https://genepi.qimr.edu.au/contents/p/staff/CVPV051.pdf

Bias and Power in the Estimation of a Maternal Family Variance Component in the Presence of Incomplete and Incorrect Pedigree Information

Data from the official milk recording scheme of the Austrian Simmental population were analysed to estimate variance components due to genomic imprinting. Traits regarded were milk yield, fat and protein content, persistency, days open (first, second and third lactation) and herd life. All dairy traits were preadjusted for BLUP herd-year effects. After applying some data restrictions, the number of records ranged from 3391 (persistency, third lactation) to 33 993 (days open, first lactation). Two different estimation approaches were used: (i) estimation of the maternal and paternal gametic component by a dam and sire model, respectively, and (ii) estimation of the animal and an additional gametic component (maternal or paternal) by treating gametes as homozygous diploid individuals. All models also accounted for year of first calving and the cytoplasmic effect of maternal lineages. In tendency, the results of both approaches were fairly well in line with each other. For the majority of the investigated traits, no substantial imprinting effects were detected. Significant evidence of genomic imprinting on a multiple type I error ≤ 0.10 was only found for protein content and days open. For protein content in the second and third lactation, the proportions of variance due to the paternal gametic effect exceeded those of the maternal by 0.096 and 0.152, respectively. For days open in the second lactation, however, the proportion of variance of the maternal gamete effect exceeded that of the paternal by 0.036. In tendency, indication of paternal imprinting was found for all fitness-related traits. For true and functional herd life, significant differences (pairwise type I error ≤ 0.05) of 0.040 and 0.032 were found between the proportions of variance due to the maternal and paternal gamete effect. Significant variance components of cytoplasmic effects (multiple type I error ≤ 0.01) were found for first lactation of milk yield (0.020), for first, second and third lataction of persistency (0.026, 0.035 and 0.033) and of days open (0.029, 0.016 and 0.022) and for true and functional herd life (0.019 and 0.029).

Genomic imprinting effects on dairy- and fitness-related traits in cattle

Treating gametes as homozygous diploid individuals, TIER and SOLKNER (Theor. Appl. Genet. 85: 868–872, 1993) proposed a method which manages the use of available computer programs with a common animal model to estimate variance components caused by imprinting effects. Despite some relevant model restrictions, this approach has already been used in some field data analyses by an adapted version of the widely used DFREML computer program, subsequently indicated by DFREMLa. The main objective of this study was to ascertain the properties of DFREMLa by computer simulation and to examine other alternative estimation approaches. The most important results may be summarized as follows:



(1) Treating gametes as homozygous diploid individuals has the consequence that one-half of the actually realized gametic effect is totally abstracted in variance component estimation. Thus, an additional adjustment of the phenotypic variance calculated by DFREMLa is necessary to get correct values of estimated variance component ratios.



(2) Adjusted DFREMLa estimates yielded correct results when animals were unselected and only maternal or paternal imprinting (not both simultaneously) occurred.



(3) When the model did not adequately account for the additive genetic component within a maternal lineage, significant upward biases for the cytoplasmic component were observed.



(4) The use of a simple dam and sire model with appropriate relationship matrices can be recommended when only the difference of maternal and paternal imprinting effects is of primary interest and the covariance between maternal halfsibs is not substantially increased by common environmental effects.



(5) An adequate estimation of variance components for all possible imprinting situations requires the use of an animal model augmented by both maternal and paternal gametic effects. Unfortunately, a computer program on the basis of such a model does not yet exist.



Schatzung von Varianzkomponenten fur Imprintingeffekte mittels DFREML und VCE: Ergebnisse einer Simulationsstudie



TIER and SOLKNER (Theor. Appl. Genet. 85: 868–872, 1993) schlugen eine Methode zur Schatzung von imprintingbedingten Varianzkomponenten vor, die mit einem einfach zu adaptierenden Computerprogramm auf der Basis eines ublichen Tiermodells vorgenommen werden kann, indem sie Gameten wie homozygot diploide Individuen behandelten. Obwohl dieser Ansatz einige praxisrelevante Einschrankungen hat, wurde er bereits bei einigen Felddatenanalysen verwendet. Fur diesen Zweck wurde eine entsprechend adaptierte Version des haufig verwendeten Computerprogrammes DFREML eingesetzt, die im folgenden mit DFREMLa bezeichnet wird. Das Ziel der vorliegen Untersuchung lag darin, die Eigenschaften von DFREMLa bei verschiedenen Imprintingsituationen zu uberprufen und weiters die Brauchbarkeit anderer moglicher Schatzansatze zu uberprufen.



(1) Werden Gameten wie diploide homozygote Individuen aufgefast, dann geht bei der Schatzung von Varianzkomponenten mit DFREMLa eine Halfte des tatsachlich wirksamen Gameteneffektes vollig verloren. Das heist, die von DFREMLa ausgewiesenen Ergebnisse mussen nachtraglich entsprechend adjustiert werden, um korrekte Schatzergebnisse fur alle jene Quotienten von Varianzkomponenten zu erhalten, bei denen die gesamte phanotypische Varianz im Nenner steht.



