Genomic evaluation for calf wellness traits in Holstein cattle

Abstract

Reducing calf morbidity and mortality is important for attaining financial sustainability and improving animal welfare on commercial dairy operations. Zoetis (Kalamazoo, MI) has developed genomic predictions for calf wellness traits in Holsteins that include calf respiratory disease (RESP; recorded between 0 and 365 d of age), calf scours (DIAR; recorded between 2 and 50 d of age), and calf livability (DEAD; recorded between 2 and 365 d of age). Phenotype and pedigree data were from commercial dairies and provided directly by producers upon obtaining their permission. The number of records ranged from 741,484 for DIAR to 1,926,261 for DEAD. The number of genotyped animals was 325,025. All traits were analyzed using a univariate threshold animal model including fixed effect of year of birth × calving season × region, and random effects of herd × year of birth and animal. A total of 45,425 SNP were used in genomic analyses. Animals genotyped with low-density chips were imputed to the required number of SNP. All analyses were conducted using single-step genomic BLUP implementing the "algorithm for proven and young" (APY) animals designed to accommodate very large numbers of genotypes. Estimated heritabilities were 0.042, 0.045, and 0.060 for RESP, DIAR, and DEAD, respectively. The genomic predicted transmitting abilities ranged between −8.0 and 24.0, −11.5 and 28.5, and −6.5 to 22.8 for RESP, DIAR, and DEAD, respectively. Reliabilities of breeding values were obtained by approximation based on partitioning of a function of reliability into contributions from records, pedigree, and genotypes, where the genotype contribution was approximated using the diagonal value of the genomic relationship matrix. The average reliabilities for the genotyped animals were 41.9, 42.6, and 47.3% for RESP, DIAR, and DEAD, respectively. Estimated genomic predicted transmitting abilities and reliabilities were approximately normally distributed for all analyzed traits. Approximated genetic correlations of calf wellness with Zoetis dairy wellness traits and traits included in the US national genetic evaluation were low to moderate. The results indicate that direct evaluation of calf wellness traits under a genomic threshold model is feasible and offers predictions with average reliabilities comparable to other lowly heritable traits. Genetic selection for calf wellness traits presents a compelling opportunity for dairy producers to help manage herd replacement costs and improve overall profitability.

Large-Scale Phenotyping of Livestock Welfare in Commercial Production Systems: A New Frontier in Animal Breeding

“…In this context, various livestock breeding programs have started to incorporate welfare and resilience indicators in their breeding programs. Examples of welfare indicators that have been investigated or included in selection schemes in livestock breeding programs around the world are: aggression ( Løvendahl et al, 2005 ); behavior ( Rohrer et al, 2013 ); boar taint (to avoid castration; Tajet et al, 2006 ; Zadinová et al, 2016 ), calf wellness ( Gonzalez-Peña et al, 2019 ), calving ease ( Jamrozik and Miller, 2014 ; Vanderick et al, 2014 ; Li and Brown, 2016 ), cortisol levels ( Mormède et al, 2011 ); docility ( Norris et al, 2014 ); feather pecking ( Dawkins and Layton, 2012 ), feet and leg health ( Kapell et al, 2012 , 2017 ); fertility disorders ( Guarini et al, 2018 ; Fleming et al, 2019 ), hoof health [in cattle ( Chapinal et al, 2013 ; Häggman and Juga, 2013 ; Heringstad et al, 2018 ), sheep ( Conington et al, 2008 ), and pigs ( Quintanilla et al, 2006 )]; lesion scores ( Wurtz et al, 2017 ; Angarita et al, 2019 ), longevity ( Serenius and Stalder, 2006 ; Ramos et al, 2020 ), mastitis ( Martin et al, 2018 ); maternal behavior and progeny survival ( Gäde et al, 2008 ; Hellbrügge et al, 2008a , b ), metabolic diseases ( Egger-Danner et al, 2014 ; Jamrozik et al, 2016 ; Pryce et al, 2016 ), nematode resistance ( Doeschl-Wilson et al, 2008 ), overall resilience ( Berghof et al, 2019 ), paratuberculosis ( Brito et al, 2018 ; Mallikarjunappa et al, 2020 ); pre-weaning survival ( Su et al, 2007 ; Nielsen et al, 2013 ); social dominance ( Tong et al, 2020 ); tail or ear biting ( Breuer et al, 2005 ), and thermal tolerance ( Fragomeni et al, 2016 ; Misztal, 2017 ; Nguyen et al, 2017 ; Xu et al, 2017 ). Genetic selection and modern genomic techniques (e.g., gene editing) might also be an alternative to eliminate the need for stressful procedures in commercial applications such as cattle dehorning ( Van Eenennaam and Young, ...…”

Genomics: the host's genotype and its relevance to bovine respiratory disease

“…Heritability estimates for BRD susceptibility vary based on how the trait was measured, if the trait was binary or ordinal and if the estimates were based on pedigree information or genomic (single nucleotide polymorphism or SNP) data. Heritability estimates range from 0.02 to 0.29 for BRD susceptibility in beef and dairy cattle (Lyons et al ., 1991; Snowder et al ., 2005; Heringstad et al ., 2008; Taylor et al ., 2010; Neibergs et al ., 2014; Buchanan et al ., 2016; Gonzalez-Pena et al ., 2019). Higher heritability estimates tend to be identified in data sets with precise phenotypes and phenotypes that are ordinal rather than binary (Buchanan et al ., 2016).…”

“…A third GWAA of 45,425 SNP was used to analyze 67,289 animals that had genotypic and BRD treatment data using a single-step BLUP method taken from 326 dairy producers in the United States (Gonzalez-Pena et al ., 2019). In this cohort, the incidence of BRD was 21% in calves from birth to 1 year of age, with most cases occurring prior to 30 days of age (Gonzalez-Pena et al ., 2019). The mean reliability (accuracy) for the prediction of respiratory disease was 0.419 with a range of 0.189–0.99 and the heritability was 0.042.…”

“…The PTA of bulls with a minimum of 100 offspring in the 326 dairies identified bulls with large differences in the PTA for BRD susceptibility. Bulls with the worst PTA (high values) for respiratory disease reported up to 50.4% of their progeny were affected by BRD (Gonzalez-Pena et al ., 2019). Selection of bulls with low BRD PTAs would be beneficial in reducing the incidence of disease with similar levels of management.…”

Genomic analysis of bovine respiratory disease and lung consolidation in preweaned Holstein calves using clinical scoring and lung ultrasound

“…Heritability estimates for BRD in Holstein calves in the study Vukasinovic et al (2018) (Gonzalez-Peña et al, 2019).…”