Genetic grouping for direct and maternal effects with differential assignment of groups

HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés. Genetic grouping for direct and maternal effects with differential assignment of groups Rjc Cantet, Rl Fernando, D Gianola, I Misztal

Summary -Genetic grouping in additive models with maternal effects is extended to cover differential assignment of groups for direct and for maternal effects. Differential grouping provides a means for including genetic groups in animal evaluations when, for example, genetic trends for additive direct and for maternal effects are different. The cxl l 'lIsion is based on including the same animals in both vectors of additive direct and additive maternal effects, and on exploiting the resulting Kronecker structure so as to adapt the rules of Quaas when maternal effects are absent. Computations can be performed while reading pedigree data, and no matrix manipulations are involved. An example is presented to illustrate the computations. Extension of the procedure to accommodate multiple traits is indicated. genetic groups / direct and maternal effects / animal model / best linear unbiased prediction (BLUP) Résumé -La constitution de groupes génétiques avec affectation différentielle selon les effets directs et maternels. La constitution de groupes génétiques dans le cadre de modèles additifs avec effet maternel est généralisée à une affectation différentielle à des groupes selon les effets directs et maternels. Ce regroupement différentiel fournit une méthode pour inclure les groupes génétiques dans l'évaluation des animaux quand, par exemple, les progrès génétiques pour les effets directs et maternels sont différents. Cette généralisation est basée sur l'inclusion des mêmes animaux dans les 2 vecteurs d'effets additifs directs et maternels et sur l'exploitation des structures de Kronecker résultantes, INTRODUCTION Genetic grouping is a means for dealing with incomplete pedigree information in genetic evaluation (Quaas, 1988). The theory developed for additive effects (Quaas, 1988;Westel et al, 1988) was extended to accommodate maternal effects by Van Vleck (1990), but this author considered only the situation where the unknown parents are assigned to the same groups for direct and maternal effects. He also warned about possible singularities introduced by grouping when solving the mixed model equations (Henderson, 1984).
Grouping animals is often a subjective process (Quaas and Pollak, 1981;Henderson, 1984;Quaas, 1988) in which individuals are assigned to different populations (groups) based on some attribute such as year of birth. Genetic grouping is somewhat less arbitrary in the sense that only unknown parent animals are assigned to groups (Quaas, 1988). When there are maternal effects, every unknown parent must be assigned to a group for direct effects and to a group for maternal effects, and there may be situations in which the criteria for constructing groups for the direct effects differ from those used for the maternal effects. An example is when genetic trends for direct and for maternal effects are different. The objective of this study is to extend the theory of genetic grouping in models with maternal effects so as to allow for differential criteria to be used when assigning groups for directs effects and groups for maternal effects. THEORY Let y j be a record made by individual i with dam j. After Willham (1963) and Quaas and Pollak (1980), an additive model for the maternally influenced record Yi j is: where x' is a row of the incidence matrix relating the record of individual i to an unknown vector p of fixed effects, aoi is the direct breeding value (BV) of i for direct effects, a mj is the BV of dam j for maternal effects, e mj is an environmental contribution common to all progeny raised by j and e oi is an environmental deviation peculiar to the record made by individual i. The model is such that a oi , a mj , e oi are random variables with Var(a o i) _ o-2 A o , Var(a mj ) !A!m cov(aoi, anx!) = rijUAoAm! Var(en,!) _ u2 , m and Va r ( eoi ) _ o,20;rij is the additive relationship between i and j, a ij being equal to 1/2 in this case. All random variables are assumed to be mutually independent, with the exception of a oi and a mj . The E(y2!) is described in Mixed model equations.
