Limits...
Maximizing crossbred performance through purebred genomic selection.

Esfandyari H, Sørensen AC, Bijma P - Genet. Sel. Evol. (2015)

Bottom Line: Estimated breeding values for CP can be calculated from additive and dominance effects of alleles that are estimated using pure line data.However, for a high correlation of LD phase, marker effects that were estimated using a single combined reference population increased the gain in CP.Furthermore, if the correlation of LD phase between pure lines is high, accuracy of selection can be increased by combining the two pure lines into a single reference population to estimate marker effects.

View Article: PubMed Central - PubMed

Affiliation: Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark. Hadi.esfandyari@mbg.au.dk.

ABSTRACT

Background: In livestock production, many animals are crossbred, with two distinct advantages: heterosis and breed complementarity. Genomic selection (GS) can be used to select purebred parental lines for crossbred performance (CP). Dominance being the likely genetic basis of heterosis, explicitly including dominance in the GS model may be an advantage to select purebreds for CP. Estimated breeding values for CP can be calculated from additive and dominance effects of alleles that are estimated using pure line data. The objective of this simulation study was to investigate the benefits of applying GS to select purebred animals for CP, based on purebred phenotypic and genotypic information. A second objective was to compare the use of two separate pure line reference populations to that of a single reference population that combines both pure lines. These objectives were investigated under two conditions, i.e. either a low or a high correlation of linkage disequilibrium (LD) phase between the pure lines.

Results: The results demonstrate that the gain in CP was higher when parental lines were selected for CP, rather than purebred performance, both with a low and a high correlation of LD phase. For a low correlation of LD phase between the pure lines, the use of two separate reference populations yielded a higher gain in CP than use of a single reference population that combines both pure lines. However, for a high correlation of LD phase, marker effects that were estimated using a single combined reference population increased the gain in CP.

Conclusions: Under the hypothesis that performance of crossbred animals differs from that of purebred animals due to dominance, a dominance model can be used for GS of purebred individuals for CP, without using crossbred data. Furthermore, if the correlation of LD phase between pure lines is high, accuracy of selection can be increased by combining the two pure lines into a single reference population to estimate marker effects.

Show MeSH

Related in: MedlinePlus

Decay of averager2over distance for a low (a) and a high correlation of LD phase (b). Average r2 between SNPs in breed A and breed B at various distances in base pairs ranging from 1 to 100 cM. The plots are the result of one replicate.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4358869&req=5

Fig3: Decay of averager2over distance for a low (a) and a high correlation of LD phase (b). Average r2 between SNPs in breed A and breed B at various distances in base pairs ranging from 1 to 100 cM. The plots are the result of one replicate.

Mentions: To estimate LD, we used SNP genotypes of animals in the training set of both breeds. An average r2 of 0.43 and 0.42 for adjacent SNPs was found for breeds A and B, respectively. These average r2 between adjacent SNPs are similar to those reported by Badke et al. [21] for four US pig breeds that ranged from 0.36 to 0.46 for animals genotyped using the Illumina PorcineSNP60 (number of markers M = 62 163). Another study by Du et al. [24] that investigated the range and extent of LD in six commercial pig lines (two terminal sire lines and four maternal lines) for 4500 autosomal SNPs, reported an average r2 of 0.2 and 0.07 for all pairs of SNPs that were approximately 1 and 5 cM apart, respectively, whereas we found average r2 of 0.29 and 0.08 at those distances. Figure 3 displays an overview of the decline of r2 over distance in both breeds. As expected, in both breeds the most tightly linked SNP pairs had the highest average r2, and the observed average r2 decreased rapidly as the map distance increased.Figure 3


Maximizing crossbred performance through purebred genomic selection.

Esfandyari H, Sørensen AC, Bijma P - Genet. Sel. Evol. (2015)

Decay of averager2over distance for a low (a) and a high correlation of LD phase (b). Average r2 between SNPs in breed A and breed B at various distances in base pairs ranging from 1 to 100 cM. The plots are the result of one replicate.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4358869&req=5

Fig3: Decay of averager2over distance for a low (a) and a high correlation of LD phase (b). Average r2 between SNPs in breed A and breed B at various distances in base pairs ranging from 1 to 100 cM. The plots are the result of one replicate.
Mentions: To estimate LD, we used SNP genotypes of animals in the training set of both breeds. An average r2 of 0.43 and 0.42 for adjacent SNPs was found for breeds A and B, respectively. These average r2 between adjacent SNPs are similar to those reported by Badke et al. [21] for four US pig breeds that ranged from 0.36 to 0.46 for animals genotyped using the Illumina PorcineSNP60 (number of markers M = 62 163). Another study by Du et al. [24] that investigated the range and extent of LD in six commercial pig lines (two terminal sire lines and four maternal lines) for 4500 autosomal SNPs, reported an average r2 of 0.2 and 0.07 for all pairs of SNPs that were approximately 1 and 5 cM apart, respectively, whereas we found average r2 of 0.29 and 0.08 at those distances. Figure 3 displays an overview of the decline of r2 over distance in both breeds. As expected, in both breeds the most tightly linked SNP pairs had the highest average r2, and the observed average r2 decreased rapidly as the map distance increased.Figure 3

Bottom Line: Estimated breeding values for CP can be calculated from additive and dominance effects of alleles that are estimated using pure line data.However, for a high correlation of LD phase, marker effects that were estimated using a single combined reference population increased the gain in CP.Furthermore, if the correlation of LD phase between pure lines is high, accuracy of selection can be increased by combining the two pure lines into a single reference population to estimate marker effects.

View Article: PubMed Central - PubMed

Affiliation: Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark. Hadi.esfandyari@mbg.au.dk.

ABSTRACT

Background: In livestock production, many animals are crossbred, with two distinct advantages: heterosis and breed complementarity. Genomic selection (GS) can be used to select purebred parental lines for crossbred performance (CP). Dominance being the likely genetic basis of heterosis, explicitly including dominance in the GS model may be an advantage to select purebreds for CP. Estimated breeding values for CP can be calculated from additive and dominance effects of alleles that are estimated using pure line data. The objective of this simulation study was to investigate the benefits of applying GS to select purebred animals for CP, based on purebred phenotypic and genotypic information. A second objective was to compare the use of two separate pure line reference populations to that of a single reference population that combines both pure lines. These objectives were investigated under two conditions, i.e. either a low or a high correlation of linkage disequilibrium (LD) phase between the pure lines.

Results: The results demonstrate that the gain in CP was higher when parental lines were selected for CP, rather than purebred performance, both with a low and a high correlation of LD phase. For a low correlation of LD phase between the pure lines, the use of two separate reference populations yielded a higher gain in CP than use of a single reference population that combines both pure lines. However, for a high correlation of LD phase, marker effects that were estimated using a single combined reference population increased the gain in CP.

Conclusions: Under the hypothesis that performance of crossbred animals differs from that of purebred animals due to dominance, a dominance model can be used for GS of purebred individuals for CP, without using crossbred data. Furthermore, if the correlation of LD phase between pure lines is high, accuracy of selection can be increased by combining the two pure lines into a single reference population to estimate marker effects.

Show MeSH
Related in: MedlinePlus