The big challenge for livestock genomics is to make sequence data pay

Abstract

This paper will argue that one of the biggest challenges for livestock genomics is to make whole-genome sequencing and functional genomics applicable to breeding practice. It discusses potential explanations for why it is so difficult to consistently improve the accuracy of genomic prediction by means of whole-genome sequence data, and three potential attacks on the problem.

Recent advances in the genomic resources for sheep

“…However, the majority of health, welfare and resilience traits, are polygenic and any causative variants are likely to have small effects, which makes detecting them more difficult (Georges et al 2019 ). Functional genomic data can help enrich for variance in quantitative traits reviewed in (Johnsson 2023 ). Since most causal variants for complex traits are likely to be located in regulatory regions of the genome and will impact complex traits by changing gene expression (Tam et al 2019 ) improvements in prediction accuracy could be achieved by filtering the genetic marker information, used for genomic selection, based upon whether the genetic variants reside in regulatory regions of the genome and then developing robust prediction models that can accommodate information about genome function (Georges et al 2019 ).…”

“…The primary challenge facing the sheep and wider farmed animal genomics community now is harnessing the power of a highly accurate reference genome with functional genomics data, at a population scale, and from there how to leverage this information to enhance genomic prediction reviewed in (Johnsson 2023 ). The potential to go ‘beyond the genome’ by using epigenetic modifications to predict genetic merit also shows significant potential, reviewed in (Clarke et al 2021 ).…”