Source: WASHINGTON STATE UNIVERSITY submitted to
WORKSHOP ON THE CENTRAL DOGMA OF PHENOMICS
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
ACTIVE
Funding Source
AFRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
1030645
Grant No.
2023-67015-40080
Cumulative Award Amt.
$50,000.00
Proposal No.
2022-12085
Multistate No.
(N/A)
Project Start Date
Jul 1, 2023
Project End Date
Dec 31, 2025
Grant Year
2023
Program Code
[A1201]- Animal Health and Production and Animal Products: Animal Breeding, Genetics, and Genomics
Recipient Organization
WASHINGTON STATE UNIVERSITY
240 FRENCH ADMINISTRATION BLDG
PULLMAN,WA 99164-0001
Performing Department
(N/A)
Non Technical Summary
The USDA blueprint for Animal Genome Research 2018 - 2027 has generated worldwide interests in understanding the complex relationships between an organism's genome and phenome. Generally speaking, there are two separate approaches to determine genome-phenome relationships. The central dogma of quantitative genetics describes phenotype (P) as a function of genotype (G), environment (E) and their interaction or P = G + E + G x E, while the central dogma of molecular genetics states that DNA makes RNA makes protein. Therefore, we are so pleased to organize a symposium that will be held in conjunction with the 2023 ASAS-CSAS-WSASAS Annual Meeting, July 16 - 20 in Albuquerque, New Mexico with a goal to merge both dogmas of quantitative and molecular genetics into a dogma of phenomics. The specific objective of the symposium is to provide a unique platform for both quantitative and molecular genetics communities to think about advanced theories and strategies in order to delineate the complex, nonlinear, multivariate and multi-level networks between genome and phenome. As organizers, we are committed to ensuring that the symposium is held in a high quality, efficient and safe manner in an environment that fosters diversity, equity and inclusion.
Animal Health Component
(N/A)
Research Effort Categories
Basic
(N/A)
Applied
(N/A)
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
30439991081100%
Knowledge Area
304 - Animal Genome;

Subject Of Investigation
3999 - Animal research, general;

Field Of Science
1081 - Breeding;
Goals / Objectives
Phenomics is an independent discipline to study phenotypic dynamics during the life span of an organism. No doubt, its key component is to collect phenomes: a full set of phenotypes of an individual, to provide a foundation to characterize genomes. During the last several years, the USDA/NIFA Animal Breeding, Genetics, and Genomics program has heavily solicitated proposals to determine "the connection and causation between the genetic makeup of an animal (genome) and the totality of all phenotypes, or the observable physical or physiological traits or characteristics (phenome)." Therefore, the overall goal of the symposium on the central dogma of phenomics is to review current genome-to-phenome (G2P) research progress and provide strategies, tools, and resources to take the program to the next level.The specific objectives of this symposium are to 1) provide updates on the latest accomplishments and the current progress in G2P research using both quantitative and molecular genomic approaches; 2) foster knowledge, technology and experience disseminations among program directors, researchers, students and professionals in the fields; and 3) form an international consortium and publish a book or a journal special issue on the central dogma of phenomics for global collaboration to address emerging issues related to animal agriculture for generations to come. Completion of the approved symposium will, therefore, provide unique opportunities for both quantitative and molecular genetic/genomic communities to explore joint interests in advancing our understanding of the complex relationships between an organism's genome and phenome for improved whole genome selection and accelerated genetic gains.
Project Methods
We will have leaders from the 2023 ASAS Animal Breeding and Genetics committee; the 2023 NRSP8 Animal Genome Workshop committee; the 2023 Gordon Research Conference and Seminar on Quantitative Genetics and Genomics committee, the 2023 Ruminant Telomere to Telomere Workshop committee and the 2023 AG2PI Conference Committee to speak at our symposium. As such, information that can be relied on to develop the central dogma of phenomics will be current, accurate and comprehensive. In addition, this funded symposium will take advantage of NMSU's Hispanic Serving Institution status and faculty member alliances with other institutions serving underrepresented groups to recruit participants.Efforts. We will advertise our symposium by distributing our schedules at least to all ASAS (American Society of Animal Science), AnGenMap (Animal Gene Mapper), FAANG (functional annotation of animal genome), AGDG (Animal Geneticist's Discussion Group) and ISAG (International Society of Animal Genetics) members.Evaluation. we expect a big crowd to attend our symposium on the central dogma of phenomics with a balance across countries of origin, expertise, age and sex. We will perform a post-symposium evaluation.

Progress 07/01/23 to 06/30/24

Outputs
Target Audience:The target sudiences include scientists, researchers, students and scholars in nutrition, reproduction, welfare, precision management, genetics/genomics, meat quality/healthfulness and veterinary medicine, for example. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?In addition to our three-half day workshop, we also organized a special event for our distinguished speakers and selected travel award trainees to interact and get to know each other in a friendly environment. Most of our trainee participants were Ph.D. students. How have the results been disseminated to communities of interest?Our workshop on the central dogma of phenomics was very attractive to scientists, researchers, students and scholars in nutrition, reproduction, welfare, precision management, genetics/genomics, and meat quality/healthfulness fields, for example, at the ASAS annual meeting 2023. What do you plan to do during the next reporting period to accomplish the goals?We plan to 1) officially form an international consortium on animal phenomics, 2) develop a white paper for the community to advance the field and 3) continue the workshop on the central dogma of phenomics held in 2025.

