http://guidelines.beefimprovement.org/index.php?title=Expected_Progeny_Difference&feed=atom&action=historyExpected Progeny Difference - Revision history2024-03-29T08:19:22ZRevision history for this page on the wikiMediaWiki 1.35.2http://guidelines.beefimprovement.org/index.php?title=Expected_Progeny_Difference&diff=2428&oldid=prevBgolden at 16:16, 16 April 20212021-04-16T16:16:00Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Category:Genetic Evaluation]]</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Category:Genetic Evaluation]]</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The prediction of the value of an animal as a parent for the next generation, or Expected Progeny Difference (EPD), which is simply half of the animal's breeding value, was a major advancement in the ability to select animals to fit production goals. Prior to the development of EPDs the primary method for genetic improvement was some form of subjective visual appraisal<ref name="milestone" <ref>Golden, BL, DJ Garrick, and LL Benyshek. 2009. Milestones in beef cattle genetic evaluation. J Anim Sci. 87(E. Suppl.):E3-E10.</ref>. Since the development of methodology to implement Genetic Evaluation in the beef industry (launched in the 1970s)<ref name="milestone" />, EPDs have been the gold standard for genetic selection. Regardless of their associated [[Accuracy | accuracy]] value, they are the best selection tool that producers have to improve genetic merit in a single trait, though [[Selection Index| indices]] incorporate EPD information and are the best tools for multiple-trait selection. Nevertheless, there is often confusion surrounding the best tools and information on which to make selection decisions. </div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The prediction of the value of an animal as a parent for the next generation, or Expected Progeny Difference (EPD), which is simply half of the animal's breeding value, was a major advancement in the ability to select animals to fit production goals. Prior to the development of EPDs the primary method for genetic improvement was some form of subjective visual appraisal<ref name="milestone" <ref>Golden, BL, DJ Garrick, and LL Benyshek. 2009. Milestones in beef cattle genetic evaluation. J Anim Sci. 87(E. Suppl.):E3-E10.</ref>. Since the development of methodology to implement Genetic Evaluation in the beef industry (launched in the 1970s)<ref name="milestone" />, EPDs have been the gold standard for <ins class="diffchange diffchange-inline">[[Selection | </ins>genetic selection<ins class="diffchange diffchange-inline">]]</ins>. Regardless of their associated [[Accuracy | accuracy]] value, they are the best selection tool that producers have to improve genetic merit in a single trait, though [[Selection Index| indices]] incorporate EPD information and are the best tools for multiple-trait selection. Nevertheless, there is often confusion surrounding the best tools and information on which to make selection decisions. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Phenotypes for quantitative traits are a combination of influences from both genetics (additive, dominance, epistatic) and the environment (permanent and temporary). Alternatively, we can write this as an equation as follows:</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Phenotypes for quantitative traits are a combination of influences from both genetics (additive, dominance, epistatic) and the environment (permanent and temporary). Alternatively, we can write this as an equation as follows:</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
</table>Bgoldenhttp://guidelines.beefimprovement.org/index.php?title=Expected_Progeny_Difference&diff=2301&oldid=prevBgolden at 17:08, 12 April 20212021-04-12T17:08:16Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 17:08, 12 April 2021</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The challenge with selection on measures of phenotype is that they include both genetic and environmental effects, even if weights are adjusted and/or ratios (which limit comparisons to within contemporary groups) are utilized. When selection decisions are made on these metrics, selection emphasis is also placed on nongenetic factors, which reduces the efficacy of selection and reduces genetic progress. Superiority of selection using EPDs (or breeding values) as compared to phenotypes has been demonstrated<ref>Gall, GAE and Y Bakar. 2002. Application of mixed-model techniques to fish breed improvement: analysis of breeding-value selection to increase 98-day body weight in tilapia. Aquaculture. 212(1-4):93-113.</ref><ref>Kuhlers, DL and BW Kennedy. 1992. Effect of culling on selection response using phenotypic selection or best linear unbiased prediction of breeding values in small, closed herds of swine. J Anim Sci. 70(8):2338-2348.</ref><ref>Belonsky, GM and BW Kennedy. 1988. Selection on individual phenotype and best linear unbiased predictor of breeding values in a closed swine herd. J. Anim Sci. 66:1124-1131.</ref><ref>Hagger, C. 1991. Effects of selecting on phenotype, on index, or on breeding values, on expected response, genetic relationships, and accuracy of breeding values in an experiment. J Anim Breed Genet. 108:102-110.</ref>. </div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The challenge with selection on measures of phenotype is that they include both genetic and environmental effects, even if weights are adjusted and/or ratios (which limit comparisons to within contemporary groups) are utilized. When selection decisions are made on these metrics, selection emphasis is also placed on nongenetic factors, which reduces the efficacy of selection and reduces genetic progress. Superiority of selection using EPDs (or breeding values) as compared to phenotypes has been demonstrated<ref>Gall, GAE and Y Bakar. 2002. Application of mixed-model techniques to fish breed improvement: analysis of breeding-value selection to increase 98-day body weight in tilapia. Aquaculture. 212(1-4):93-113.</ref><ref>Kuhlers, DL and BW Kennedy. 1992. Effect of culling on selection response using phenotypic selection or best linear unbiased prediction of breeding values in small, closed herds of swine. J Anim Sci. 70(8):2338-2348.