Abstract
Ticks cause substantial production losses for beef and dairy cattle. Cattle resistance to ticks is one of the most important factors affecting tick control, but largely neglected due to the challenge of phenotyping. In this study, we evaluate the pooling of tick resistance phenotyped reference populations from multi-country beef cattle breeds to assess the possibility of improving host resistance through multi-trait genomic selection. Data consisted of tick counts or scores assessing the number of female ticks at least 4.5 mm length and derived from seven populations, with breed, country, number of records and genotyped/phenotyped animals being respectively: Angus (AN), Brazil, 2,263, 921/1,156, Hereford (HH), Brazil, 6,615, 1,910/2,802, Brangus (BN), Brazil, 2,441, 851/851, Braford (BO), Brazil, 9,523, 3,062/4,095, Tropical Composite (TC), Australia, 229, 229/229, Brahman (BR), Australia, 675, 675/675, and Nguni (NG), South Africa, 490, 490/490. All populations were genotyped using medium density Illumina SNP BeadChips and imputed to a common high-density panel of 332,468 markers. The mean linkage disequilibrium (LD) between adjacent SNPs varied from 0.24 to 0.37 across populations and so was sufficient to allow genomic breeding values (GEBV) prediction. Correlations of LD phase between breeds were higher between composites and their founder breeds (0.81 to 0.95) and lower between NG and the other breeds (0.27 and 0.35). There was wide range of estimated heritability (0.05 and 0.42) and genetic correlation (-0.01 and 0.87) for tick resistance across the studied populations, with the largest genetic correlation observed between BN and BO. Predictive ability was improved under the old-young validation for three of the seven populations using a multi-trait approach compared to a single trait within-population prediction, while whole and partial data GEBV correlations increased in all cases, with relative improvements ranging from 3% for BO to 64% for TC. Moreover, the multi-trait analysis was useful to correct typical over-dispersion of the GEBV. Results from this study indicate that a joint genomic evaluation of AN, HH, BN, BO and BR can be readily implemented to improve tick resistance of these populations using selection on GEBV. For NG and TC additional phenotyping will be required to obtain accurate GEBV.
Highlights
Ticks and tick-borne diseases are among the most important causes of production losses for beef and dairy cattle
Allele Frequencies and Principal Components Pearson correlations were calculated between allele frequencies of all populations across the 332,468 SNP markers used in the present study and a principal components analysis (PCA) plot of all animals by breed was obtained from genotype data using PreGSf90 software [17]
This method measures the correlation of estimated breeding values (u)̂ between whole (w) and partial (p) datasets between subsequent genetic evaluations when phenotypes are added for validation animals, ÀÁ rw,p = qffiffifficffiffioffiffivffiffiffiffiuffi^ffiffiwffiffiffi,ffiu^ffiffiffipffiÀffiffiffiffiffiffiffiffiÁffi, varðu^wÞvar u^p which is a function of the prediction accuracy with expected value of E(rw,p)≈ accp/accw
Summary
Ticks and tick-borne diseases are among the most important causes of production losses for beef and dairy cattle. Recent estimates of those losses range from US$22 to 30 billion per year [1]. Pooling reference populations across countries has previously been demonstrated to improve accuracy for traits such as dry matter intake [6]. We pool tick resistance phenotyped reference populations from beef cattle breeds in Australia, Brazil, and South Africa. We jointly analyze existing tick infestation datasets to assess the possibility of improving host resistance in cattle through multi-population, multi-trait genomic selection
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