Genomic Selection: Status in Different Species and Challenges for Breeding

Abstract

Contents Technical advances and development in the market for genomic tools have facilitated access to whole‐genome data across species. Building‐up on the acquired knowledge of the genome sequences, large‐scale genotyping has been optimized for broad use, so genotype information can be routinely used to predict genetic merit. Genomic selection (GS) refers to the use of aggregates of estimated marker effects as predictors which allow improved individual differentiation at young age. Realizable benefits of GS are influenced by several factors and vary in quantity and quality between species. General characteristics and challenges of GS in implementation and routine application are described, followed by an overview over the current status of its use, prospects and challenges in important animal species. Genetic gain for a particular trait can be enhanced by shortening of the generation interval, increased selection accuracy and increased selection intensity, with species‐ and breed‐specific relevance of the determinants. Reliable predictions based on genetic marker effects require assembly of a reference for linking of phenotype and genotype data to allow estimation and regular re‐estimation. Experiences from dairy breeding have shown that international collaboration can set the course for fast and successful implementation of innovative selection tools, so genomics may significantly impact the structures of future breeding and breeding programmes. Traits of great and increasing importance, which were difficult to improve in the conventional systems, could be emphasized, if continuous availability of high‐quality phenotype data can be assured. Equally elaborate strategies for genotyping and phenotyping will allow tailored approaches to balance efficient animal production, sustainability, animal health and welfare in future.

Genetic parameters for milk yield and reproduction traits in the Chilean Dairy Overo Colorado cattle breed

“…However, these increased heritability values were found only for milk yield traits, not for reproduction traits. Relatively high heritability values for yield traits allow reliable genomic predictions to be obtained even with moderately sized reference populations (Buch et al, 2012;Stock & Reents, 2013).…”

On the History of Cattle Genetic Resources

“…A comprehensive study compares the performance of nearly 40 American, British, European, zebu and Criollo beef breeds [195,196]. Worldwide progress in quantitative and molecular genetics intensifies the selective breeding with genomic selection, which becomes more and more realistic for several traits [197,198].…”

Genomic selection in pigs: state of the art and perspectives

“…longevity) or after death on the same animals or on carcasses of relatives, like meat quality parameters (i.e. Stock & Reents 2013;Van Eenennaam et al 2014). On the other hand, accuracy of GEBV is influenced by other factors defined in the genomic selection approach.…”

“…Genomic selection is advantageous for performance traits as phenotypic information can be leveraged across all selection candidates and, potentially, generations (e.g. Stock & Reents 2013) and the collection of phenotypic data on a routine basis might be reduced with large flexibility possible concerning the pigs that should be phenotyped (Dekkers 2010). Nevertheless, as the accuracy of GEBV might decline rapidly over generations a continuous collection of phenotypes over generations, especially in animals related to selection candidates, is always needed to update the genomic selection prediction models (Muir 2007;Sonesson & Meuwissen 2009;Dekkers 2010).…”

“…To overcome this problem, various approaches were proposed as by e.g. the pre-selection of animals to be genotyped (Stock & Reents 2013) or the recording of phenotypic data only in a limited part of the selection candidates (Okeno et al 2014). Henryon et al (2012) evaluated the amount of marginal returns derived by the introduction of genomic selection in a population with increasing proportion of selection candidates with genotyping data and in which the selection candidates to be genotyped were defined based on their breeding value calculated on a priori information.…”