</ref><ref>Belonsky, GM and BW Kennedy. 1988. Selection on individual phenotype and best linear unbiased predictor of breeding values in a closed swine herd. J. Anim Sci. 66:1124-1131.</ref><ref>Hagger, C. 1991. Effects of selecting on phenotype, on index, or on breeding values, on expected response, genetic relationships, and accuracy of breeding values in an experiment. J Anim Breed Genet. 108:102-110.</ref>. </div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>EPDs also simplify selection decisions. Selection using phenotypes can involve the individual’s own phenotype as well as phenotypes on relatives (including progeny, parents, and siblings, as an example). With [[Genetic Evaluation]], all of this information is combined and weighted appropriately in a single value, the EPD, which simplifies selection. This same value is even more relevant in the genomics era, because genomic testing provides another source of information for selection. </div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>EPDs also simplify selection decisions. Selection using phenotypes can involve the individual’s own phenotype as well as phenotypes on relatives (including progeny, parents, and siblings, as an example). With [[<ins class="diffchange diffchange-inline">:Category:</ins>Genetic Evaluation <ins class="diffchange diffchange-inline">| genetic evaluation</ins>]], all of this information is combined and weighted appropriately in a single value, the EPD, which simplifies selection. This same value is even more relevant in the genomics era, because genomic testing provides another source of information for selection. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The Beef Improvement Federation recommends using genomically-enhanced EPDs (see [[Single-step Genomic BLUP]] and [[Single-step Hybrid Marker Effects Models]]), as opposed to using disjoined marker scores and EPDs separately, as the best method for utilizing genomic data for selection<ref>Muir, WM. 2007. Comparison of genomic and traditional BLUP-estimated breeding value accuracy and selection response under alternative trait and genomic parameters. J. Anim Brdg Genet. 124(6):342-355.</ref>. Genetic Evaluation methodologies are always evolving and improving, but all of these methods incorporate all available data on an animal into EPD prediction, including genomic data, and weight it appropriately so that there is a single metric for genetic selection that represents the best prediction of that animal’s genetic merit using all available data. </div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The Beef Improvement Federation recommends using genomically-enhanced EPDs (see [[Single-step Genomic BLUP]] and [[Single-step Hybrid Marker Effects Models]]), as opposed to using disjoined marker scores and EPDs separately, as the best method for utilizing genomic data for selection<ref>Muir, WM. 2007. Comparison of genomic and traditional BLUP-estimated breeding value accuracy and selection response under alternative trait and genomic parameters. J. Anim Brdg Genet. 124(6):342-355.</ref>. Genetic Evaluation methodologies are always evolving and improving, but all of these methods incorporate all available data on an animal into EPD prediction, including genomic data, and weight it appropriately so that there is a single metric for genetic selection that represents the best prediction of that animal’s genetic merit using all available data. </div></td></tr>
</table>Bgoldenhttp://guidelines.beefimprovement.org/index.php?title=Expected_Progeny_Difference&diff=2269&oldid=prevBgolden at 13:38, 11 April 20212021-04-11T13:38:31Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 13:38, 11 April 2021</td>
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<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">[[Category:Genetic Evaluation]]</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The prediction of the value of an animal as a parent for the next generation, or Expected Progeny Difference (EPD), which is simply half of the animal's breeding value, was a major advancement in the ability to select animals to fit production goals. Prior to the development of EPDs the primary method for genetic improvement was some form of subjective visual appraisal<ref name="milestone" <ref>Golden, BL, DJ Garrick, and LL Benyshek. 2009. Milestones in beef cattle genetic evaluation. J Anim Sci. 87(E. Suppl.):E3-E10.</ref>. Since the development of methodology to implement Genetic Evaluation in the beef industry (launched in the 1970s)<ref name="milestone" />, EPDs have been the gold standard for genetic selection. Regardless of their associated [[Accuracy | accuracy]] value, they are the best selection tool that producers have to improve genetic merit in a single trait, though [[Selection Index| indices]] incorporate EPD information and are the best tools for multiple-trait selection. Nevertheless, there is often confusion surrounding the best tools and information on which to make selection decisions. </div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The prediction of the value of an animal as a parent for the next generation, or Expected Progeny Difference (EPD), which is simply half of the animal's breeding value, was a major advancement in the ability to select animals to fit production goals. Prior to the development of EPDs the primary method for genetic improvement was some form of subjective visual appraisal<ref name="milestone" <ref>Golden, BL, DJ Garrick, and LL Benyshek. 2009. Milestones in beef cattle genetic evaluation. J Anim Sci. 87(E. Suppl.):E3-E10.</ref>. Since the development of methodology to implement Genetic Evaluation in the beef industry (launched in the 1970s)<ref name="milestone" />, EPDs have been the gold standard for genetic selection. Regardless of their associated [[Accuracy | accuracy]] value, they are the best selection tool that producers have to improve genetic merit in a single trait, though [[Selection Index| indices]] incorporate EPD information and are the best tools for multiple-trait selection. Nevertheless, there is often confusion surrounding the best tools and information on which to make selection decisions. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Phenotypes for quantitative traits are a combination of influences from both genetics (additive, dominance, epistatic) and the environment (permanent and temporary). Alternatively, we can write this as an equation as follows:</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Phenotypes for quantitative traits are a combination of influences from both genetics (additive, dominance, epistatic) and the environment (permanent and temporary). Alternatively, we can write this as an equation as follows:</div></td></tr>
