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

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

doi:10.1186/s12711-023-00850-x

Genetics Selection Evolution

Table 2 Description of the genomic prediction scenarios evaluated for foot angle (FA) and claw set (CS) in Australian (AU) and United States (US) Angus cattle

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

Abbreviation	Description	Scenarios	N_TOT	Target
WC-TT	Within-country two-trait model	FA_US.WC	44,421	2020^a:4142
	Single-country analysis (no correlation between US and AU traits) for FA and CS (FA and CS are correlated traits)	CS_US.WC	46,408	2020:4429
		FA_AU.WC	70,464	2020:325
				2019:3678
		CS_AU.WC	70,909	2020:339
				2019:3675
MC-TT	Multi-country two-trait model	FA_US.MC	44,421	2020³:4142
	Two-country and two traits (FA and CS from US and AU are correlated) model	CS_US.MC	46,408	2020:4429
		FA_AU.MC	70,464	2020:325
				2019:3678
		CS_AU.MC	70,909	2020:339
				2019:3675
JC-TT	Joint countries two-trait model	FA_JC	114,885	2020:4467
	Single-trait analysis in which the phenotypic records for each trait (FA and CS) from both countries were combined as if the US and AU were the same population (FA and CS are correlated)			2019:3678
		CS_JC	117,317	2020:4768
				2019:3675
AC	Across-country two-trait model	FA_{AC-EsetUS.TargetAU}	44,421	2020:325
	Across-country analysis for FA and CS (FA and CS are correlated traits). In this case, two scenarios:			2019:3678
	(1) Genomic model predicting AU and Canadian Angus (CA) (AU and CA are the prediction target—Target) based on genomic and phenotypic information from US animals (US is the Training estimation set—Eset)	FA_{AC-EsetUS.TargetCA}	44,421	700
	(2) Genomic model predicting US and CA (US and CA are the Target) based on a genomic and phenotypic information from AU animals (AU is the Eset)	FA_{AC-EsetAU.TargetUS}	70,464	2020:4142
		FA_{AC-EsetAU.TargetCA}	70,464	700
		CS_{AC-EsetUS.TargetAU}	46,408	2020:339
				2019:3675
		CS_{AC-EsetUS.TargetCA}	46,408	700
		CS_{AC-EsetAU.TargetUS}	70,909	2020:4429
		CS_{AC-EsetAU.TargetCA}	70,909	700

For the target population numbers presented in this table, all the target animals had both phenotypic and genotypic information. Furthermore, for the purpose of the forward validation, the remaining animals born in 2020 for US or in 2019–20 for AU with phenotype and no genotype were removed from the partial-dataset analyses to avoid biasing the results
N_TOT : number of animals included in the whole-dataset analyses; Target: animals in the target population, in which their phenotypic records were masked in the partial-dataset analyses
^aYear of birth of the target animals

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ISSN: 1297-9686

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