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Genetic Security Research and Resources: Acquiring, Evaluating, Preserving, and Distributing Critical Genetic Resources

HARVEY BLACKBURN

NATIONAL COORDINATOR

NAGP/ARS/USDA

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Genetic Resources Drive the Livestock Industry.�

  • U.S. is the most important purveyor of genetically productive livestock (60% of global broiler genetics come from one U. S. company)

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  • But – in general genetic diversity is contracting

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Establishment of NAGP

  • 1999 – National Animal Germplasm Program established and placed in Fort Collins, Colorado
  • Funded by U.S. Congress as part of USDA’s regular budget
  • Late 1999 ASDS Discover Conference – University, Industry and Government

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NAGP Objectives, Structure & Operation

  • Goal - a repository to protect all breeds from epidemics to genetic diversity loss through routine use
  • An integrated system not just one discipline
    • Information system, genetic assessment & cryobiology all work in unison
  • Input & collaboration with stakeholders is key

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Collection Development Over Time. �

1,158,494

59,812

191

369

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Animal – GRIN Information System https://agrin.ars.usda.gov/collection_overview_page_dev?language=EN&record_source=US

  • Real time web-based, publically accessible
  • Contains: pedigree, genotypic, phenotypic, management, and environmental descriptors
  • Facilitates
    • Industry and research queries
    • All incoming/outgoing shipments
    • Identification of collection gaps
    • Collection storage and management

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Timeline of Animal GRIN (A-GRIN) Development

A-GRIN V1 Initiated

2000

A-GRIN V1 Delivered

2005-2006

A-GRIN V2 Initiated

2006

A-GRIN V2 Delivered

2010

A-GRIN Web-interface Redesign

2015

A-GRIN Mapping & Photos initiated

2017

A-GRIN Capacity to Store Genomic Data

2018 – ongoing

A-GRIN Capacity for GIS

2019 - ongoing

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Early Steps in Developing A-GRIN

  • Realized early on collection transparency was key to garnering stakeholder support
    • Internet based and real time
  • Species committee members (n = 50) were asked what data they would like to have in the database
  • Programming was performed by an ARS plant database group in Maryland
  • Initial data base was done using Oracle under the license held by programming team

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A-GRIN V1 Delivered

  • Staff found data entry too cumbersome, better data entry features needed
  • Web-interface for public was minimal
  • Oracle license expensive
  • Plant based programming team not willing to make needed changes in a timely manner
  • Result – we started A-GRIN V2

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A-GRIN V2 Started

  • Agriculture and Agri Foods Canada and EMBRAPA (Brazil) joined development effort
  • Each country provided a programmer to work on the development team
  • Subject mater experts from all three countries are members of the development team
  • Programmers meet every two weeks & pre-covid programmers co-located for 2-3 weeks per year
  • Only freeware used

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Web-Interface Redesign

  • Goals
    • Modern look
    • Increase intuitiveness
    • Each page is an educational opportunity

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Responding to New Demands – Animal Photos

Identifications

Type

Value

Registration Number

HOUSA000001491007

Name

ROUND OAK RAG APPLE ELEVATION

NAAB Code

7HO58

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Identifications

Type

Value

Registration Number

HOUSA000143308649

Name

CALORI-D CL MONTEREY RAV

NAAB Code

14HO7776

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Description

Repository Number:  1671

Taxonomy:  Bovidae Bos taurus - beef Simmental

Species Common Name:  Beef Cattle

Gender:  M

Date of Birth:  02/16/1966

Breeder:  Rossin, Henri

Origin:  France,

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Responding to New Demands�Mapping animals’ origin & GIS�

Holstein Collection

THI Zones and Beef Collection

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Responding to New Demands – �Genomic Data

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Has the Investment in the Database Been Successful/Useful?

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Impact of Collection Use – over 11,000 animals used

Purdue University – reconstituting Napole + Halothane line; reduce research costs

Dairy samples for original genomic predictions. $400 million per year added to U.S. Dairy industry

Adding genetic variation to rare breeds

e.g., Dexter & Milking Shorthorn

Determining genetic lethal carriers from1980s sires:

Angus $2.2 million

Brangus $1million

Lost Y chromosomes reintroduction to Holstein

From 1960’s era bulls. Progeny at breed average for milk

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Reviving Lost Y Chromosomes in Holstein

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Lost Y Chromosome Progeny Performance

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Collection Use:

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Rito 707 of Ideal 7075 (1996)

  • Sale average ~$7,000, this bull $23,000
  • Largest breeder/seller of bulls requests 5 repository bulls born before 2000 to mate with 150 cows

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Future Challenges for Database Development

  • Cyber Security
  • Increasing A-GRIN profile
  • Storing and accessing sequence data
  • Build more tools to assess germplasm and genetic resources
  • Adding new countries
  • Keeping the consortium together

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