</table>Bgoldenhttp://guidelines.beefimprovement.org/index.php?title=Expected_Progeny_Difference&diff=2263&oldid=prevBgolden at 22:44, 22 March 20212021-03-22T22:44:25Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 22:44, 22 March 2021</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1" >Line 1:</td>
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<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The <del class="diffchange diffchange-inline">estimation </del>of the value of an animal as a parent for the next generation, or Expected Progeny Difference (EPD), which is simply half of the animal's breeding value, was a major advancement in the ability to select animals to fit production goals. Prior to the development of EPDs the primary method for genetic improvement was some form of subjective visual appraisal<ref name="milestone" <ref>Golden, BL, DJ Garrick, and LL Benyshek. 2009. Milestones in beef cattle genetic evaluation. J Anim Sci. 87(E. Suppl.):E3-E10.</ref>. Since the development of methodology to implement Genetic Evaluation in the beef industry (launched in the 1970s)<ref name="milestone" />, EPDs have been the gold standard for genetic selection. Regardless of their associated [[Accuracy | accuracy]] value, they are the best selection tool that producers have to improve genetic merit in a single trait, though [[Selection Index| indices]] incorporate EPD information and are the best tools for multiple-trait selection. Nevertheless, there is often confusion surrounding the best tools and information on which to make selection decisions. </div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The <ins class="diffchange diffchange-inline">prediction </ins>of the value of an animal as a parent for the next generation, or Expected Progeny Difference (EPD), which is simply half of the animal's breeding value, was a major advancement in the ability to select animals to fit production goals. Prior to the development of EPDs the primary method for genetic improvement was some form of subjective visual appraisal<ref name="milestone" <ref>Golden, BL, DJ Garrick, and LL Benyshek. 2009. Milestones in beef cattle genetic evaluation. J Anim Sci. 87(E. Suppl.):E3-E10.</ref>. Since the development of methodology to implement Genetic Evaluation in the beef industry (launched in the 1970s)<ref name="milestone" />, EPDs have been the gold standard for genetic selection. Regardless of their associated [[Accuracy | accuracy]] value, they are the best selection tool that producers have to improve genetic merit in a single trait, though [[Selection Index| indices]] incorporate EPD information and are the best tools for multiple-trait selection. Nevertheless, there is often confusion surrounding the best tools and information on which to make selection decisions. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Phenotypes for quantitative traits are a combination of influences from both genetics (additive, dominance, epistatic) and the environment (permanent and temporary). Alternatively, we can write this as an equation as follows:</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Phenotypes for quantitative traits are a combination of influences from both genetics (additive, dominance, epistatic) and the environment (permanent and temporary). Alternatively, we can write this as an equation as follows:</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>EPDs also simplify selection decisions. Selection using phenotypes can involve the individual’s own phenotype as well as phenotypes on relatives (including progeny, parents, and siblings, as an example). With [[Genetic Evaluation]], all of this information is combined and weighted appropriately in a single value, the EPD, which simplifies selection. This same value is even more relevant in the genomics era, because genomic testing provides another source of information for selection. </div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>EPDs also simplify selection decisions. Selection using phenotypes can involve the individual’s own phenotype as well as phenotypes on relatives (including progeny, parents, and siblings, as an example). With [[Genetic Evaluation]], all of this information is combined and weighted appropriately in a single value, the EPD, which simplifies selection. This same value is even more relevant in the genomics era, because genomic testing provides another source of information for selection. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The Beef Improvement Federation recommends using genomically-enhanced EPDs (see [[Single-step Genomic BLUP]] and [[Single-step Hybrid Marker Effects Models]]), as opposed to using disjoined marker scores and EPDs separately, as the best method for utilizing genomic data for selection<ref>Muir, WM. 2007. Comparison of genomic and traditional BLUP-estimated breeding value accuracy and selection response under alternative trait and genomic parameters. J. Anim Brdg Genet. 124(6):342-355.</ref>. Genetic Evaluation methodologies are always evolving and improving, but all of these methods incorporate all available data on an animal into EPD prediction, including genomic data, and weight it appropriately so that there is a single metric for genetic selection that represents the best <del class="diffchange diffchange-inline">estimate </del>of that animal’s genetic merit using all available data. </div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The Beef Improvement Federation recommends using genomically-enhanced EPDs (see [[Single-step Genomic BLUP]] and [[Single-step Hybrid Marker Effects Models]]), as opposed to using disjoined marker scores and EPDs separately, as the best method for utilizing genomic data for selection<ref>Muir, WM. 2007. Comparison of genomic and traditional BLUP-estimated breeding value accuracy and selection response under alternative trait and genomic parameters. J. Anim Brdg Genet. 