The BV's for direct and maternal effects of any individual can be described as the average of the BV's of its parents plus an independently distributed Mendelian sampling residual 0 (Bulmer, 1985). Letting k be the sire of i, the direct BV of i is: In the same way, the maternal BV of i is: Following Quaas (1988), in the absence of inbreeding Var(<p o i) = 1/2 cr!, and Var ( § mj ) = 1/2lT!m' Also: because k and j are unrelated. From the preceding, cov(<!ot)!mt) == 1/2(TAoAn7,-Let the positive-definite matrix Go be: The animal model with groups and relationships (Robinson, 1986;Quaas, 1988;Westell et al 1988; is based on arranging BV's of all animals into 2 different vectors, a and a b . Every identified individual in the pedigree has a direct BV in the a x 1 vector a o and a maternal BV in the a x 1 vector a m such that a' = [a!, a' ) . Unknown animals (parents) from which individuals in a are derived have their BV's represented in the 2b x 1 vector ab = [a 0 , ab&dquo;1!. These are the &dquo;base&dquo; population animals, and they are assumed each to have a single progeny represented in a. Let P 6 (of order a x b) and P (of order a x a) be matrices relating BV of progeny to BV of unknown and identified individuals, respectively.
If base animals were known, a matrix version of [2] and [3] would be given by a = (1 2 0 P)a + !, where. is a vector that results from stacking the Mendelian residuals for direct and maternal effects. As in Quaas (1988), it will be assumed that Mendelian residuals have expectation E(!) = 0 and, because no inbreeding is assumed, Var (!) = 1/2 Go 0 I a . This variance-covariance matrix follows from expression (4!. If there is inbreeding, the matrix I a must be replaced by a diagonal matrix with elements d ii = 1/2 -(F si + F D: )/4, where Fs i and F Di are the inbreeding coefficients of the sire and the dam of individual i.
The vector a is better represented conceptually (Quaas, 1988) by the expression: Rearranging: and solving for a: The base animals are assumed to be drawn at random from the distribution where Q 6 relates base animals to the &dquo;base&dquo; population means, g. Hence, base animals are unrelated but do not necessarily have the same mean. More explicitly: where go and g m are the &dquo;base&dquo; mean vectors for direct and maternal effects, respectively, and the matrices Q bo and Q bm relate base animals to their respective population means. In general, Q bo and Qb! may be different, even though including the same animals in a o and in a m forces a bo and a bm to correspond to the same base animals.
To exemplify, consider the following pedigree: Capital letters denote identified individuals and lower case letters the unknown or &dquo;phantom&dquo; parents. Symbols in parentheses indicate group (direct, maternal) of the unknown parents. There are 2 groups for direct effects (D 1 and D 2 ) and 2 groups for maternal effects (M i and M 2 ); note that some unknown parents (a, d) have been assigned to different groups for direct and maternal effects. The matrix The matrix Q 6 is: This formulation allows the rules of Quaas to be extended (1988) for writing the mixed model equations for an animal model with genetic groups for direct and maternal effects in a simple way.
Expectation of a Using [5], we have: for Q = 11 2 &reg; (I a -P) !P;)]Qb. The rectangular matrix Q is made of 2 blocks: (I a -P P bQbo and (I a -P)-'P bQb ,,,. The first block is the same as in Quaas (1988) (William, 1963). If an animal with a record in y has an unidentified (&dquo;phantom&dquo;) dam, mis-specification of Var (y) results due to taking those additive relationships as if there were zero. One solution is to include the BV for direct and maternal effects of the &dquo;phantom&dquo; dam of the individual in a o and a!, respectively. Note that this has the effect of increasing the size of the system of equations by twice the number of unknown dams of individuals with records in y. Maternal environmental effects of &dquo;phantom&dquo; dams may also be included in e m to force u5!__ to be present in the variance of animals with a record in y and with an unknown dam, as discussed by Henderson (1988 and, on using Q = (I 2 &reg; (I a -P)-1 P b )Q b and G-1 as in (10), the above expression is equal to: Note that H can be written as: where d-1 is diagonal element k of matrix D-1 and h!:k (see 14) is the kth row of H i . Most elements in each of these rows are zeroes except for 2 negative halves (corresponding to a sire or a sire base group and to a dam or a base dam group) and a one (corresponding to the individual). The first a rows correspond to direct effects and the rest to maternal effects.
