NRCAM, PNPLA8, and CTTNBP2 and Developement of a diagnostic SNP haplotype. PLoS One. 8(3): e59251.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Luo, J., Yu, Y., Mitra, A., Chang, S., Zhang, H., Liu, G., Yang, N., Song, J. 2013. Genome-wide copy number variant analysis in inbred chicken lines with different susceptibility to Mareks disease. Genes, Genomes, and Genomics. 3:217-223.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2012 Citation: Hou, Y., Connor, E.E., Liu, G. 2012. Initial analysis of copy number variations in Holstein cattle selected for high or low feed efficiency. Meeting Proceedings. No. 2.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2012 Citation: Liu G. Mapping cattle copy number variation by population-scale genome sequencing at the 33rd Conference of the International Society of Animal Genetics in Cairns, Australia on July 15-20, 2012. Poster Abstract. p. 146.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2012 Citation: Hou, Y., Bickhart, D.M., Hvinden, M.L., Li, C., Song, J., Boichard, D.A., Fritz, S., Eggen, A., Denise, S., Wiggans, G.R., Sonstegard, T.S., Van Tassell, C.P., Liu, G. 2012. Fine mapping of copy number variations on two cattle genome assemblies using high density SNP array at the 33rd Conference of the International Society of Animal Genetics in Cairns, Australia on July 15-20, 2012. Poster Abstract. p. 6007.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Luo, J., Yu, Y., Mitra, A., Zhang, H., Liu, G., Song, J. 2013. Genome-wide copy number variant analysis in inbred chickens lines with different susceptibility to Marek's disease. Plant and Animal Genome XXI Conference, January 12-16, 2013, San Diego, California. Abstract. P0649.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Liu, G., Bickhart, D.M. 2013. Mapping cattle copy number variations in water buffalo. Plant and Animal Genome XXI Conference, January 12-16, 2013, San Diego, California. Meeting Abstract. W115.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Bickhart, D.M., Liu, G. 2013. Combined arms: a full spectrum approach to structural variant discovery in livestock populations. Plant and Animal Genome XXI Conference, January 12-16, 2013, San Diego, California. Meeting Abstract. W145.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Bickhart, D.M., Hutchison, J.L., Xu, L., Song, J., Liu, G. 2013. Open source tools to exploit DNA sequence data from livestock species. BARC Poster Day. p. 9, Abstract 4.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Xu, L., Huson, H.J., Hou, Y., Bickhart, D.M., Song, J., Sonstegard, T.S., Van Tassell, C.P., Liu, G. 2013. Analysis of population structure and genetic history of cattle breeds based on high-density SNP data. BARC Poster Day. p.55 Abstract 48.
  • Type: Book Chapters Status: Published Year Published: 2013 Citation: Liu, G., Bickhart, D.M. 2013. The trappin gene family: structure, function and evolution. In: G.E. Liu, Editor. Cattle: Domestication, Disease and Environment. Nova Science Publishers Inc. Hauppauge, NY. Chapter 2, p. 25-38.


Progress 05/01/11 to 04/30/12

Outputs
OUTPUTS: Activities: Its objectives are (1) Develop an integrated tool (ArraySeq) to detect, classify and compare CNV by jointly using existing next generation sequencing (NGS), aCGH and SNP genotyping data; (2) Apply ArraySeq to existing human and cattle datasets; (3) Evaluate ArraySeq's performance by computational and experimental confirmation; and (4) Test functional impacts of cattle CNVs on animal production and health. All objectives are partially met. For objectives 1, 2 and 3, we performed the first comprehensive discovery of CNVs using NGS from six cattle individuals. We identified over 1,265 CNV regions comprising ~55.6 Mbp sequence - 476 of which (~38%) had not been previously reported. We validated this sequence-based CNV call set with aCGH, qPCR and FISH, achieving a validation rate of 82% and a false positive rate of 8%. We are developing and improving an integrated tool/algorithm to merge CNV across various discovery platforms. For objective 4, over 30,000 Bovine50K SNP data were collected and processed by PennCNV. We are associating resultant CNVs with animal production and health traits. Teach and mentor 2 technicians, 2 postdoc, and 2 Ph.D. students. Events: Invited talk titled "Search for copy number variation in the Water Buffalo genome" in the Water Buffalo Workshop during Plant and Animal Genome (PAG) XIX Conference in San Diego, CA, 2012. Invited talk titled "Structural and functional impacts of copy number variation on the cattle genome" in the Annual Project Director (PD) Meeting for the NRI's Animal Genome Program in San Diego, CA, 2012. Services: collaboration with and consulting for University Maryland, College Park. Products: The first individualized CNV maps were generated using NGS from six cattle. 2 websites: http://bfgl.anri.barc.usda.gov/cattleCNV/ and http://bfgl.anri.barc.usda.gov/BovineTFBS/. PARTICIPANTS: Teach and mentor 2 postdoc, 2 technicians and 2 Ph.D. students. 1. Yali Hou, Postdoc, contributed to CNV call algorithms using SNP array; 2. Derek Bickhart, Postdoc, contributed to CNV call algorithms using NGS; 3. Reuben Anderson, technician, contributed to qPCR, aCGH and NGS; 4. Alexander Dimtchev, technician, contributed to qPCR, aCGH and BAC isolation; 5. Fei Tian, Ph. D. student, contributed to CNV call algorithms; 6. Fei Zan, Ph. D. student, contributed to CNV call algorithms. Internal collaboration with Drs. E.C. Connor, C.P. Van Tassell, T.S. Sonstegard (BFGL-ANRI-ARS-USDA), J.B. Cole, P.M. VanRaden, G. Wiggans (AIPL), J.W. Keele, T.P. Smith, T.G. McDaneld, D.J. Nonneman (USDA-MARC); L.J. Alexander (USDA-Mile City, Montana). External collaborations with researchers: J.F. Garcia from Brazil, J.F. Taylor and R.D. Schnabel at University of Missouri Columbia, J. Williams of Parco Tecnologico Padano from Italy, L. Iannuzzi of Institute for Animal Production Systems in Mediterranean Environments, National Research Council from Italy. TARGET AUDIENCES: Stakeholders and general audiences PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
By providing the first individualized cattle CNV and segmental duplication maps and genome-wide gene copy number estimates, we enable future CNV studies into highly duplicated regions in the cattle genome.

