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Research Project: ENHANCING GENETIC MERIT OF RUMINANTS THROUGH GENOME SELECTION AND ANALYSIS

Location: Animal Genomics and Improvement Laboratory

Title: The Second Report on the State of the World's Animal Genetic Resources for Food and Agriculture, Part 4, The State of the Art: Box 4A4: A digital enumeration method for collecting phenotypic data for genome association

Author
item Woodward-Greene, Jennifer
item KINSER, JASON - George Mason University
item HUSON, HEATHER - Cornell University - New York
item Sonstegard, Tad
item SOELKNER, J - University Of Natural Resources & Applied Life Sciences - Austria
item VAISMAN, I - George Mason University
item Van Tassell, Curtis - Curt

Submitted to: Food and Agriculture Organization of the United Nations
Publication Type: Government Publication
Publication Acceptance Date: 2/27/2015
Publication Date: 2/27/2015
Citation: Woodward Greene, M.J., Kinser, J.K., Huson, H.J., Sonstegard, T.S., Soelkner, J., Vaisman, I.I., Van Tassell, C.P. 2015. The Second Report on the State of the World's Animal Genetic Resources for Food and Agriculture, Part 4, The State of the Art: Box 4A4: A digital enumeration method for collecting phenotypic data for genome association. Food and Agriculture Organization of the United Nations. Available: http://www.fao.org/publications/sowangr/en/, page 424, http://fao.org/3/ai4787e.pdf#page=465.

Interpretive Summary:

Technical Abstract: Consistent data across animal populations are required to inform genomic science aimed at finding important adaptive genetic variations. The ADAPTMap Digital Phenotype Collection- Prototype Method will yield a new procedure to provide consistent phenotypic data by digital enumeration of categorical and continuous values. It is an easy to use, low-cost procedure to collect phenotypic data for genome association and general breed characterization:health status indicators (anemia status, age, and weight),body measurements, shapes, coat colour and pattern; via digital images using mobile technology. The prototype collection protocol calls for six photos: four for body-measurement followed by two for health indicators. The animal walks directly into a simple photo set, and makes only two right one-quarter turns to achieve all six photos. The final two health indicators are close-ups of the teeth (tooth age) and eye (FAMACHA score). Novel calibration signs designed to affirm size and colour are fabricated of sturdy, light-weight metal, and employ dry erase pens to record sample data captured by the images. Phenotype values will be enumerated via complementary software developed to process ADAPTMap images. Twelve sampling teams have employed the method in 12 countries, sampling roughly 2 000 goats and collecting over 12 000 images. An ADAPTMap Quick Start Guide was developed and proved valuable to sampling teams in proper set up and photographing. The basic equipment needed (calibration signs and ropes; blue tarpaulins, securing rope and clips; duct tape and livestock markers; FAMACHA card; blue surgical scrubs; the full protocol and Quick Start Guide; etc.) were organized into a convenient kit for easy transport from one site to another. Samplers supplied the camera, and generally had little difficulty applying the method; however the FAMACHA and tooth shots were challenging. In conjunction with DNA sampling, the method aims to provide consistent phenotypes over a variety of sampling teams and conditions. The data may be used to inform genomics research, guide animal selection for breeding programmes and facilitate animal genetic conservation decisions, by enabling countries to take advantage of state-of-the-art science and support identification of their most important animal genetic resources for conservation. The data may also be useful regionally in One Health detection and surveillance; or as an on-farm herd record keeping management and animal health care tool. The protocol is under continual development and the Modified Method will be simplified with a redesign of the small calibration sign for standalone use rather than being worn by the handler, and fewer images. The FAMACHA and tooth poses will continue unchanged. The associated digital phenotyping software under development could be integrated into other mobile livestock management applications.