Estimation of covariance components between one continuous and one binary trait

International audienc

Comparison of traditional and genomic breeding programs for organic and low input dairy cattle accounting for traits relevant in different macro-climatic zones

In the past decade, successful selection on production traits for dairy cattle has greatly increased milk production. Recently, selection indices for female fertility were gradually and increasingly introduced into the overall breeding goals for dairy cattle (Miglior et al., 2005). As a by-product of fermention in ruminants, enteric methane emissions (ME) should also be controlled and mitigated due to their contribution to global warming (Forster et al., 2007) and as a cause for inefficient use of dietary energy. Moderate heritabilities ranging between 0.30 and 0.35 for predicted and real measurements of ME were reported for dairy cows and ewe lambs (de Haas et al., 2011; Pinares-Patiño et al., 2011), indicating that a heritable component for ME is available for implementing sustainable breeding strategies to reduce ME in dairy farms. In dairy cattle production systems, the traditional progeny testing substantially increases accuracy of selection especially for bulls. However, availability of high-density SNP arrays enable dairy cattle breeders to apply genomic selection in their breeding strategies. Consequently, the objective of this study was to compare selection response for a complex breeding goal comprising ME, milk yield (MY), days open (DO), clinical mastitis (CM), body condition score (BCS) and milking temperament (MT) and total discounted return for organic and low input dairy cattle (with organic Brown Swiss as an example) from progeny testing and genomic breeding program by applying ZPLAN+ (Täubert et al., 2010)

Genetische Parameter für verschiedene euterviertelspezifische Merkmale beim Schweizer Braunvieh

Fragestellung: - Gibt es Unterschiede und Regelmäßigkeiten in den genetischen Parametern für die Milchinhaltsstoffe zwischen den Eutervierteln? - Lassen sich diese Informationen züchterisch nutzen

Estimation of genomic breeding values for traits with high and low heritability in Brown Swiss bulls

This paper was written in the framework of the LowInputBreeds project: “Development of integrated livestock breeding and management strategies to improve animal health, product quality and performance in European organic and ‘low input’ milk, meat and egg production”. The LowInputBreeds project unites 21 partners from Europe and further afield and will develop integrated breeding and management strategies to tackle the issue of improved animal health and food quality. It will run until 2014 and is co-funded by the European Union’s Seventh Framework Programme for Research and Technological Development

Accuracy of 54K to HD gebotype imputation in Brown Swiss cattle

Imputation of genotypes can be used to reduce the implementation costs of genomic selection. In this study, we evaluated the accuracy of genotype imputation from Illumina 54k to Illumina High Density (HD) in Brown Swiss cattle. Genotype data comprised 6,106 54k and 880 HD genotyped bulls and cows of Brown Swiss and Original Braunvieh cattle. Genotype data was checked for parentage conflicts and SNP were excluded if MAF was below 0.5% and SNP call rate was lower than 90%. The final data set included 39,004 SNP for the 54k and 627,306 SNP for the HD chip. HD genotypes of animals born between 2004 and 2008 (n=365) were masked to mimic animals genotyped with the 54k chip. Methods used for imputation were FImpute and Findhap V2. Both programs use pedigree information for imputation. The accuracy of imputation was assessed by the correlation (r) between true and imputed genotypes, the percentage of correctly and incorrectly imputed genotypes. Both programs gave high imputation accuracy with FImpute outperforming Findhap. Accuracy of imputation increased with increasing relationship between the HD genotyped reference population and 54k genotyped imputation candidates. Average r for FImpute and Findhap were 0.992 and 0.988 when both parents of the 54k genotyped candidate were HD genotyped, respectively. Correlations were lower when no direct relatives were HD genotyped (0.971 and 0.918 for FImpute and Findhap, respectively). Accuracy of imputation highly depended on MAF of the imputed SNP. For FImpute, average r ranged between 0.89 (MAF <0.025) and 0.99 (MAF between 0.4 and 0.5)