124(6):342-355.</ref>. Genetic Evaluation methodologies are always evolving and improving, but all of these methods incorporate all available data on an animal into EPD prediction, including genomic data, and weight it appropriately so that there is a single metric for genetic selection that represents the best <ins class="diffchange diffchange-inline">prediction </ins>of that animal’s genetic merit using all available data. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>===Interim EPDs===</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>===Interim EPDs===</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Most beef breed organizations and companies have transitioned to routinely perform their genetic evaluation. Often these routine analyses are performed as frequently as weekly. Prior to this change, many organizations performed genetic evaluations either annually or semi-annually, and thus interim EPD<ref>Wilson, D. E. and R. L. Willham. 1988. Interim Expected Progeny Differences for Young Animals Not Included in National Cattle Evaluations. Journal of Animal Science, Volume 66, Issue 3, March 1988, Pages 618–625, https://doi.org/10.2527/jas1988.663618x</ref> computations were done so that breeders could have at least an early <del class="diffchange diffchange-inline">estimate </del>of genetic merit for selection decisions. As noted above with more routine runs of the genetic evaluation, interim EPDs now exist for shorter periods in an animal's life.</div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Most beef breed organizations and companies have transitioned to routinely perform their genetic evaluation. Often these routine analyses are performed as frequently as weekly. Prior to this change, many organizations performed genetic evaluations either annually or semi-annually, and thus interim EPD<ref>Wilson, D. E. and R. L. Willham. 1988. Interim Expected Progeny Differences for Young Animals Not Included in National Cattle Evaluations. Journal of Animal Science, Volume 66, Issue 3, March 1988, Pages 618–625, https://doi.org/10.2527/jas1988.663618x</ref> computations were done so that breeders could have at least an early <ins class="diffchange diffchange-inline">predictions </ins>of genetic merit for selection decisions. As noted above with more routine runs of the genetic evaluation, interim EPDs now exist for shorter periods in an animal's life.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>===Genetically Identical Animals===</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>===Genetically Identical Animals===</div></td></tr>
</table>Bgoldenhttp://guidelines.beefimprovement.org/index.php?title=Expected_Progeny_Difference&diff=2258&oldid=prevMspangler at 20:00, 29 December 20202020-12-29T20:00:51Z<p></p>
<table class="diff diff-contentalign-left diff-editfont-monospace" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 20:00, 29 December 2020</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l22" >Line 22:</td>
<td colspan="2" class="diff-lineno">Line 22:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Most beef breed organizations and companies have transitioned to routinely perform their genetic evaluation. Often these routine analyses are performed as frequently as weekly. Prior to this change, many organizations performed genetic evaluations either annually or semi-annually, and thus interim EPD<ref>Wilson, D. E. and R. L. Willham. 1988. Interim Expected Progeny Differences for Young Animals Not Included in National Cattle Evaluations. Journal of Animal Science, Volume 66, Issue 3, March 1988, Pages 618–625, https://doi.org/10.2527/jas1988.663618x</ref> computations were done so that breeders could have at least an early estimate of genetic merit for selection decisions. As noted above with more routine runs of the genetic evaluation, interim EPDs now exist for shorter periods in an animal's life.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Most beef breed organizations and companies have transitioned to routinely perform their genetic evaluation. Often these routine analyses are performed as frequently as weekly. Prior to this change, many organizations performed genetic evaluations either annually or semi-annually, and thus interim EPD<ref>Wilson, D. E. and R. L. Willham. 1988. Interim Expected Progeny Differences for Young Animals Not Included in National Cattle Evaluations. Journal of Animal Science, Volume 66, Issue 3, March 1988, Pages 618–625, https://doi.org/10.2527/jas1988.663618x</ref> computations were done so that breeders could have at least an early estimate of genetic merit for selection decisions. As noted above with more routine runs of the genetic evaluation, interim EPDs now exist for shorter periods in an animal's life.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>References: </div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">===Genetically Identical Animals===</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">There are instances where genetically identical animals are in the pedigree (i.e. identical twins and clones). BIF recommends that, where genetically identical animals exist in the pedigree, for purposes of routine genetic evaluation, each set of genetically identical individuals is assigned a common identifier so they have identical EPDs. Periodic test runs with the genetic identicals individually identified and the differences between them evaluated would be prudent. BIF recommends that genetically identical individuals should be assigned different permanent identification numbers.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">===</ins>References:<ins class="diffchange diffchange-inline">=== </ins> </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>----</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>----</div></td></tr>