(2) Die adjustierten DFREMLa Schatzwerte lieferten in all jenen Fallen korrekte Ergebnisse, wo keine Selektion der Tiere erfolgte und entweder nur maternales oder paternales Imprinting (nicht beide gleichzeitig) auftrat.



(3) Alle Modelle, bei denen die additiv genetische Komponente innerhalb einer Kuhfamilie keine adaquate Berucksichtigung fand, fuhrten zu einer systematischen Uberschatzung der zytoplasmatischen Varianzkomponente.



(4) Ist nur jene Varianzkomponente von Interesse, die durch unterschiedlich starkes maternales bzw. paternales Imprinting erklart werden kann, dann kann auch die Verwendung einfacher Vater-bzw. Muttermodelle empfohlen werden. Voraussetzung hierfur ist allerdings, das die Kovarianz zwischen mutterlichen Halbgeschwistern durch keine gemeinsame Umwelt erhoht ist.



(5) Eine fur alle Imprintingsituationen problemadaquate Schatzung von Varianzkomponenten verlangt die Anwendung eines Tiermodelles, erweitert um beide imprintingbedingten Gameteneffekte. Leider fehlt gegenwartig hierfur noch ein entsprechendes Computerprogramm.

Estimation of variance components due to imprinting effects with DFREML and VCE: results of a simulation study

Data on 4477 mares born between 1932 and 1995 from six studs were recorded. Three exterior traits were included: height at wither, chest girth, circumference of cannon. (Co)variance components were estimated by the DFREML procedure on the basis of four linear models. Model I included the fixed effects: period of birth, place of birth, breed effect (as covariable) and random effects: direct additive genetic and residuals. Model II was expanded by taking into account the maternal additive genetic effect. Third model included cytoplasmic effect as fixed (model IIIa) and random (model IIIb). Direct heritability estimates varied from 0.4 to 0.6 whereas maternal heritability estimates ranged between 0.01 and 0.25, cytoplasmic heritabilities were close to zero. Negative correlations between direct and maternal effects were estimated for all traits under study. Akaike Information Criterion suggested the highest adequacy of model I. However, other criteria (likelihood ratio test and error variance estimate) and negative covariance between direct and maternal genetic effects indicate that maternal effects should be included in the genetic evaluation of horses. In general, genetic trends were positive for the traits studied.

http://www.jafs.com.pl/pdf-67135-6285?filename=Maternal effects on the.pdf

Maternal effects on the conformation traits in half-bred horses

Fil: Mezzadra, Carlos Alberto. Instituto Nacional de Tecnologia Agropecuaria. Centro Regional Buenos Aires; Argentina

/pdf/effects-of-cytoplasmic-inheritance-on-preweaning-traits-of-4xcbran89z.pdf

Effects of cytoplasmic inheritance on preweaning traits of Hereford cattle

Field data of the Austrian Simmental population were analysed using restricted maximum likelihood (REML) with an animal model where additive direct, additive maternal and cytoplasmic effects were treated as random and the effect of the year of first calving as fixed. Traits analysed were milk yield, fat and protein content, persistency, days open and herd life. All dairy traits were pre-adjusted for best linear unbiased prediction (BLUP) herd-year effects, milk yield additionally for season, age at first calving and days open. After applying specific data restrictions, the number of records for the various traits ranged from 3360 to 51889. Identification of cow lineages was based on pedigree information from the official milk recording scheme, with a span of at least four and up to 16 generations. The number of lineages per trait varied and ranged from 484 to 3195, with an average size of 15 members (for herd life 7). Evaluations of the relevant variance components for the dairy and fitness-related traits investigated were separate for the first three lactations. The estimated variance components for cytoplasmic effects were close to zero for all dairy traits with the exception of first lactation milk yield, where a significant value of 2.0% of the total phenotypic variance was found. Significant contributions of cytoplasmic lineages to total variance in all lactations, however, were estimated for persistency (2·6 to 3.8%), days open (1·8 to 2.9%) and for both true and functional herd life (4.6% each). The portions of additive maternal variance and covariance between additive direct and additive maternal effects on total variance were very close to zero for all traits investigated. The maximum differences between BLUP lineage effects were 373 kg for first lactation milk yield, 44 days for days open (first lactation), 1·6 and 2·8 years for true and functional herd life and, on average, 1·0 kg for standard deviation of test day milk yields (persistency) of the first three lactations. Removing the cytoplasmic effect from the model led to increased estimates of the additive direct heritability. Further model aspects such as interaction between additive and cytoplasmic gene effects and possible confounding between cytoplasmic and herd effects are discussed.

Field data analysis of cytoplasmic inheritance of dairy and fitness-related traits in cattle

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Field data analysis of cytoplasmic inheritance of dairy and fitness-related traits in cattle