Approximate Reliability of Genetic Evaluations Under an Animal Model

Harris, B. L.; Johnson, D. L.

doi:10.3168/jds.s0022-0302(98)75829-1

Cited by 71 publications

(71 citation statements)

References 5 publications

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“…There are at least two reasons that can cause non-accumulative gains in reliability. One is that the information sources (cow information and US bull information here) are not independent (Harris and Johnson, 1998), and the other is that the increase of reliability with increase of reference population size is not linear (Daetwyler et al, 2008;Goddard, 2009;Goddard and Hayes, 2009). …”

Section: Discussionmentioning

confidence: 99%

Sharing reference data and including cows in the reference population improve genomic predictions in Danish Jersey

Nielsen

et al. 2016

Animal

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Small reference populations limit the accuracy of genomic prediction in numerically small breeds, such like Danish Jersey. The objective of this study was to investigate two approaches to improve genomic prediction by increasing size of reference population in Danish Jersey. The first approach was to include North American Jersey bulls in Danish Jersey reference population. The second was to genotype cows and use them as reference animals. The validation of genomic prediction was carried out on bulls and cows, respectively. In validation on bulls, about 300 Danish bulls (depending on traits) born in 2005 and later were used as validation data, and the reference populations were: (1) about 1050 Danish bulls, (2) about 1050 Danish bulls and about 1150 US bulls. In validation on cows, about 3000 Danish cows from 87 young half-sib families were used as validation data, and the reference populations were: (1) about 1250 Danish bulls, (2) about 1250 Danish bulls and about 1150 US bulls, (3) about 1250 Danish bulls and about 4800 cows, (4) about 1250 Danish bulls, 1150 US bulls and 4800 Danish cows. Genomic best linear unbiased prediction model was used to predict breeding values. De-regressed proofs were used as response variables. In the validation on bulls for eight traits, the joint DK-US bull reference population led to higher reliability of genomic prediction than the DK bull reference population for six traits, but not for fertility and longevity. Averaged over the eight traits, the gain was 3 percentage points. In the validation on cows for six traits (fertility and longevity were not available), the gain from inclusion of US bull in reference population was 6.6 percentage points in average over the six traits, and the gain from inclusion of cows was 8.2 percentage points. However, the gains from cows and US bulls were not accumulative. The total gain of including both US bulls and Danish cows was 10.5 percentage points. The results indicate that sharing reference data and including cows in reference population are efficient approaches to increase reliability of genomic prediction. Therefore, genomic selection is promising for numerically small population.

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Section: Discussionmentioning

confidence: 99%

Sharing reference data and including cows in the reference population improve genomic predictions in Danish Jersey

Nielsen

et al. 2016

Animal

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“…The EBV combining different sources of information were standardized to a mean of 0 and a genetic standard deviation corresponding to the square root of the estimated breed genetic variance. For each animal, the reliability of the combined EBV was computed using the Harris and Johnson (1998) approach. This reliability was compared with the one obtained when only CM information is included or when correlated traits are added one at a time.…”

Section: Modelsmentioning

confidence: 99%

Multiple trait genetic evaluation of clinical mastitis in three dairy cattle breeds