Efficiency of different selection strategies against boar taint in pigs

The breeding scheme of a Swiss sire line was modeled to compare different target traits and information sources for selection against boar taint. The impact of selection against boar taint on production traits was assessed for different economic weights of boar taint compounds. Genetic gain and breeding costs were evaluated using ZPlan+, a software based on selection index theory, gene flow method and economic modeling. Scenario I reflected the currently practiced breeding strategy as a reference scenario without selection against boar taint. Scenario II incorporated selection against the chemical compounds of boar taint, androstenone (AND), skatole (SKA) and indole (IND) with economic weights of −2.74, −1.69 and −0.99 Euro per unit of the log transformed trait, respectively. As information sources, biopsy-based performance testing of live boars (BPT) was compared with genomic selection (GS) and a combination of both. Scenario III included selection against the subjectively assessed human nose score (HNS) of boar taint. Information sources were either station testing of full and half sibs of the selection candidate or GS against HNS of boar taint compounds. In scenario I, annual genetic gain of log-transformed AND (SKA; IND) was 0.06 (0.09; 0.02) Euro, which was because of favorable genetic correlations with lean meat percentage and meat surface. In scenario II, genetic gain increased to 0.28 (0.20; 0.09) Euro per year when conducting BPT. Compared with BPT, genetic gain was smaller with GS. A combination of BPT and GS only marginally increased annual genetic gain, whereas variable costs per selection candidate augmented from 230 Euro (BPT) to 330 Euro (GS) or 380 Euro (both). The potential of GS was found to be higher when selecting against HNS, which has a low heritability. Annual genetic gain from GS was higher than from station testing of 4 full sibs and 76 half sibs with one or two measurements. The most effective strategy to reduce HNS was selecting against chemical compounds by conducting BPT. Because of heritabilities higher than 0.45 for AND, SKA and IND and high genetic correlations to HNS, the (correlated) response in units of the trait could be increased by 62% compared with scenario III with GS and even by 79% compared with scenario III, with station testing of siblings with two measurements. Increasing the economic weights of boar taint compounds amplified negative effects on average daily gain, drip loss and intramuscular fat percentag

Ökologische Milchviehzucht: Entwicklung und Bewertung züchterischer Ansätze unter Berücksichtigung der Genotyp x Umwelt-Interaktion und Schaffung eines Informationssystems für nachhaltige Zuchtstrategien

In dem Projekt wurden für verschiedene Merkmalskomplexe an zwei verschiedenen Datensätzen Genotyp x Umwelt-Interaktionen zwischen ökologischen und konventionellen Produktionssystemen geschätzt. Anhand Schweizer Daten wurden für Braunvieh und Fleckvieh für Milchleistungsmerkmale Korrelationen > 0.9 zwischen beiden Betriebsformen geschätzt, wohingegen die genetische Korrelationen für funktionale Merkmale (Rastzeit, Zellzahl) geringer (0.8 bis 0.9) waren. Diese Korrelationen konnten für die Rasse Holstein Friesian auf Grund einer Auswertung Deutscher Daten bestätigt werden. Generell liegt für Leistungsmerkmale keine und für funktionale Merkmale eine geringe Genotyp x Umwelt-Interaktion zwischen ökologischen und konventionellen Betrieben vor, wobei insbesondere für letztere die Informationsbasis begrenzt ist. Auswertungen der Betriebsdaten von > 450 ökologisch wirtschaftenden Milchviehbetrieben und Befragungen der Betriebsleiter haben ergeben, dass sich diese Betriebe in ihren züchterischen Zielen kaum und in ihrem züchterischen Handeln gar nicht von konventionellen Betrieben unterscheiden. Zuchtplanerische Rechnungen haben ergeben, dass unter den gefundenen genetischen Parametern weder ein geschlossenes noch ein offenes eigenes Zuchtprogramm im ökologischen Sektor wirtschaftlich gerechtfertigt ist. Vielmehr ist anzustreben, dass sich ökologisch wirtschaftende Milchviehbetriebe stärker aktiv an etablierten Zuchtprogrammen beteiligen, z.B. durch den stärkeren Einsatz von Testbullen. Es wird vorgeschlagen, aufgrund der bestehenden Teilzuchtwerte einen Ökologischen Gesamtzuchtwert zu entwickeln, in dem funktionale Merkmale stärker gewichtet werden. Ein im Projekt entwickeltes Internetportal und eine entsprechend angepasste Anpaarungssoftware kann die Umsetzung dieses Vorschlags unterstützen. Erforderlich ist allerdings eine vollständigere Erfassung der ökologischen Milchviehbetriebe als Voraussetzung für eine bessere Unterstützung der ökologischen Milchviehzucht