Progress 09/01/23 to 08/31/24
Outputs Target Audience:Genome research, education and service community; Animal breeding and genetics companies; Organic and conventional dairy producers, processors and retailers; Veterinarians. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?The award has provided training opportunities for two PhD students, one Master's degree student and five undergraduate students. The training includes laboratory and farm safety, animal care and use, DNA and RNA extraction, WTTS-seq library construction, and sample/data collection, analysis and storage, for example. How have the results been disseminated to communities of interest?Results have been regularly disseminated to the USDA/NIFA National Program Leaders, the USDA National Organic Program funded project directors and/or participants, the US bovine FAANG group members, WSU Animal Biology and Biomedicine group members and graduate and undergraduate students who take the Perspectives in Biotechnology class at Washington State University in Fall semesters. What do you plan to do during the next reporting period to accomplish the goals?We will continue our collection of samples from Aurora Organic Dairy in Colorado, Clover Sonoma in California and potential expansion to other states and accumulation of our datasets in genome, transcriptome, metabolome, microbiome and phenome. We will work on data analysis and prepare manuscripts for publication. We will report to our advisory board members and national program leaders and solicit their advice for further improvement of the study design, public engagement and education/extension activities.
Impacts What was accomplished under these goals?
In year 2 of the funded research, we focused on collecting both endometrial cells and blood from organic dairy cows at 7 ± 2 days post-partum and again at 21± 2 days post-partum. The sampling involved both Holstein and Holstein x Jersey cows at two time periods: cool season (November - December) and warm season (May - July). In addition, we collected health-related phenotypes from each cow at sampling by measuring 1) body temperature; 2) mucus scores (uterine discharge score: 0 - clear, 1 - flakes of purulent exudate, 2 - >50% purulent exudate and 3 - hemorrhagic discharge mixed with purulent exudate), 3) reproductive ultrasound measurements (uterine, right ovary, left ovary and cervix) and 4) body condition scores. Because we tried to pair healthy-sick cows for sampling on the same day, our datasets cannot be used to examine seasonal effects on metritis and endometritis in organic dairies. However, cows sampled in the cool season had higher body condition scores (2.75 vs. 2.22, respectively; P<0.0001), but lower body temperatures (101.1 vs 101.7oF, respectively; P<0.01) compared to those sampled in the warm season. Uterine swabs were sent to Washington Animal Disease Diagnosis Laboratory for identification of pathogens, such as mixed bacteria, Escherichia coli and Trueperella pyogenes. Interestingly, the pathogen profiles are hard to distinguish between healthy and unhealthy cows. A method for isolation of both RNA and DNA from the same sample was successfully established. An initial set of DNA samples were sent to GeneSeek for low genome coverage sequencing for genotyping. RNA isolation and construction of WTTS-seq (whole transcriptome termini site sequencing) libraries are underway. As planned, Dr. Maquivar prepared "Organic Animal Production" training materials to educate the public, college students and extension specialists, for example. The current topics include: 1) Introduction to Organic Animal Production, 2) National Organic Program; 3) Nutritional management in Organic Systems, 4) Animal health management in organic animal production systems; 5) Animal welfare assessment in Organic Animal Production systems, 6) Organic Animal Production systems and Economics, 7) Organic food marketing, 8) Organic dairy production, 9) Organic meat production, 10) Organic poultry production and 11) Other organic animal products. In collaboration with USAID Farmer to Farmer Program, Dr. Maquivar developed a training program to dairy producers in the south region of Madagascar in the town of Toliara. The program included 1) Dairy cow husbandry best practices, 2) Assessment of health and disease prevention of dairy cows (including administering veterinary medicines and detection and treatment of metabolic, infectious and reproductive diseases), 3) Production of silage and hay and utilization of forage resources, 4) Reproductive management and 5) Appropriate equipment for milking and milk transportation. As a result, producers got a training certificate in basic dairy cattle management and they continue to improve the management practices.
