Prediction of expected long-term genetic contributions
Our prediction method is based on the concept of long-term genetic contributions. The long-term genetic contribution of individual i (
ri) in generation t
1 is defined as the proportion of genes from individual i that are present in individuals in generation t
2 deriving by descent from individual i, where (t
2–t
1) →∞ [
5]. That is, after several generations, the genetic contributions of ancestors stabilize and become equal for all descendants, i.e., the ultimate proportional contribution of an ancestor to its descendants is reached.
Selection is performed in four categories of selection path (SS, SD, DS, and DD). Rates of inbreeding can be expressed in terms of the expected contributions of these categories [
6,
9–
11]:
where 1′ = (1 1 1 1), N is a 4×4 diagonal matrix containing the number of selected parents for element (i, i) as Ni,i, N1,1 is the number of sires in SS and is referred to as NSS, N2,2 is the number of sires in SD and is referred to as NSD, N3,3 is the number of dams in DS and is referred to as NDS, and N4,4 is the number of dams in DD and is referred to as NDD. In addition,
u2=(ui,SS2 ui,SD2 ui,DS2 ui,DD2), where ui,SS is the expected lifetime long-term genetic contribution of individual i in category SS conditional on its selective advantage (which in mass selection is the genomically enhanced breeding value [GEBV]), and ui,SD, ui,DS, and ui,DD are the expected lifetime long-term genetic contributions of individual i in categories SD, DS, and DD, respectively. Furthermore, δ = (δSS δSD δDS δDD), where δSS is the correction factor for deviations of the variance of family size from independent Poisson variances in the selected offspring from sires in SS; δSD, δDS, and δDD are corrections for deviations of the variance of the family size from independent Poisson variances in the selected offspring from parents in SD, DS, and DD, respectively.
The selective advantage of the ith sire in SS (Si,SS) and in SD (Si,SD) in the linear model is:
where Ai,SS is the breeding value of sire i in SS or SD, Āi,DS and DD is the average breeding value of dams mated to the ith sire in SS and SD, respectively; the dams mated to the ith sire in SS belong to the DS category, and the dams mated to the ith sire in SD belong to the DD category; and Āi,SS, Āi,SD, Āi,DS, and Āi,DD, are the average breeding values of the individuals in the SS, SD, DS, and DD categories.
The selective advantage of the ith dam in DS (Si,DS) and in DD (Si,DD) in the linear model is:
where Ai,DS and DD is the breeding value of dam i in DS and DD, respectively; Ai,SS and SD is the breeding value of a sire mated to the ith dam in DS and DD, respectively; the sires mated to the ith dam in DS belong to the SS category; and the sires mated to the ith dam in DD belong to the SD category.
Expected contributions (ui,SS,SD,DS,or DD) are predicted by linear regression on the selective advantage. That is,
where
αx is the expected contribution of an average parent in
x, and
βx is the regression coefficient of the contribution of i on its selective advantage (
Si,x). In addition,
αx can be obtained according to Woolliams et al [
9]:
where G is a 4×4 matrix representing the parental origin of genes of selected offspring in the order of SS, SD, DS, and DD category, i.e., representing rows offspring and columns parental categories. That is,
However,
where
α′N is the left eigenvector of
G with eigenvalue 1; the left eigenvector is obtained according to Bijma and Woolliams [
11] and is equal to (0.25 0.25 0.25 0.25).
Solutions for
βx are obtained according to Woolliams et al [
9]:
note that the right hand side of (
1) is unaffected by the number of parents, so that
βx is inversely proportional to the number of parents (that is,
1NSS,1NSD,1NDS and
1NDD), where,
I4 is a 4×4 identity matrix,
Π is a 4×4 matrix of regression coefficients with
πxy being the regression coefficient of
Si,x of a selected offspring i of category
x (SS, SD, DS, DD) on
sj,y of its parent j of category
y (SS, SD, DS, DD). For example,
πSD,SS is the regression coefficient of
Si,SD of a selected offspring i of SD on
Sj,SS of its parent j of SS. Given that SS is the sires to breed sons category, we have non-zero elements,
πSS,SS and
πSD,SS, in
Π as elements (1,1) and (2,1), respectively. In the same way, since SD is the sires to breed daughters category, we have non-zero elements,
πDS,SD and
πDD,SD, in
Π as elements (3,2) and (4,2), respectively. Because DS is the dams to breed sons category, we have non-zero elements,
πSS,DS and
πSD,DS, in
Π as elements (1,3) and (2,3), respectively. And given that DD is the dams to breed daughters category, we have non-zero elements,
πDS,DD and
πDD,DD, in
Π as elements (3,4) and (4,4), respectively.
In addition, Λ is a 4×4 matrix of regression coefficients, with λxy being the regression coefficient of the number of selected offspring of category x on Sj,y of its parent j of category y. In the same way as Π, we have non-zero elements, λSS,SS and λSD,SS, λDS,SD and λDD,SD, λSS,DS and λSD,DS, and λDS,DD and λDD,DD in Λ as elements (1,1) and (2,1), (3,2) and (4,2), (1,3) and (2,3), and (3,4) and (4,4), respectively. Consequently,
representing rows as offspring and columns as parental categories.
