Across-country genetic and genomic analyses of foot score traits in American and Australian Angus cattle

Amanda B Alvarenga; Kelli J Retallick; Andre Garcia; Stephen P Miller; Andrew Byrne; Hinayah R Oliveira; Luiz F Brito

doi:10.1186/s12711-023-00850-x

Across-country genetic and genomic analyses of foot score traits in American and Australian Angus cattle

Genet Sel Evol. 2023 Nov 2;55(1):76. doi: 10.1186/s12711-023-00850-x.

Authors

Amanda B Alvarenga¹, Kelli J Retallick², Andre Garcia², Stephen P Miller^{2

3}, Andrew Byrne⁴, Hinayah R Oliveira¹, Luiz F Brito⁵

Affiliations

¹ Department of Animal Sciences, Purdue University, 270 South Russell Street, West Lafayette, IN, 47907, USA.
² American Angus Association, Angus Genetics Inc., 3201 Frederick Avenue, Saint Joseph, MO, 64506, USA.
³ AGBU, a Joint Venture of NSW Department of Primary Industries and University of New England, Armidale, NSW, 2351, Australia.
⁴ Angus Australia, 86 Glen Innes Road, Armidale, NSW, 2350, Australia.
⁵ Department of Animal Sciences, Purdue University, 270 South Russell Street, West Lafayette, IN, 47907, USA. britol@purdue.edu.

Abstract

Background: Hoof structure and health are essential for the welfare and productivity of beef cattle. Therefore, we assessed the genetic and genomic background of foot score traits in American (US) and Australian (AU) Angus cattle and investigated the feasibility of performing genomic evaluations combining data for foot score traits recorded in US and AU Angus cattle. The traits evaluated were foot angle (FA) and claw set (CS). In total, 109,294 and ~ 1.12 million animals had phenotypic and genomic information, respectively. Four sets of analyses were performed: (1) genomic connectedness between US and AU Angus cattle populations and population structure, (2) estimation of genetic parameters, (3) single-step genomic prediction of breeding values, and (4) single-step genome-wide association studies for FA and CS.

Results: There was no clear genetic differentiation between US and AU Angus populations. Similar heritability estimates (FA: 0.22-0.24 and CS: 0.22-0.27) and moderate-to-high genetic correlations between US and AU foot scores (FA: 0.61 and CS: 0.76) were obtained. A joint-genomic prediction using data from both populations outperformed within-country genomic evaluations. A genomic prediction model considering US and AU datasets as a single population performed similarly to the scenario accounting for genotype-by-environment interactions (i.e., multiple-trait model considering US and AU records as different traits), even though the genetic correlations between countries were lower than 0.80. Common significant genomic regions were observed between US and AU for FA and CS. Significant single nucleotide polymorphisms were identified on the Bos taurus (BTA) chromosomes BTA1, BTA5, BTA11, BTA13, BTA19, BTA20, and BTA23. The candidate genes identified were primarily from growth factor gene families, including FGF12 and GDF5, which were previously associated with bone structure and repair.

Conclusions: This study presents comprehensive population structure and genetic and genomic analyses of foot scores in US and AU Angus cattle populations, which are essential for optimizing the implementation of genomic selection for improved foot scores in Angus cattle breeding programs. We have also identified candidate genes associated with foot scores in the largest Angus cattle populations in the world and made recommendations for genomic evaluations for improved foot score traits in the US and AU.

MeSH terms

Animals
Australia
Cattle / genetics
Genome*
Genome-Wide Association Study* / veterinary
Genomics
Genotype
Phenotype
Polymorphism, Single Nucleotide