Publications

  • Y. Hou, G. E. Liu, D. M. Bickhart, L. K. Matukumalli, C. Li, J. Song, L. C. Gasbarre, C. P. Van Tassell, and T. S. Sonstegard. Genomic regions showing copy number variations associate with resistance or susceptibility to gastrointestinal nematodes in Angus cattle. The BARC-UMD Fall Symposium 2011, National Wildlife Visitor Center, Laurel, MD, 2011. (Abstract)
  • G. Partipilo, P. D'Addabbo, G. M. Lacalandra, G. E. Liu, and M. Rocchi. Refinement of Bos taurus sequence assembly based on BAC-FISH experiments. BMC Genomics 12:639, 2011.
  • D. M. Bickhart, Y. Hou, S. G. Schroeder, C. Alkan, M. F. Cardone, L. K. Matukumalli, J. Song, R. D. Schnabel, M. Ventura, J. F. Taylor, J. F. Garcia, C. P. Van Tassell, T. S. Sonstegard, E. E. Eichler, and G. E. Liu. Copy number variation of individual cattle genomes using next-generation sequencing. Genome Res. 22 (4):778-790, 2012.
  • N. Lawless, J. D. Lippolis, T. A. Reinhardt, K. G. Meade, M. McCabe, G. E. Liu, M. C. Zody, T. S. Sonstegard, C. O'Farrelly, and D. J. Lynn. Innate immune response to a bovine mastitis pathogen profiled in milk and blood monocytes using a systems biology approach. The International Symposium on Animal Functional Genomics, Dublin, Ireland, October 10-12, 2011., 2011. (Abstract)
  • D. M. Bickhart, Y. Hou, S. G. Schroeder, C. Alkan, M. F. Cardone, L. K. Matukumalli, J. Song, R. D. Schnabel, M. Ventura, J. F. Taylor, J. F. Garcia, E. E. Eichler, T. S. Sonstegard, C. P. Van Tassell, and G. E. Liu. Individualized Cattle Copy Number and Segmental Duplication Maps using Next Generation Sequencing. The BARC-UMD Fall Symposium 2011, National Wildlife Visitor Center, Laurel, MD, 2011. (Abstract)
  • D. M. Bickhart, Y. Hou, S. G. Schroeder, C. Alkan, M. F. Cardone, L. K. Matukumalli, J. Song, R. D. Schnabel, M. Ventura, J. F. Taylor, J. F. Garcia, E. E. Eichler, T. S. Sonstegard, C. P. Van Tassell, and G. E. Liu. Copy Number Variation of Individual Cattle Genomes using Next Generation Sequencing. Plant and Animal Genome XX Conference, January 14-18, 2012, San Diego, CA, 2012. (Abstract)
  • Y. Hou, D. M. Bickhart, X. Fang, J. Song, C. P. Van Tassell, T. S. Sonstegard, E. eroussi, and G. E. iu. Copy number variations related to reproduction traits in Holstein cattle. The BARC-UMD Fall Symposium 2011, National Wildlife Visitor Center, Laurel, MD, 2011. (Abstract)
  • G. E. Liu and D. M. Bickhart. Searching for copy number variations in the buffalo genome. Plant and Animal Genome XX Conference, January 14-18, 2012, San Diego, CA, 2012. (Abstract)
  • G. E. Liu. Analyses of cattle DNA methylation patterns in diverse tissues. Keystone Symposia Conference Epigenomics (J3) January 17 - 22, 2012, Keystone Resort, Keystone, Colorado, 2012. (Abstract)
  • D. M. Bickhart, Y. Hou, S. G. Schroeder, C. Alkan, M. F. Cardone, L. K. Matukumalli, J. Song, R. D. Schnabel, M. Ventura, J. F. Taylor, J. F. Garcia, E. E. Eichler, T. S. Sonstegard, C. P. Van Tassell, and G. E. Liu. Copy Number Variation Detection in Cattle Reveals Potential Breed-Specific Differences. 2012 BARC Poster Day, Beltsville, MD, 2012. (Abstract)