In our current study, elements in matrices
Π and
λ were calculated from Woolliams et al [
9] and Bijma and Woolliams [
11], as outlined in
Appendices A and B.
The sires in the SS category are included among the sires in SD category. That is, the sires in the SS category are selected not only to breed sons but as sires in the SD category to breed daughters. Similarly the dams in the DS category are included among the dams in the DD category. The dams in the DS category are selected not only to breed sons but as dams in the DD category to breed daughters. Therefore, after applying the procedure of Bijma and Woolliams [
6], the number of sires in SD is larger than that of sires in SS, and the number of dams in DD is larger than that of dams in DS. Therefore,
E (ΔF)=12(1′N0U01), where
E denotes the expectation with respect to the selective advantage,
and E(ĀDS – ĀDD) = (iDS – iDD)σA,f,
note that variance of selective advantage (
σSS2,σSD2,σDS2, and
σDD2) is not affected greatly by the number of parents (
NSS,
NSD,
NDS, and
NDD), since the term of
(1-1Nx) is adjustment for finite population size, where
σA,m2 and
σA,f2 are the equilibrium genetic variance in the male and female populations, respectively;
rA^,m2 and
rA^f2 are the equilibrium reliability of GEBV in the male and female populations, respectively; and
kSS,
kSD,
kDS, and
kDD are variance reduction coefficients for offspring selection in SS, SD, DS, and DD, respectively. Note that covariances of mates between SS and SD and between DS and DD are zero, because of random mating. General predictions of expected genetic contributions was developed using equilibrium genetic variances instead of second generation genetic variances [
9]. Therefore, variances thereafter refer to those in equilibrium.
The accounting percentage derived from SS, SD, DS, and DD for the rate of inbreeding (ΔF) is obtained,
When the effect of selection on inbreeding is ignored, i.e., β = 0,
E (ΔF)=12(1′N0U01)=132(1NSS+3NSD+1NDS+3NDD).
This result is in agreement with the formula from Gowe et al [
8], which likewise neglects the effects of selection on ΔF.
Example applications of the formula
To demonstrate the application of our formula, we assumed only two quantitative traits: trait 1 was assumed to be moderately heritable, with h2 = 0.3, whereas trait 2 was assumed to have low heritability, with h2 = 0.1. These traits are selected as single traits expressed as GEBV. Furthermore, we assumed an aggregate genotype as a linear combination of genetic values, each weighted by the relative economic weights, which was expressed as a1g1 + a2g2, where g1 is the true genetic value for trait i, ai is the relative economic weight for trait i, and the genetic correlation between traits 1 and 2 was assumed as 0.4. Index selection was performed to select a1g1 + a2g2, that is, breeding goal (H), under the assumption that the relative economic weight between traits 1 and 2 is 1:1. Breeding value (A) was defined as described earlier in the Methods; for example, the breeding value of sire i in SS was defined as Ai,SS. Similarly, the breeding goal value (H) of sire i in SS can be expressed as Hi,SS; note that the formula that we developed in Methods can be applied not only to breeding value (A) but also to breeding goal value (H).
In our example, we assumed the reliabilities of the GEBVs for traits 1 and 2 to be 0.5721 and 0.4836, respectively [
3]. Index selection (
I) was performed as
I =
a1 GEBV1 +
a1 GEBV2, because GEBVs are assumed to be derived from multiple-trait BLUP (MT BLUP) genetic evaluation methods in the current study (as done for single-step genomic BLUP [
13]). We calculated equilibrium genetic variances and reliabilities based on Togashi et al [
3]. The initial (generation 0) and equilibrium genetic variances and reliabilities for single-trait selection (
h2 = 0.3 or
h2 = 0.1) and index selection are shown in
Table 1. Rates of inbreeding were calculated based on equilibrium genetic variances and reliabilities, because regression coefficients of the number or breeding value of selected offspring on the breeding value of the parent are equal for the parental and offspring generations under equilibrium genetic variances and reliabilities.
We considered two scenarios for the selection percentages for SS, SD, DS, and DD—5%-12.5%–1%-70% and 1%-5%–1%-70%—and three scenarios for the numbers of selected parents of SS, SD, DS, and DD—namely 20-50–100-7,000, 40-100–200-14,000, and 60-150–300-21,000. Therefore, we considered six scenarios (two scenarios of selection percentage and three scenarios of the number of parents in SS, SD, DS, DD) in total. Note that the two scenarios for selection percentage for SS, SD, DS, and DD differ only in the selection percentage along the SS and SD selection paths, because under actual breeding conditions, selection intensity can be adjusted more easily in male selection paths (SS and SD) than in female selection paths (DS and DD). The numbers of male and female offspring from a dam of DS, i.e., fmds and ffds, were set at 4. The number of female offspring from a dam of DD, i.e., ffdd, was set at 1.4. These numbers are derived from the years of usage of a dam and the reproduction method (ovum collection, in vitro fertilization, or embryo transfer). When DS and DD parents are used with constant selection intensity and in equal numbers over several years, they belong to a single or exclusive category. The numbers are used to compute the deviation of the variance of the family size from Poisson variance.