Publications
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Maquivar M. Genetic and clinical aspects of uterine diseases in dairy cattle. Instituto Tecnol�gico de Costa Rica. Santa Clara, Alajuela, Costa Rica. Curso internacional de reproducci�n bovina. October 2023.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Maquivar M. The social license and animal welfare of bovine production systems and husbandry procedures. Instituto Tecnol�gico de Costa Rica. Santa Clara, Alajuela, Costa Rica. Curso internacional de reproducci�n bovina. October 2023.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Maquivar M. Genetic regulation of endometritis and repeater breeder syndrome in dairy cattle. Congreso Binacional de la Leche. Universidad Polit�cnica Estatal del Carch�. Tulc�n, Ecuador. November 2023
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2024
Citation:
Maquivar M. Animal Health & the immune system. University of Toliara, Toliara, Madagscar. June 2024
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2024
Citation:
Maquivar M. Phenome to genome of uterine diseases. The case of early lactation diseases and repeat breeder cows. National Autonomous University of Mexico. School of Veterinary Medicine. Mexico City, Mexico. November 2024
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2024
Citation:
Stotts MJ, Zhang Y, Michal JJ, Velez J, Hans B, Maquivar M, Jiang Z. Genomically Optimized Organic Dairy (GOOD): Genome Selection against Uterine Diseases to Improve Fertility and Longevity in Cattle. USDA National Institute of Food and Agriculture 2024 Organic Agriculture Annual Project Director Meeting. 04/24 04/25, 2024 Orlando, Florida.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Jiang Z. Invited Plenary Speaker. Research Frontiers in Animal Phenomics. International Conference on Genetics and Genomics Research Fronts in Animals and Poultry, December 9 10, 2023. Shandong Agricultural University, China.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2024
Citation:
Jiang Z. Invited Seminar. Trust your gut or trust your RNA? Department of Animal Science, University of Maryland. 10/18/2024. Baltimore, MD.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2024
Citation:
Jiang Z. Guest Speaker. Want to be healthy? Look to RNA for solutions! Center for Birth Defects Research, University of Maryland School of Medicine. 10/17/2024. Baltimore, MD.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2024
Citation:
Jiang Z. Invited Seminar. You do what RNA does. Biotechnology Faculty, University of Ljubljana. 06/24/2024. Ljubljana, Slovenia.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2024
Citation:
Jiang Z. Invited Seminar. Go abroad and learn more broadly. Animal Science Spring Seminar Series. February 7, 2024. Washington State University.
- Type:
Peer Reviewed Journal Articles
Status:
Published
Year Published:
2024
Citation:
Beiki H, Murdoch BM, Park CA, Kern C, Kontechy D, Becker G, Rincon G, Jiang H, Zhou H, Thorne J, Koltes JE, Michal JJ, Davenport K, Rijnkels M, Ross PJ, Hu R, Corum S, McKay S, Smith TPL, Liu W, Ma W, Zhang X, Xu X, Han X, Jiang Z, Hu ZL, Reecy JM. Enhanced bovine genome annotation through integration of transcriptomics and epi-transcriptomics datasets facilitates genomic biology. Gigascience. 2024;13:giae019.
- Type:
Peer Reviewed Journal Articles
Status:
Published
Year Published:
2024
Citation:
de Jong TV, Pan Y, Rastas P, Munro D, Tutaj M, Akil H, Benner C, Chen D, Chitre AS, Chow W, Colonna V, Dalgard CL, Demos WM, Doris PA, Garrison E, Geurts AM, Gunturkun HM, Guryev V, Hourlier T, Howe K, Huang J, Kalbfleisch T, Kim P, Li L, Mahaffey S, Martin FJ, Mohammadi P, Ozel AB, Polesskaya O, Pravenec M, Prins P, Sebat J, Smith JR, Solberg Woods LC, Tabakoff B, Tracey A, Uliano-Silva M, Villani F, Wang H, Sharp BM, Telese F, Jiang Z, Saba L, Wang X, Murphy TD, Palmer AA, Kwitek AE, Dwinell MR, Williams RW, Li JZ, Chen H. A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats. Cell Genom. 2024;4(4):100527.
