Coordinated effort to advance genomes-to-phenomes through the integration of bioinformatics with aquaculture research

Authors: Abernathy, Jason; Fuller, Adam; Green, Bartholomew - Bart; Lange, Miles; Rawles, Steven - Steve; Straus, David - Dave; Webster, Carl

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 3/30/2018
Publication Date: 4/23/2018
Citation: Abernathy, J.W., Fuller, S.A., Green, B.W., Lange, M.D., Rawles, S.D., Straus, D.L., Webster, C.D. 2018. Coordinated effort to advance genomes-to-phenomes through the integration of bioinformatics with aquaculture research [abstract]. Meeting Abstract, 4th Annual Meeting of the Arkansas Bioinformatics Consortium AR-BIC 2018, April 23-24th, 2018, Little Rock, Arkansas. p. 45.

Interpretive Summary:

Technical Abstract: Aquaculture is the fastest growing food production system in the world. The research program at the USDA-ARS-SNARC strives to improve the efficiency and sustainability of warmwater U.S. aquaculture. SNARC scientists have impacted the catfish (#1 U.S. aquaculture industry), tilapia (#3) and hybrid striped bass (#4) industries among others throughout decades of research. Our current efforts focus on the hybrid striped bass industry, a major industry for the state of Arkansas. By integrating computational approaches coupled with basic and applied aquaculture research we strive to further advance the hybrid striped bass industry through the genetic improvement of the hybrid parental species, the white bass and striped bass. Toward this effort, our work addresses selective breeding of white bass to improve agriculturally-important traits including growth and alternative feeds utilization. Molecular genetics platforms and bioinformatics pipelines are being developed concurrently. The white bass and striped bass genomes are being sequenced and assembled. Transcriptomic resources across white and hybrid striped bass are being characterized in response to variables including diet formulation, diseases and their treatments, and the aquatic ecosystem. We are mapping microbiome and mycobiome changes throughout production. With reciprocal crossbreeding we are examining quantitative trait loci, the transmissibility of traits to their hybrids as well as maternal and paternal effects. We also use a dynamic systems approach to aid our understanding of host-pathogen interactions. Our long-term goal is to increase genetic gains via the integration of molecular genetics with our selective breeding program. An update on our progress toward mapping functional variation across our multidisciplinary projects as well as the computational approaches utilized at SNARC will be presented.