Expression [14] shows that the 3 non-zero elements in each row of H make each known individual to &dquo;contribute&dquo; 36 times (= 3 2 x 2 x 2) to the &dquo;genetic&dquo; part of A * . The contributions can be described letting i, f, j, k, I and m represent the row or column or A * associated with: i = direct effect of an individual; f = maternal genetic effect of the same individual; j = direct effect of the sire of the individual if the sire is known, or group for direct effects of the unknown sire; k = direct effect of the dam of the individual if the dam is known, or group for direct effects of the unknown dam; I = genetic maternal effect of the sire of the individual if the sire is known, or group for maternal effects of the unknown sire; m = genetic maternal effect of the dam of the individual if the dam is known, or group for maternal effects of the unknown dam. Therefore, the 36 contributions result from all pairwise combinations of the above subscripts. As in Quaas (1988), let , = 0, 1 or 2 be the number of unknown parents of i and x = 4/(!, + 2) and put: Then, each known individual makes the following contributions which are added to the &dquo;genetic&dquo; part of A&dquo;: Using these rules plus !15!, the contributions of each animal to elements of the &dquo;genetic&dquo; part of A&dquo;, for the example, are displayed in table I.
Using these contributions the &dquo;genetic&dquo; part of A * is: The algorithm can,,,be extended to multiple.traits, <as pomted= out ' -by -a referee, as follows. Let: i i = equation number of individual i for the lth trait; j i = equation number of the sire of i or its sire's group (if base sire) for trait l ; k i = equation number of the dam of i or its dam's group (if base dam) for trait I.
Let s = d, l, 2, be the number of base parents of i. For each animal calculate -! = 41(s + 2). Finally, letting t be the number of traits, for m = 1 to t and n = 1 to t, add to A * the following 9 contributions: where gmn is element (m, n) of the inverse of the t x t matrix of additive variances and covariance among the t traits. Note that for t = 2 there are 4 passes through the loops of m and n, resulting in 9 x 4 = 36 contributions, as in the case of direct and maternal effects.

DISCUSSION
The procedure presented here allows for different criteria to be used when assigning genetic groups for direct and for maternal effects. If groups for direct and maternal effects are assigned using the same criterion, our formulation gives the same results as those of Van Vleck (1990). The method can be implemented by a simple modification of existing algorithms for direct effects only. The modification requires different addressing for genetic groups. This can be accomplished by writing extra columns on a file containing pedigree information indicating the group assignment for maternal effects of the &dquo;phantom&dquo; parents.
Assigning different groups may be used to account for different genetic trends on a maternally influenced trait. For example, Benyshek et al (1988) analyzed weaning weight records of beef calves and found a positive genetic trend for direct effects, whereas the trend for maternal effects was practically null. In this case, unknown animals may be assigned to just one group (or none) for maternal effects while being assigned to several groups for direct effects. Differential genetic grouping can also be employed when genetic trends display genetic (piecewise) patterns throughout the years. For other situations, assigning different groups to direct and maternal effects may not be feasible. Quaas (1988) warned about using complex strategies to assign groups to missing individuals so that confounding between genetic groups and other effects in the model is avoided. If groups for direct and maternal effects are to be fitted there is_ also the possibility of confounding between genetic groups for both types of effects A referee pointed out an example indicating that lack of estimatibility may not always be produced by confounding but also due to lack of expression of the maternal effects. The problem arises when there are animals with records and unknown sires and males and females are grouped separately. Whereas the direct effect for the &dquo;phantom&dquo; sire group would be estimable the maternal effect would not, because none of these sires has female descendents with recorded progeny. As direct effects are expressed long before maternal effects, direct group effects will be estimable well in advance of maternal group effects, the referee indicated. He goes further to suggest that, in this case, one can resort to form groups with both males and females or have the last maternal group correspond to a much longer time period.
In the present work breeding values for direct and maternal effects of missing or &dquo;phantom&dquo; dams of individuals with records are suggested to be included in the vector of solutions to correctly specify the variance-covariance matrix of the observations, as in Van Vleck (1990). As a consequence the number of equations to be solved increases. However, the procedure of differential grouping is independent of enlarging the vector of breeding values to include those of the &dquo;phantom&dquo; dams. If other methods of specifying the variance of the records are found, the procedure presented here may still be applicable.

ACKNOWLEDGMENTS
The referees provided many comments that greatly improved the original version of this paper. Any remaining mistake is the responsibility of the first author. RJC Cantet wishes to thank the University of Illinois and Universidad de Buenos Aires for financial support throughout his graduate studies.