{"id":5414,"date":"2022-09-29T10:12:18","date_gmt":"2022-09-29T08:12:18","guid":{"rendered":"https:\/\/qualitasag.ch\/?p=5414"},"modified":"2022-09-29T10:12:18","modified_gmt":"2022-09-29T08:12:18","slug":"wcgalp-methodology","status":"publish","type":"post","link":"https:\/\/qualitasag.ch\/en\/wcgalp-methodology\/","title":{"rendered":"WCGALP – Methodology"},"content":{"rendered":"

The topic of methodology in genomic EBVs was also very prominent at this conference. Already in the first plenary session, Mario Calus pointed out that this year, for the first time, more papers were submitted on genomic prediction than on GWAS and QTL prediction (Figure 1).<\/span><\/span><\/span>\u00a0<\/span><\/p>\n

On the one hand, there were sessions that were specifically dedicated to the topic of \u201cMethods and Tools\u201d. <\/span>T<\/span>he topic \u201cGenomic Selection\u201d, <\/span>in particular single<\/span>–<\/span>step<\/span> breeding value estimation, was also repeatedly addressed in <\/span>additional<\/span> sessions. <\/span><\/span>\u00a0<\/span><\/p>\n<\/div><\/div>

As a first <\/span>example<\/span>, Daniela Lourenco from the <\/span>University<\/span> of Georgia <\/span>presented<\/span> the further development of <\/span>the BLUPF90 programs<\/a><\/span><\/span>. This well-known program package was fundamentally revised. It can be used mainly for variance component estimation and traditional and genomic <\/span><\/span><\/span>breeding value estimation. However, it can also be used to perform many upstream and downstream processes that are important for the above methods.<\/span><\/span><\/span><\/p>\n<\/div><\/div><\/div><\/div><\/div>

\"\"<\/div><\/div>
<\/div><\/div>

Figure 1: <\/span>M.Calus<\/span> WCGALP 2022 Number of submitted papers on GWAS\/QTL (blue) and Genomic Prediction (red)<\/span>.<\/span><\/span>\u00a0<\/span><\/em><\/p>\n<\/div><\/div><\/div><\/div><\/div><\/div><\/div><\/section>

\"\"<\/div><\/div>

Figure 2: (Frischknecht et al. 2016, EAAP Belfast): Accuracy of genomic EBV with different marker densities compared to 50k density for the traits NRH: non-return rate bovine, SCS: somatic cell score and STA: sacral height.<\/span><\/span><\/span>\u00a0<\/span><\/em><\/p>\n<\/div><\/div><\/div><\/div><\/div>

In the session \u201cChallenges \u2013 Use of whole genome sequence information\u201d several contributions were shown on how to optimize the selection of markers for genomic selection. Several years ago, we argued that there is little gain in accuracy if all imputed sequence variants are considered. This basic finding <\/span><\/span><\/span>was<\/span><\/span><\/span> confirmed by several presentations in this session and new methods for the selection of an optimal marker set <\/span><\/span><\/span>were<\/span><\/span><\/span> presented.\u00a0<\/span><\/span><\/span>\u00a0<\/span><\/p>\n<\/div><\/div><\/div><\/div><\/div><\/div><\/div><\/section>

\"\"<\/div>

single-step breeding value estimation<\/h1>
\n

In singl<\/span>e<\/span>–<\/span>step breeding value estimation, genomic and phenotypic information is processed simultaneously. <\/span>This new methodology is becoming the gold standard for new<\/span>,<\/span> as well as<\/span> for<\/span> traditional<\/span>,<\/span> traits<\/span>.<\/span><\/p>\n<\/blockquote>\n

 <\/p>\n

Minna Koivula from LUKE gave a short presentation on how breeding values for milk yield traits were estimated in the Nordic Holstein breeds using the so-called <\/span>ssGTBLUP<\/span> model (a special form of single-step breeding value estimation) and Meta-Founders. Meta-Founders is used to model the genetics of animals that have no parental information in the pedigree. In this presentation<\/a>, it was additionally shown how the information of foreign animals can be considered<\/span>.<\/span><\/span>\u00a0<\/span><\/p>\n

Single step breeding value estimation does not stop at beef cattle. The presentation <\/span><\/span><\/span>\u201cAccuracy of pedigree and genomic predictions of meat quality in a multi-breed cattle using single and two step model\u201d<\/a> <\/span><\/span><\/span>highlighted the importance of this new methodology for traits that are difficult to capture, such as “meat eating quality”, which includes tenderness, juiciness and flavor. This set of traits is extremely relevant to consumers. The reliability of <\/span><\/span><\/span>EBVs<\/span><\/span><\/span> can be improved with genomic information. The genomic breeding values for “meat eating quality” with the single-step method are now routinely published in Ireland.<\/span><\/span><\/span>\u00a0<\/span><\/p>\n<\/div><\/div><\/div><\/div><\/div><\/div><\/div><\/div><\/section>

\"\"<\/div>

“beef-on-dairy”<\/h1>

Increasingly, dairy cows are being bred with beef cattle. This is called <\/span><\/span><\/span>“beef-on-dairy”. Tools are being developed to obtain good predictions for this as well. An example of this was presented at the talk “Decision support tools to support a more sustainable beef-on-dairy industry”<\/a><\/span><\/span><\/span>. Three methods have been developed in Ireland. The first is the Dairy Beef Index (DBI), which identifies elite beef cattle for dairy. Thanks to this index, birth traits and slaughter traits can be improved simultaneously. The second tool allows ranking of <\/span>matings<\/span>. With the third, the resulting progeny are ranked according to their market value. By combining these three tools, both the profitability and sustainability of the beef-on-dairy system can be improved.\u00a0<\/span><\/span><\/span>\u00a0<\/span><\/p>\n<\/div><\/div><\/div><\/div><\/div><\/div><\/div><\/div><\/section>

\"\"<\/div>

Conclusion<\/h1>

In summary, the full range of developments and applications of single-step breeding value estimation were presented at the World Congress. It is worth looking through the program<\/a> and reading individual papers.<\/span><\/span><\/span>\u00a0<\/span><\/p>\n<\/div><\/div><\/div><\/div><\/div><\/div><\/div><\/div><\/section>\n","protected":false},"excerpt":{"rendered":"The topic of methodology in genomic EBVs was also very prominent at this conference. Already in the first plenary session, Mario Calus pointed out that this year, for the first time, more papers were submitted on genomic prediction than on GWAS and QTL prediction (Figure 1).\u00a0 On the one hand, there were sessions that were...","protected":false},"author":17,"featured_media":5091,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[291],"tags":[409,407,408],"class_list":["post-5414","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-uncategorized","tag-beef-on-dairy-en","tag-methodology","tag-single-step"],"yoast_head":"\nWCGALP - Methodology - Qualitas AG<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/qualitasag.ch\/en\/wcgalp-methodology\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"WCGALP - 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