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Large-Scale Phenotyping and Genotyping: State of the Art and Emerging Challenges

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Smart Livestock Nutrition

Part of the book series: Smart Animal Production ((SMANPR,volume 1))

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Abstract

The genome and phenome are both forms of big data in that they can be characterised by volume, variety, velocity, value, veracity and variability. A direct relationship exists between the phenotype and the genotype; the proportion of the variability in the phenotype due to differences in the genotype of a (sample) population is termed heritability. Phenomics in livestock generally relate to (a) animal identification, (b) measurements of performance (either output or inputs) and (c) measures of the prevailing environmental conditions. The use of genomics in livestock production includes: (1) genomic predictions, (2) parentage assignment, (3) animal/product traceability, (4) monitoring of major genes and congenital defects including karyotype disorders, (5) estimating coancestry or inbreeding, (6) quantifying breed composition and, importantly (7) facilitating more precise mating and management (e.g. nutrition) decisions. Facilitated by developments in agri-tech, such information will enable the development of tailored genotype-specific nutritional and management regimes. Such a strategy is not at all novel and is the basis for the diversity of production systems for generations; genotype in such situations was, however, synonymous only with breed. Genomics and phenomics will simply improve the granularity of differentiation from being among breeds to being within breeds. Challenges include (a) the return-on-investment, especially for phenomics, although from a breeding perspective, the cost of phenotyping is incurred by few but realised by many, (b) how to distil the masses of data to support decisions by diagnosing and prescribing management and nutritional strategies, and (c) data ownership and use. As more data accumulates on both the genotypes and phenotypes of individuals, the ability to estimate the genetic potential of individual animals more accurately will improve.

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  1. Teagasc, Animal & Grassland Research and Innovation Centre, Co. Cork, Ireland

    Donagh P. Berry

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    Ilias Kyriazakis

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Berry, D.P. (2023). Large-Scale Phenotyping and Genotyping: State of the Art and Emerging Challenges. In: Kyriazakis, I. (eds) Smart Livestock Nutrition. Smart Animal Production, vol 1. Springer, Cham. https://doi.org/10.1007/978-3-031-22584-0_5

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