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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.

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Correlation of gametic phase compared across two breeds over distance for a low (a) and a high correlation of LD phase (b). Correlation of LD phase between the two breeds for SNP pairs grouped by distance in intervals of 1 cM and covering 0 to 50 cM across the genome. The plots are the result of one replicate.
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Fig4: Correlation of gametic phase compared across two breeds over distance for a low (a) and a high correlation of LD phase (b). Correlation of LD phase between the two breeds for SNP pairs grouped by distance in intervals of 1 cM and covering 0 to 50 cM across the genome. The plots are the result of one replicate.

Mentions: Persistence of LD phase among breeds can be used to infer on the history of a species and relatedness of breeds within that species, as well as on the reliability of across-population prediction of genome-wide association studies (GWAS) and GEVB [25]. Figure 4 shows the persistence of LD phase between adjacent SNPs, measured by the correlation of r between the two breeds. A greater correlation implies that the SNP-SNP (and most probably the SNP-QTL) LD is more consistent between the two breeds. As distance in time between subpopulations increases, there is a greater chance for recombination to break down the LD that was present in the ancestral population and for drift to create new LD within each subpopulation. Both mechanisms decrease the correlation of LD phase between the two breeds [26,27]. For SNPs with a pairwise distance of 1 cM, persistence of LD phase between breeds A and B was estimated 0.2 and 0.7 for cases with a low and high correlation of LD phase, respectively. Persistence of LD phase has been reported for Duroc, Landrace, Yorkshire pig breeds. For SNPs with a pairwise distance less than 50 kb, Badke et al. [21] reported a correlation of LD of 0.85 between Landrace and Yorkshire breeds and of 0.82 between Duroc and Landrace and between Duroc and Yorkshire breeds. Assuming 1 cM is approximately 1 Mb, we found correlations of LD phase equal to 0.38 and 0.87 for SNPs with a pairwise distance less than 50 kb for cases with low and high correlations of LD phase between two breeds, respectively. The correlation of LD phase between pig breeds in different studies ranged from 0.80 to 0.92 for SNPs with a pairwise distance less than 10 kb. In a study on the extent and persistence of LD phase in Holstein-Friesian, Jersey, and Angus cattle, de Roos et al. [25] reported a correlation of LD phase that ranged from 0.7 to 0.97 between two breeds for SNPs with a pairwise distance less than 10 kb and a decline of this correlation as the distance between SNPs or divergence between breeds increased. In our study, as distance between SNPs increased, the correlation of LD phase between the two breeds decreased (0.5 at an average pairwise SNP distance of 1 cM). It has been reported that, while correlation of LD phase is similar for pig breeds and dairy cattle at short distance ranges (<10 kb), pig breeds generally show greater correlations of LD phase than dairy cattle at larger SNP distances [21].Figure 4


Maximizing crossbred performance through purebred genomic selection.

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

Correlation of gametic phase compared across two breeds over distance for a low (a) and a high correlation of LD phase (b). Correlation of LD phase between the two breeds for SNP pairs grouped by distance in intervals of 1 cM and covering 0 to 50 cM across the genome. 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

Fig4: Correlation of gametic phase compared across two breeds over distance for a low (a) and a high correlation of LD phase (b). Correlation of LD phase between the two breeds for SNP pairs grouped by distance in intervals of 1 cM and covering 0 to 50 cM across the genome. The plots are the result of one replicate.
Mentions: Persistence of LD phase among breeds can be used to infer on the history of a species and relatedness of breeds within that species, as well as on the reliability of across-population prediction of genome-wide association studies (GWAS) and GEVB [25]. Figure 4 shows the persistence of LD phase between adjacent SNPs, measured by the correlation of r between the two breeds. A greater correlation implies that the SNP-SNP (and most probably the SNP-QTL) LD is more consistent between the two breeds. As distance in time between subpopulations increases, there is a greater chance for recombination to break down the LD that was present in the ancestral population and for drift to create new LD within each subpopulation. Both mechanisms decrease the correlation of LD phase between the two breeds [26,27]. For SNPs with a pairwise distance of 1 cM, persistence of LD phase between breeds A and B was estimated 0.2 and 0.7 for cases with a low and high correlation of LD phase, respectively. Persistence of LD phase has been reported for Duroc, Landrace, Yorkshire pig breeds. For SNPs with a pairwise distance less than 50 kb, Badke et al. [21] reported a correlation of LD of 0.85 between Landrace and Yorkshire breeds and of 0.82 between Duroc and Landrace and between Duroc and Yorkshire breeds. Assuming 1 cM is approximately 1 Mb, we found correlations of LD phase equal to 0.38 and 0.87 for SNPs with a pairwise distance less than 50 kb for cases with low and high correlations of LD phase between two breeds, respectively. The correlation of LD phase between pig breeds in different studies ranged from 0.80 to 0.92 for SNPs with a pairwise distance less than 10 kb. In a study on the extent and persistence of LD phase in Holstein-Friesian, Jersey, and Angus cattle, de Roos et al. [25] reported a correlation of LD phase that ranged from 0.7 to 0.97 between two breeds for SNPs with a pairwise distance less than 10 kb and a decline of this correlation as the distance between SNPs or divergence between breeds increased. In our study, as distance between SNPs increased, the correlation of LD phase between the two breeds decreased (0.5 at an average pairwise SNP distance of 1 cM). It has been reported that, while correlation of LD phase is similar for pig breeds and dairy cattle at short distance ranges (<10 kb), pig breeds generally show greater correlations of LD phase than dairy cattle at larger SNP distances [21].Figure 4

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