- Claudia A. Sevillano(older publications) (1)
- Claudia A. Sevillano (1)
- Henk Bovenhuis (1)
- Simone E.F. Guimarães (1)
- Fabyano F. Silva (1)
Genomic evaluation for a crossbreeding system implementing breed-of-origin for targeted markers
Sevillano, Claudia A. ; Bovenhuis, Henk ; Calus, Mario P.L. - \ 2019
Frontiers in Genetics Livestock Genomics 10 (2019)MAY. - ISSN 1664-8021
Crossbred - Finisher - Genomic prediction - Origin of alleles - Pig
The genome in crossbred animals is a mosaic of genomic regions inherited from the different parental breeds. We previously showed that effects of haplotypes strongly associated with crossbred performance are different depending upon from which parental breed they are inherited, however, the majority of the genomic regions are not or only weakly associated with crossbred performance. Therefore, our objective was to develop a model that distinguishes between selected single nucleotide polymorphisms (SNP) strongly associated with crossbred performance and all remaining SNP. For the selected SNP, breed-specific allele effects were fitted whereas for the remaining SNP it was assumed that effects are the same across breeds (SEL-BOA model). We used data from three purebred populations; S, LR, and LW, and the corresponding crossbred population. We selected SNP that explained together either 5 or 10% of the total crossbred genetic variance for average daily gain in each breed of origin. The model was compared to a model where all SNP-alleles were allowed to have different effects for crossbred performance depending upon the breed of origin (BOA model) and to a model where all SNP-alleles had the same effect for crossbred performance across breeds (G model). Across the models, the heritability for crossbred performance was very similar with values of 0.29-0.30. With the SEL-BOA models, in general, the purebred-crossbred genetic correlation (rpc) for the selected SNP was larger than for the non-selected SNP. For breed LR, the rpc for selected SNP and non-selected SNP estimated with the SEL-BOA 5% and SEL-BOA 10% were very different compared to the rpc estimated with the G or BOA model. For breeds S and LW, there was not a big discrepancy for the rpc estimated with the SEL-BOA models and with the G or BOA model. The BOA model calculates more accurate breeding values of purebred animals for crossbred performance than the G model when rpc differs (≈10%) between the G and the BOA model. Superiority of the SEL-BOA model compared to the BOA model was only observed for SEL-BOA 10% and when rpc for the selected and non-selected SNP differed both (≈20%) from the rpc estimated by the G or BOA model.
Effects of alleles in crossbred pigs estimated for genomic prediction depend on their breed-of-origin
Sevillano, Claudia A. ; Napel, Jan ten; Guimarães, Simone E.F. ; Silva, Fabyano F. ; Calus, Mario P.L. - \ 2018
BMC Genomics 19 (2018)1. - ISSN 1471-2164
Breed-of-origin - Crossbred - Genomic prediction - Pig
Background: This study investigated if the allele effect of a given single nucleotide polymorphism (SNP) for crossbred performance in pigs estimated in a genomic prediction model differs depending on its breed-of-origin, and how these are related to estimated effects for purebred performance. Results: SNP-allele substitution effects were estimated for a commonly used SNP panel using a genomic best linear unbiased prediction model with breed-specific partial relationship matrices. Estimated breeding values for purebred and crossbred performance were converted to SNP-allele effects by breed-of-origin. Differences between purebred and crossbred, and between breeds-of-origin were evaluated by comparing percentage of variance explained by genomic regions for back fat thickness (BF), average daily gain (ADG), and residual feed intake (RFI). From ten regions explaining most additive genetic variance for crossbred performance, 1 to 5 regions also appeared in the top ten for purebred performance. The proportion of genetic variance explained by a genomic region and the estimated effect of a haplotype in such a region were different depending upon the breed-of-origin. To illustrate underlying mechanisms, we evaluated the estimated effects across breeds-of-origin for haplotypes associated to the melanocortin 4 receptor (MC4R) gene, and for the MC4Rsnp itself which is a missense mutation with a known effect on BF and ADG. Although estimated allele substitution effects of the MC4Rsnp mutation were very similar across breeds, explained genetic variance of haplotypes associated to the MC4R gene using a SNP panel that does not include the mutation, was considerably lower in one of the breeds where the allele frequency of the mutation was the lowest. Conclusions: Similar regions explaining similar additive genetic variance were observed across purebred and crossbred performance. Moreover, there was some overlap across breeds-of-origin between regions that explained relatively large proportions of genetic variance for crossbred performance; albeit that the actual proportion of variance deviated across breeds-of-origin. Results based on a missense mutation in MC4R confirmed that even if a causal locus has similar effects across breeds-of-origin, estimated effects and explained variance in its region using a commonly used SNP panel can strongly depend on the allele frequency of the underlying causal mutation.
Interval from last insemination to culling : I: The genetic background in crossbred sows
Grevenhof, E.M. van; Knol, E.F. ; Heuven, H.C.M. - \ 2015
Livestock Science 181 (2015). - ISSN 1871-1413 - p. 103 - 107.
Crossbred - Culling reason - Heritability - Interval last insemination to culling - Longevity - Sows
Improving longevity of sows is hampered by the lack of accurate and early recording of factors that contribute to reduced longevity. Besides, phenotypic data of parity number at culling or culling reason are potentially collected in purebred individuals, while these animals are not able to show full potential of their longevity due to EBVs, which makes the culling to take place earlier. In contrast to crossbred animals, of which usually very little information is collected, as phenotypes are expensive and difficult to obtain. Longevity is influenced by several culling reasons of which fertility and leg weakness are known to be the most important, although culling reason is unknown or unreliably recorded in crossbreds. To distinguish different reasons for (in)voluntary culling, interval from last insemination to culling (IL2C) might be able to function as an indicator, which could potentially enable us to breed for sow able to fulfil a complete production cycle. The aim is to quantify and understand the mechanism of parity number at culling by analysing the IL2C, in relation to parity number at culling. The results show that IL2C is a heritable trait that can be used in selection, in addition to parity number at culling. Parity number at culling and IL2C are not significantly correlated, which shows the potential to take both traits into account in breeding. By combining improvement of IL2C with improved longevity, economics and welfare of crossbred sows will even further be increased.