Genomic analyses provide insights into breed-of-origin effects from purebreds on three-way crossbred pigs.
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ABSTRACT:
SUBMITTER: Lin Y
PROVIDER: S-EPMC6855203 | biostudies-literature | 2019
REPOSITORIES: biostudies-literature
Publications
Genomic analyses provide insights into breed-of-origin effects from purebreds on three-way crossbred pigs.
Lin Yu Y Tang Qianzi Q Li Yan Y He Mengnan M Jin Long L Ma Jideng J Wang Xun X Long Keren K Huang Zhiqing Z Li Xuewei X Gu Yiren Y Li Mingzhou M
PeerJ 20191111
Crossbreeding is widely used aimed at improving crossbred performance for poultry and livestock. Alleles that are specific to different purebreds will yield a large number of heterozygous single-nucleotide polymorphisms (SNPs) in crossbred individuals, which are supposed to have the power to alter gene function or regulate gene expression. For pork production, a classic three-way crossbreeding system of Duroc × (Landrace × Yorkshire) (DLY) is generally used to produce terminal crossbred pigs wit ...[more]
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Project description:Broiler breeding programs rely on crossbreeding. With genomic selection, widespread use of crossbred performance in breeding programs comes within reach. Commercial crossbreds, however, may have unknown pedigrees and their genomes may include DNA from 2 to 4 different breeds. Our aim was, for a broiler dataset with a limited number of sires having both purebred and crossbred offspring generated using natural mating, to rapidly derive parentage, assess the distribution of the sire contribution to the offspring generation, and to assess breed-of-origin of alleles in crossbreds. The dataset contained genotypes for 56,075 SNPs for 5,882 purebred and 10,943 3-way crossbred offspring generated by natural mating of 164 purebred sires to 1,016 purebred and 1,386 F1 crossbred hens. Using our algorithm FindParents, joint parentage derivation for the offspring and parent generations required only 1 m 29 s to retrieve parentage for 20,253 animals considering 4,504 possible parents. FindParents was similarly accurate as a maximum likelihood based method, apart from situations where settings of FindParents did not match the genotyping error rate in the data. Numbers of offspring per sire had a very skewed distribution, ranging from 1 to 270 crossbreds and 1 to 154 purebreds. Derivation of breed-of-origin of alleles relied on phasing all genotypes, including 8,205, 372, and 720 animals from the 3 pure lines involved, and allocating haplotypes in the crossbreds to purebred lines based on observed frequencies in the purebred lines. Breed-of-origin could be derived for 96.94% of the alleles of the 1,386 F1 crossbred hens and for 91.88% of the alleles of the 10,943 3-way crossbred offspring, of which 49.49% to the sire line. The achieved percentage of assignment to the sire line was sufficient to proceed with subsequent analyses requiring only the breed-of-origin of the paternal alleles to be known. Although required number of animals may be population dependent, to increase the total percentage of assigned alleles, it seems advisable to use at least approx. 1,000 genotyped purebred animals for each of the lines involved.
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Project description:BackgroundThis 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.ResultsSNP-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.ConclusionsSimilar 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.
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