- Type:
Peer Reviewed Journal Articles
Status:
Published
Year Published:
2023
Citation:
Wheeler EC, Choi P, De Howitt J, Gill S, Watson S, Yu S, Wahl P, Diaz C, Mohr C, Zinski A, Jiang Z, Rossi D, Davis JF. Cannabis Sativa targets mediobasal hypothalamic neurons to stimulate appetite. Sci Rep. 2023;13(1):22970.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Maquivar M. NCBA - USRSB (U.S Roundtable For Sustainable Beef) General Assembly Meeting Collaborating for Continuous Improvement May 2023 Boise, Idaho
Title of the talk: Impact Of Hispanic Employees On The Sustainability Of Livestock Production Systems In The United States Of America: BQA example.
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Progress 09/01/22 to 08/31/23
Outputs Target Audience:Genome research, education and service community; Animal breeding and genetics companies; Organic and conventional dairy producers, processors and retailers; Veterinarians. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?The award has provided training opportunities for one PhD student, one visiting PhD student, one Master's degree student and three undergraduate students. The training includes laboratory safety, animal care and use, RNA extraction, APA profiling library construction, data analysis and SOP training, for example. How have the results been disseminated to communities of interest?Results have been regularly disseminated to the US bovine FAANG group members, WSU Animal Biology and Biomedicine group members and graduate and undergraduate students who take the Perspectives in Biotechnology class at Washington State University. The information was also shared with broad international communities through a selected talk at the Ruminant Genetics Workshop, 39th International Society for Animal Genetics Conference, Cape Town, South Africa and an invited talk at the Central Dogma of Phenomics Workshop, the American Society of Animal Science Annual meeting 2023, Albuquerque, NM. What do you plan to do during the next reporting period to accomplish the goals?We have a plan to collect samples from Aurora Organic Dairy in Colorado and Clover Sonoma in California and accumulate our datasets in genome, transcriptome, metabolome, microbiome and phenome. We will continue fine-tuning of new statistical models and novel pipelines for data analyses. We will develop cost-effective tools for our industry partners to pursue diagnosis of both metritis and endometritis on farm. We will organize a symposium on organic dairy and facilitate knowledge and technology transfer from research to application.
Impacts What was accomplished under these goals?
We started this funded research project by completing a preliminary study. We have strong evidence to show that alternative polyadenylation (APA) profiles can be used to generate an endometritis progression panel for exploring the bridges between genome and the disease. Especially, pathogens force the host to execute more up-regulated APA sites. In comparison to healthy cows, unhealthy cows tend to use more intronic, but less distal APA sites. Four genes: CD59 molecule, Fc fragment of IgG receptor IIa, lymphocyte antigen 75 and plasminogen may serve as initial contacts or combats with pathogens on cell surfaces, followed by activation of nuclear receptor subfamily 1 group H member 4 to regulate AXL receptor tyrosine kinase, FGR proto-oncogene, Src family tyrosine kinase, HCK proto-oncogene, Src family tyrosine kinase and integrin subunit beta 2 for anti-inflammation. In addition, we also observed that microRNA genes: MIR21 and MIR30A might be a good pair of antagonistic biomarkers for diagnosis of either inflammation or anti-inflammation in the uterus. During this transition stage from a small-scale study to large-scale research, we focused on development of our protocols, procedures and processes before heading to farms for sampling. Specifically, it is our priority to efficiently use samples collected from each animal and thus maximize data collection in genome, transcriptome and phenome to develop the bridge maps for both metritis and endometritis in organic cows. For each cow, we will have pedigree information, production records and reproduction performance plus ultrasonic measurements collected as phenome. Blood samples will be used to produce metabolome and genome datasets, while uterine samples are expected to have both microbiome and transcriptome profiles. The standard operation procedures (SOPs) have been drafted for collection of these datasets for the funded project. In fact, we have been designing a database to include all of these datasets plus sample management systems, including sample storage location, sample processing method and sample analyses