</table>Mspanglerhttp://guidelines.beefimprovement.org/index.php?title=Expected_Progeny_Difference&diff=1888&oldid=prevMnielsen at 04:49, 17 December 20192019-12-17T04:49:43Z<p></p>
<table class="diff diff-contentalign-left diff-editfont-monospace" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 04:49, 17 December 2019</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l15" >Line 15:</td>
<td colspan="2" class="diff-lineno">Line 15:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The challenge with selection on measures of phenotype is that they include both genetic and environmental effects, even if weights are adjusted and/or ratios (which limit comparisons to within contemporary groups) are utilized. When selection decisions are made on these metrics, selection emphasis is also placed on nongenetic factors, which reduces the efficacy of selection and reduces genetic progress. Superiority of selection using EPDs (or breeding values) as compared to phenotypes has been demonstrated<ref>Gall, GAE and Y Bakar. 2002. Application of mixed-model techniques to fish breed improvement: analysis of breeding-value selection to increase 98-day body weight in tilapia. Aquaculture. 212(1-4):93-113.</ref><ref>Kuhlers, DL and BW Kennedy. 1992. Effect of culling on selection response using phenotypic selection or best linear unbiased prediction of breeding values in small, closed herds of swine. J Anim Sci. 70(8):2338-2348.</ref><ref>Belonsky, GM and BW Kennedy. 1988. Selection on individual phenotype and best linear unbiased predictor of breeding values in a closed swine herd. J. Anim Sci. 66:1124-1131.</ref><ref>Hagger, C. 1991. Effects of selecting on phenotype, on index, or on breeding values, on expected response, genetic relationships, and accuracy of breeding values in an experiment. J Anim Breed Genet. 108:102-110.</ref>. </div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The challenge with selection on measures of phenotype is that they include both genetic and environmental effects, even if weights are adjusted and/or ratios (which limit comparisons to within contemporary groups) are utilized. When selection decisions are made on these metrics, selection emphasis is also placed on nongenetic factors, which reduces the efficacy of selection and reduces genetic progress. Superiority of selection using EPDs (or breeding values) as compared to phenotypes has been demonstrated<ref>Gall, GAE and Y Bakar. 2002. Application of mixed-model techniques to fish breed improvement: analysis of breeding-value selection to increase 98-day body weight in tilapia. Aquaculture. 212(1-4):93-113.</ref><ref>Kuhlers, DL and BW Kennedy. 1992. Effect of culling on selection response using phenotypic selection or best linear unbiased prediction of breeding values in small, closed herds of swine. J Anim Sci. 70(8):2338-2348.</ref><ref>Belonsky, GM and BW Kennedy. 1988. Selection on individual phenotype and best linear unbiased predictor of breeding values in a closed swine herd. J. Anim Sci. 66:1124-1131.</ref><ref>Hagger, C. 1991. Effects of selecting on phenotype, on index, or on breeding values, on expected response, genetic relationships, and accuracy of breeding values in an experiment. J Anim Breed Genet. 108:102-110.</ref>. </div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>EPDs also simplify selection decisions. Selection using phenotypes can involve the individual’s own phenotype as well as phenotypes on relatives (including progeny, parents, and siblings, as an example). With Genetic Evaluation, all of this information is combined and weighted appropriately in a single value, the EPD, which simplifies selection. This same value is even more relevant in the genomics era, because genomic testing provides another source of information for selection. </div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>EPDs also simplify selection decisions. Selection using phenotypes can involve the individual’s own phenotype as well as phenotypes on relatives (including progeny, parents, and siblings, as an example). With <ins class="diffchange diffchange-inline">[[</ins>Genetic Evaluation<ins class="diffchange diffchange-inline">]]</ins>, all of this information is combined and weighted appropriately in a single value, the EPD, which simplifies selection. This same value is even more relevant in the genomics era, because genomic testing provides another source of information for selection. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The Beef Improvement Federation recommends using genomically-enhanced EPDs (see [[Single-step Genomic BLUP]] and [[Single-step Hybrid Marker Effects Models]]), as opposed to using disjoined marker scores and EPDs separately, as the best method for utilizing genomic data for selection<ref>Muir, WM. 2007. Comparison of genomic and traditional BLUP-estimated breeding value accuracy and selection response under alternative trait and genomic parameters. J. Anim Brdg Genet. 124(6):342-355.</ref>. Genetic Evaluation methodologies are always evolving and improving, but all of these methods incorporate all available data on an animal into EPD prediction, including genomic data, and weight it appropriately so that there is a single metric for genetic selection that represents the best estimate of that animal’s genetic merit using all available data. </div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The Beef Improvement Federation recommends using genomically-enhanced EPDs (see [[Single-step Genomic BLUP]] and [[Single-step Hybrid Marker Effects Models]]), as opposed to using disjoined marker scores and EPDs separately, as the best method for utilizing genomic data for selection<ref>Muir, WM. 2007. Comparison of genomic and traditional BLUP-estimated breeding value accuracy and selection response under alternative trait and genomic parameters. J. Anim Brdg Genet. 124(6):342-355.</ref>. Genetic Evaluation methodologies are always evolving and improving, but all of these methods incorporate all available data on an animal into EPD prediction, including genomic data, and weight it appropriately so that there is a single metric for genetic selection that represents the best estimate of that animal’s genetic merit using all available data. </div></td></tr>