Impacts
What was accomplished under these goals? The workshop on the central dogma of phenomics was successfully held in conjunction with the ASAS (American Society of Animal Science) annual meeting in 2023. Traditionally, a symposium is held for a half day with 4 - 6 invited speakers. However, the overall ASAS programming committee found our proposed topics very interesting, so we were asked to plan a full day workshop to thoroughly discuss the central dogma of phenomics. At the end, the enthusiasm we received during our recruitment of invited speakers made it possible to expand the workshop to three half-day sessions. The first half-day workshop was chaired by Dr. Hernandez Gifford, New Mexico State University. Topics included pangenome assemblies (Dr. Murdoch), panepigenome assemblies (Dr. McKay), CRISPR-based annotation of genome function (Dr. Phelps), neural network-based genome analysis (Dr. Cheng) and high throughput sperm phenotyping (Dr. Sutovsky). Dr. Van Goor, USDA/NIFA National Program Leader in Animal Breeding, Genetics and Genomics chaired the second half-day workshop. Five invited speakers spoke at the session, including Dr. Brito on enviromics, genomics and machine learning for precision breeding of resilient livestock; Dr. McNamara on the bigger picture of phenomics; Dr. Miller on the questto lift genomic prediction accuracy in livestock; Dr. Fragomeni on novel phenotypes and environmental factors and Dr. Murdoch on resources in agricultural genomics and phenomics. Dr. Zhihua Jiang, Washington State University led the last half-day workshop with five invited speakers who discussed 1) evolution of cis-regulatory elements in genetic control of complex traits (Dr. Zhou); 2) molecular phenomics via a multi-omics approach (Dr. Biase); 3) noncoding RNAs and interpretations of genome to phenome (Dr. Hagen); 4) animal genomes to phenomes: funding and perspectives from USDA/NIFA (Dr. Van Goor) and 5) the central dogma of phenomics: P = G + R + E + G x R x E (Dr. Jiang). As chairs of the workshop, our main goal was to create opportunities and training through scientific meetings for underrepresented students and scholars Indeed, we recruited 12 participants from underrepresented groups to participate in our workshop on the central dogma of phenomics. They were all awarded a scholarship to cover the cost of travel. We believe that they enjoyed the opportunity to learn the latest developments in the cutting-edge interdisciplinary study of genome-phenome relationships. Hopefully they will be actively involved in development of the central dogma of phenomics. No doubt, our three-half day workshop was well received by a large audience. In 2023, the European network on livestock phenomics was funded (https://eu-li-phe.eu/). Currently, the network is organized in five task groups: 1) phenotyping technologies; 2) genome-to-phenome integration; 3) computational resources and methodologies for data analysis; 4) economic impact, regulations, policies and society and 5) stakeholder engagement, communication and dissemination. Dr. Jiang has been working with the European network leadership team to develop plans for knowledge exchange and creation of joint activities to promote animal phenomic research, education and extension.

Publications

  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: The power of pangenome assemblies in ruminants Presenting Author: Brenda M. Murdoch, PhD  University of Idaho
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Establishing a pan-epigenome for cattle and sheep Presenting Author: Stephanie McKay  University of Missouri-Columbia
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Large-scale CRISPR functional characterization of genomic elements in rainbow trout (Oncorhynchus mykiss). Presenting Author: Michael Phelps, PhD  Washington State University
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Mixed-effects multilayer neural networks for genome-wide analysis including intermediate omics data in the central dogma of phenomics Presenting Author: Hao Cheng  University of California, Davis
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Biomarker-based high throughput sperm phenotyping: The good, the bad and the ugly Presenting Author: Peter Sutovsky, PhD, Dr.h.c.  University of Missouri-Columbia
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Integrating enviromics, genomics, and machine learning for precision breeding of resilient livestock Presenting Author: Luiz F. Brito  Purdue University
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: The Bigger Picture of Phenomics: Whole-system support for systems research, models and databases Presenting Author: John P. McNamara  Washington State University
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: From Big to Bigger data, the quest to lift genomic prediction accuracy in livestock Presenting Author: Steve Miller  University of New England, Australia
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: How to use novel phenotypes and environmental factors to evaluate complex traits Presenting Author: Breno O. Fragomeni  University of Connecticut
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: The AG2PI vision for resources in agricultural genomics and phenomics: How ASAS can contribute Presenting Author: Brenda M. Murdoch, PhD  University of Idaho
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Dissection of evolution of cis-regulatory elements and its application on genetic control of complex traits in farm animals Presenting Author: Huaijun Zhou  University of California, Davis
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Molecular phenomics - A multi-omics approach to understanding complex traits in cattle Presenting Author: Fernando Biase  Virginia Tech
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Noncoding RNAs alter our interpretations of genome to phenome Presenting Author: Darren E. Hagen  Oklahoma State University
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Animal genomes to phenomes: Funding and perspectives from USDA-NIFA Presenting Author: Angelica G. Van Goor, PhD (she/her/hers)  USDA-National Institute of Food and Agriculture
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: The central dogma of phenomics: P = G + R + E + G x R x E? Presenting Author: Zhihua Jiang  Washington State University