Govignon-Gion

Dassonneville

Baloche

et al. 2016

animal

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In 2010, a routine genetic evaluation on occurrence of clinical mastitis in three main dairy cattle breeds -Montbéliarde (MO), Normande (NO) and Holstein (HO) -was implemented in France. Records were clinical mastitis events reported by farmers to milk recording technicians and the analyzed trait was the binary variable describing the occurrence of a mastitis case within the first 150 days of the first three lactations. Genetic parameters of clinical mastitis were estimated for the three breeds. Low heritability estimates were found: between 2% and 4% depending on the breed. Despite its low heritability, the trait exhibits genetic variation so efficient genetic improvement is possible. Genetic correlations with other traits were estimated, showing large correlations (often > 0.50, in absolute value) between clinical mastitis and somatic cell score (SCS), longevity and some udder traits. Correlation with milk yield was moderate and unfavorable (ρ = 0.26 to 0.30). High milking speed was genetically associated with less mastitis in MO (ρ = − 0.14) but with more mastitis in HO (ρ = 0.18). A two-step approach was implemented for routine evaluation: first, a univariate evaluation based on a linear animal model with permanent environment effect led to pre-adjusted records (defined as records corrected for all non-genetic effects) and associated weights. These data were then combined with similar pre-adjusted records for others traits in a multiple trait BLUP animal model. The combined breeding values for clinical mastitis obtained are the official (published) ones. Mastitis estimated breeding values (EBV) were then combined with SCSs EBV into an udder health index, which receives a weight of 14.5% to 18.5% in the French total merit index (ISU) of the three breeds. Interbull genetic correlations for mastitis occurrence were very high (ρ = 0.94) with Nordic countries, where much stricter recording systems exist reflecting a satisfactory quality of phenotypes as reported by the farmers. They were lower (around 0.80) with countries supplying SCS as a proxy for the international evaluation on clinical mastitis.

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“…Parental contribution to the reliability of each PTA was removed using the method described by Harris and Johnson (1998)…”

Section: Phenotypic Datamentioning

confidence: 99%

Genome-wide association study for calving traits in Holstein–Friesian dairy cattle

Purfield

Bradley

Kearney

et al. 2014

Animal

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Dystocia and perinatal mortality are quantitative traits that significantly impact animal productivity and welfare. Their economic importance is reflected by their inclusion in the national breeding goals of many cattle populations. The genetic architecture that influences these traits, however, has still yet to be thoroughly defined. Regions of the bovine genome associated with calving difficulty (direct and maternal) and perinatal mortality were detected in this study using a Bayesian approach with 43 204 single nucleotide polymorphisms (SNPs) on up to 1970 Holstein-Friesian bulls. Several SNPs on chromosomes 5, 6, 11, 12, 17,18 and 28 were detected to be strongly associated with these calving performance traits. Novel genomic regions with previously reported associations with growth, stature, birth weight and bone morphology were identified in the present study as being associated with the three calving performance traits. Morphological abnormalities are a known contributor to perinatal mortality and the most significantly associated SNP for perinatal mortality in the present study was located in a region in linkage disequilibrium with the gene SLC26A7. This gene, SLC26A7, has similarities and colocalises with SLC4A2, which has previously been associated with osteoporosis and mortality in cattle populations. The HHIP gene that is known to be associated with stature in humans was strongly associated with direct calving difficulty in the present study; large calves are known to, on average, have a greater likelihood of dystocia. A stemloop microRNA, bta-mir-1256, on chromosome 12, involved in post-transcriptional regulation of gene expression was associated with maternal calving difficulty. Previously reported quantitative trait loci associated with calving performance traits in other populations were again identified in this study; with one genomic region on chromosome 18 supporting very strong evidence of an underlying causative mutation and accounting for 2.1% of the genetic variation in direct calving difficulty. Overlapping genomic regions associated with one or more of the calving traits were also detected substantiating the known genetic covariances existing between these traits. Moreover, some genomic regions were only associated with one of the calving traits implying the selective genomic breeding programs exploiting these regions could help resolve genetic antagonisms.Keywords: dystocia, mortality, calving difficulty, genomic, quantitative trait loci ImplicationsThis study contributes to the understanding of the underlying genetic architecture and aetiology of dystocia and perinatal mortality both of which are quantitative traits that have a significant economic farm impact. Moreover, the detection of quantitative trait loci associated with only one calving trait can help resolve genetic antagonisms if targeted in genomic breeding programs -for example, selecting for decreased calving difficulty without impacting maternal calving difficulty.

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Approximate Reliability of Genetic Evaluations Under an Animal Model

Cited by 71 publications

References 5 publications

Sharing reference data and including cows in the reference population improve genomic predictions in Danish Jersey

Sharing reference data and including cows in the reference population improve genomic predictions in Danish Jersey

Multiple trait genetic evaluation of clinical mastitis in three dairy cattle breeds

Genome-wide association study for calving traits in Holstein–Friesian dairy cattle

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