</table>Mnielsenhttp://guidelines.beefimprovement.org/index.php?title=Expected_Progeny_Difference&diff=1788&oldid=prevMnielsen at 03:12, 10 December 20192019-12-10T03:12:23Z<p></p>
<table class="diff diff-contentalign-left diff-editfont-monospace" data-mw="interface">
<col class="diff-marker" />
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<col class="diff-marker" />
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<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 03:12, 10 December 2019</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l20" >Line 20:</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>===Interim EPDs===</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>===Interim EPDs===</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Most beef breed organizations and companies have transitioned to routinely perform their genetic evaluation. Often these routine analyses are performed as frequently as weekly. Prior to this change, many organizations performed genetic evaluations either annually or semi-annually, and thus interim EPD<ref>Wilson, D. E. and R. L. Willham. 1988. Interim Expected Progeny Differences for Young Animals Not Included in National Cattle Evaluations. Journal of Animal Science, Volume 66, Issue 3, March 1988, Pages 618–625, https://doi.org/10.2527/jas1988.663618x</ref> computations were done so that breeders could have at least an early estimate of genetic merit for selection decisions. As noted above, interim EPDs <del class="diffchange diffchange-inline">have been phased out with frequently scheduled evaluations</del>.</div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Most beef breed organizations and companies have transitioned to routinely perform their genetic evaluation. Often these routine analyses are performed as frequently as weekly. Prior to this change, many organizations performed genetic evaluations either annually or semi-annually, and thus interim EPD<ref>Wilson, D. E. and R. L. Willham. 1988. Interim Expected Progeny Differences for Young Animals Not Included in National Cattle Evaluations. Journal of Animal Science, Volume 66, Issue 3, March 1988, Pages 618–625, https://doi.org/10.2527/jas1988.663618x</ref> computations were done so that breeders could have at least an early estimate of genetic merit for selection decisions. As noted above <ins class="diffchange diffchange-inline">with more routine runs of the genetic evaluation</ins>, interim EPDs <ins class="diffchange diffchange-inline">now exist for shorter periods in an animal's life</ins>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>References: </div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>References: </div></td></tr>
</table>Mnielsenhttp://guidelines.beefimprovement.org/index.php?title=Expected_Progeny_Difference&diff=1787&oldid=prevMnielsen at 03:04, 10 December 20192019-12-10T03:04:04Z<p></p>
<table class="diff diff-contentalign-left diff-editfont-monospace" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 03:04, 10 December 2019</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l20" >Line 20:</td>
<td colspan="2" class="diff-lineno">Line 20:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>===Interim EPDs===</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>===Interim EPDs===</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Most beef breed organizations and companies have transitioned to routinely perform their genetic evaluation. Often these routine analyses are performed as frequently as weekly. Prior to this change, many organizations performed interim EPD<ref>Wilson, D. E. and R. L. Willham. 1988. Interim Expected Progeny Differences for Young Animals Not Included in National Cattle Evaluations. Journal of Animal Science, Volume 66, Issue 3, March 1988, Pages 618–625, https://doi.org/10.2527/jas1988.663618x</ref> computations so that breeders could <del class="diffchange diffchange-inline">timely receive updates using new data</del>.</div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Most beef breed organizations and companies have transitioned to routinely perform their genetic evaluation. Often these routine analyses are performed as frequently as weekly. Prior to this change, many organizations performed <ins class="diffchange diffchange-inline">genetic evaluations either annually or semi-annually, and thus </ins>interim EPD<ref>Wilson, D. E. and R. L. Willham. 1988. Interim Expected Progeny Differences for Young Animals Not Included in National Cattle Evaluations. Journal of Animal Science, Volume 66, Issue 3, March 1988, Pages 618–625, https://doi.org/10.2527/jas1988.663618x</ref> computations <ins class="diffchange diffchange-inline">were done </ins>so that breeders could <ins class="diffchange diffchange-inline">have at least an early estimate of genetic merit for selection decisions. As noted above, interim EPDs have been phased out with frequently scheduled evaluations</ins>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>References: </div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>References: </div></td></tr>
</table>Mnielsenhttp://guidelines.beefimprovement.org/index.php?title=Expected_Progeny_Difference&diff=1786&oldid=prevMnielsen at 02:58, 10 December 20192019-12-10T02:58:26Z<p></p>
<table class="diff diff-contentalign-left diff-editfont-monospace" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 02:58, 10 December 2019</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1" >Line 1:</td>