results. We started to look at potential challenges associated with big data analysis. Currently, we use the principal component analysis (PCA) to build a disease progression panel. For our funded project, we will collect materials from 1,000 cows. As such, we see potential challenges to pursue PCA analysis on such a large dataset. Instead, we are exploring novel statistical models based on phylogenetic tree construction to overcome the challenge. A key component of transcriptome analysis is to enrich functional pathways. However, understanding the relationships among hundreds or thousands of pathways remains a challenging task. We are developing clustering approaches to make pathway classifications more meaningful to our funded research. In order to apply APA profiles in diagnosis of metritis and endometritis, we are looking into simplified approaches to do so and save costs for organic industries. Using our Department's newsletter, we have released our funded project information to the public as one of our outreach activities. Basically, our GOOD (genomically optimized organic dairy) project will engage an advisory panel of scientists, industry partners and organic dairy producers to understand gene networks underlying uterine disease and thus develop novel tools to identify cows that are resistant to both metritis and endometritis for genetic improvement. No doubt, we have been closely working with our project partners - Aurora Organic Dairy in Colorado and Clover Sonoma in California to develop protocols, procedures and processes for collection of genome, metabolome, microbiome, transcriptome and phenome datasets. We are ready now to start the large-scale sampling process.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Stotts MJ, Zhang YZ, Zhang SW, Michal JJ, Velez JS, Hans B, Maquivar M, Jiang Z. 2023. Alternative polyadenylation events in epithelial cells sense endometritis progression in dairy cows. J. Integr. Agric. 2023;22(6):18201832.
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Wu XL, Ding X, Zhao Y, Miles AM, Brito LF, Heringstad B, Zhao S, Jiang Z. Editorial: Lactation genomics and phenomics in farm animals: Where are we at? Front Genet. 2023;14:1173595.
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Carrion SA, Michal JJ, Jiang Z. Alternative Transcripts diversify Genome Function for Phenome Relevance to Health and Diseases. Genes. 2023;14(11):2051.
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Carrion SA, Michal JJ, Jiang Z. Imprinted genes, genomics conservation, transcriptomic dynamics and phenomic significance in health and diseases. Int J Biol Sci. 2023;19(10):3128-3142.
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Mikec `, Horvat S, Wang H, Michal J, Kunej T, Jiang Z. Differential alternative polyadenylation response to high-fat diet between polygenic obese and healthy lean mice. Biochem Biophys Res Commun. 2023;666:83-91.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Jiang Z. Invited Seminar. Genome Science and Healthy Longevity. Annual Advanced Science Seminar Series, Rugao Health Council. 04/18/2023. Rugao City, China.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Jiang Z. Invited Seminar. The Central Dogma of Phenomics. College of Animal Sciences and Biotechnology, Nanjing Agricultural University. 04/23/2023. Nanjing, China.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Jiang Z. Selected Speaker. Functional Mapping of Alternative Polyadenylation in Cattle. Ruminant Genetics and Genomics Workshop, 39th International Society for Animal Genetics Conference. Cape Town, South Africa. July 2-7, 2023.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Jiang Z. Invited Seminar. Central dogma of phenomics: P = G + R + E + G x R x E? Workshop on the central dogma of phenomics. 2023 American Society of Animal Science Annual Meeting. July 16 July 20, 2023. Albuquerque, NM, USA
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2023
Citation:
Jiang Z. Invited Plenary Speaker. Research Frontiers in Animal Phenomics. International Conference on Genetics and Genomics Research Fronts in Animals and Poultry, December 9 10, 2023. Shandong Agricultural University, China
- Type:
Other
Status:
Published
Year Published:
2023
Citation:
Michal JJ. GOOD: Genetically optimized organic dairy. Animal Sciences Department News Letter. https://ansci.wsu.edu/2023/05/04/good-genetically-optimized-organic-dairy/
- Type:
Other
Status:
Published
Year Published:
2023
Citation:
Zaragoza A. Genomic selection for resistance of metritis in dairy cattle to effectively increase reproductive performance in organic dairy farms. Animal Sciences Department Seminar Series. Fall 2023.
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