<td colspan="2" class="diff-lineno">Line 1:</td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The estimation of <del class="diffchange diffchange-inline">breeding values, which reflect </del>the value of an animal as a parent for the next generation, or Expected Progeny <del class="diffchange diffchange-inline">Differences </del>(EPD), which <del class="diffchange diffchange-inline">are </del>simply half of <del class="diffchange diffchange-inline">a </del>breeding value, was a major advancement in the ability to select animals to fit production goals. Prior to the development of EPDs the primary method for genetic improvement was some form of subjective visual appraisal<ref name="milestone" <ref>Golden, BL, DJ Garrick, and LL Benyshek. 2009. Milestones in beef cattle genetic evaluation. J Anim Sci. 87(E. Suppl.):E3-E10.</ref>. Since the development of methodology to implement Genetic Evaluation in the beef industry (launched in the 1970s)<ref name="milestone" />, EPDs have been the gold standard for genetic selection. Regardless of their associated [[Accuracy | accuracy]] value, they are the best selection tool that producers have to improve genetic merit in a single trait, though [[Selection Index| indices]] incorporate EPD information and are the best tools for <del class="diffchange diffchange-inline">multi</del>-trait selection. Nevertheless, there is often confusion surrounding the best tools and information on which to make selection decisions. </div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The estimation of the value of an animal as a parent for the next generation, or Expected Progeny <ins class="diffchange diffchange-inline">Difference </ins>(EPD), which <ins class="diffchange diffchange-inline">is </ins>simply half of <ins class="diffchange diffchange-inline">the animal's </ins>breeding value, was a major advancement in the ability to select animals to fit production goals. Prior to the development of EPDs the primary method for genetic improvement was some form of subjective visual appraisal<ref name="milestone" <ref>Golden, BL, DJ Garrick, and LL Benyshek. 2009. Milestones in beef cattle genetic evaluation. J Anim Sci. 87(E. Suppl.):E3-E10.</ref>. Since the development of methodology to implement Genetic Evaluation in the beef industry (launched in the 1970s)<ref name="milestone" />, EPDs have been the gold standard for genetic selection. Regardless of their associated [[Accuracy | accuracy]] value, they are the best selection tool that producers have to improve genetic merit in a single trait, though [[Selection Index| indices]] incorporate EPD information and are the best tools for <ins class="diffchange diffchange-inline">multiple</ins>-trait selection. Nevertheless, there is often confusion surrounding the best tools and information on which to make selection decisions. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Phenotypes for quantitative traits are a combination of influences from both genetics (additive, dominance, epistatic) and the environment (permanent and temporary). Alternatively, we can write this as an equation as follows:</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Phenotypes for quantitative traits are a combination of influences from both genetics (additive, dominance, epistatic) and the environment (permanent and temporary). Alternatively, we can write this as an equation as follows:</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l12" >Line 12:</td>
<td colspan="2" class="diff-lineno">Line 12:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>where P and μ are as previously defined, A represents additive genetic effects, D represents dominance, I represents epistasis, E<sub>P</sub> represents permanent environmental effects, E<sub>T</sub> represents temporary environmental effects, and GxE represents interactions between genotype and environment<ref name="Bourdon"/><ref>Pierce, BA. 2016. Genetics Essentials. Third edition. MacMillan, New York, New York.</ref>.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>where P and μ are as previously defined, A represents additive genetic effects, D represents dominance, I represents epistasis, E<sub>P</sub> represents permanent environmental effects, E<sub>T</sub> represents temporary environmental effects, and GxE represents interactions between genotype and environment<ref name="Bourdon"/><ref>Pierce, BA. 2016. Genetics Essentials. Third edition. MacMillan, New York, New York.</ref>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>EPDs <del class="diffchange diffchange-inline">describe </del>the additive genetic merit of an individual and reflect its value as a parent. It is important to remember that environmental influences are not heritable, and the only genetic influence that is known to be stably inherited <del class="diffchange diffchange-inline">at this time </del>is additive genetic variation, though dominance can be managed through crossbreeding systems. EPDs and indices are the best tools for genetic selection and do reflect average progeny performance<ref>Thrift, FA and TA Thrift. 2006. Review: Expected versus realized progeny differences for various beef cattle traits. Prof Anim Sci. 22:413-423.</ref><ref>Kuehn, LA and RM Thallman. 2017. Across-breed EPD tables for the year 2017 adjusted to breed differences for birth year of 2015. Proceedings of the Beef Improvement Federation Annual Meeting and Research Symposium. Pages 112-144.</ref>. </div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>EPDs <ins class="diffchange diffchange-inline">are a function of </ins>the additive genetic merit of an individual and reflect its value as a parent. It is important to remember that environmental influences are not heritable, and the only genetic influence that is known to be stably inherited is additive genetic variation, though dominance can be managed through crossbreeding systems. EPDs and indices are the best tools for genetic selection and do reflect average progeny performance<ref>Thrift, FA and TA Thrift. 2006. Review: Expected versus realized progeny differences for various beef cattle traits. Prof Anim Sci. 22:413-423.</ref><ref>Kuehn, LA and RM Thallman. 2017. Across-breed EPD tables for the year 2017 adjusted to breed differences for birth year of 2015. Proceedings of the Beef Improvement Federation Annual Meeting and Research Symposium. Pages 112-144.</ref>. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The challenge with selection on measures of phenotype is that they include both genetic and environmental effects, even if weights are adjusted and/or ratios (which limit comparisons to within contemporary groups) are utilized. When selection decisions are made on these metrics, selection emphasis is also placed on nongenetic factors, which reduces the efficacy of selection and reduces genetic progress. Superiority of selection using EPDs (or breeding values) as compared to phenotypes has been demonstrated<ref>Gall, GAE and Y Bakar. 2002. Application of mixed-model techniques to fish breed improvement: analysis of breeding-value selection to increase 98-day body weight in tilapia. Aquaculture. 212(1-4):93-113.</ref><ref>Kuhlers, DL and BW Kennedy. 1992. Effect of culling on selection response using phenotypic selection or best linear unbiased prediction of breeding values in small, closed herds of swine. J Anim Sci. 70(8):2338-2348.</ref><ref>Belonsky, GM and BW Kennedy. 1988. Selection on individual phenotype and best linear unbiased predictor of breeding values in a closed swine herd. J. Anim Sci. 66:1124-1131.</ref><ref>Hagger, C. 1991. Effects of selecting on phenotype, on index, or on breeding values, on expected response, genetic relationships, and accuracy of breeding values in an experiment. J Anim Breed Genet. 108:102-110.</ref>. </div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The challenge with selection on measures of phenotype is that they include both genetic and environmental effects, even if weights are adjusted and/or ratios (which limit comparisons to within contemporary groups) are utilized. When selection decisions are made on these metrics, selection emphasis is also placed on nongenetic factors, which reduces the efficacy of selection and reduces genetic progress. Superiority of selection using EPDs (or breeding values) as compared to phenotypes has been demonstrated<ref>Gall, GAE and Y Bakar. 2002. Application of mixed-model techniques to fish breed improvement: analysis of breeding-value selection to increase 98-day body weight in tilapia. Aquaculture. 212(1-4):93-113.</ref><ref>Kuhlers, DL and BW Kennedy. 1992. Effect of culling on selection response using phenotypic selection or best linear unbiased prediction of breeding values in small, closed herds of swine. J Anim Sci. 70(8):2338-2348.</ref><ref>Belonsky, GM and BW Kennedy. 1988. Selection on individual phenotype and best linear unbiased predictor of breeding values in a closed swine herd. J. Anim Sci. 66:1124-1131.</ref><ref>Hagger, C. 1991. Effects of selecting on phenotype, on index, or on breeding values, on expected response, genetic relationships, and accuracy of breeding values in an experiment. J Anim Breed Genet. 108:102-110.</ref>. </div></td></tr>
</table>Mnielsenhttp://guidelines.beefimprovement.org/index.php?title=Expected_Progeny_Difference&diff=1155&oldid=prevMrolf at 20:23, 26 June 20192019-06-26T20:23:01Z<p></p>
<table class="diff diff-contentalign-left diff-editfont-monospace" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 20:23, 26 June 2019</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l19" >Line 19:</td>
<td colspan="2" class="diff-lineno">Line 19:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The Beef Improvement Federation recommends using genomically-enhanced EPDs (see [[Single-step Genomic BLUP]] and [[Single-step Hybrid Marker Effects Models]]), as opposed to using disjoined marker scores and EPDs separately, as the best method for utilizing genomic data for selection<ref>Muir, WM. 2007. Comparison of genomic and traditional BLUP-estimated breeding value accuracy and selection response under alternative trait and genomic parameters. J. Anim Brdg Genet. 124(6):342-355.</ref>. Genetic Evaluation methodologies are always evolving and improving, but all of these methods incorporate all available data on an animal into EPD prediction, including genomic data, and weight it appropriately so that there is a single metric for genetic selection that represents the best estimate of that animal’s genetic merit using all available data. </div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The Beef Improvement Federation recommends using genomically-enhanced EPDs (see [[Single-step Genomic BLUP]] and [[Single-step Hybrid Marker Effects Models]]), as opposed to using disjoined marker scores and EPDs separately, as the best method for utilizing genomic data for selection<ref>Muir, WM. 2007. Comparison of genomic and traditional BLUP-estimated breeding value accuracy and selection response under alternative trait and genomic parameters. J. Anim Brdg Genet. 124(6):342-355.</ref>. Genetic Evaluation methodologies are always evolving and improving, but all of these methods incorporate all available data on an animal into EPD prediction, including genomic data, and weight it appropriately so that there is a single metric for genetic selection that represents the best estimate of that animal’s genetic merit using all available data. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">===Interim EPDs===</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Most beef breed organizations and companies have transitioned to routinely perform their genetic evaluation. Often these routine analyses are performed as frequently as weekly. Prior to this change, many organizations performed interim EPD<ref>Wilson, D. E. and R. L. Willham. 1988. Interim Expected Progeny Differences for Young Animals Not Included in National Cattle Evaluations. Journal of Animal Science, Volume 66, Issue 3, March 1988, Pages 618–625, https://doi.org/10.2527/jas1988.663618x</ref> computations so that breeders could timely receive updates using new data.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Most beef breed organizations and companies have transitioned to routinely perform their genetic evaluation. Often these routine analyses are performed as frequently as weekly. Prior to this change, many organizations performed interim EPD<ref>Wilson, D. E. and R. L. Willham. 1988. Interim Expected Progeny Differences for Young Animals Not Included in National Cattle Evaluations. Journal of Animal Science, Volume 66, Issue 3, March 1988, Pages 618–625, https://doi.org/10.2527/jas1988.663618x</ref> computations so that breeders could timely receive updates using new data.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
</table>Mrolf