We used a RR model based on Legendre polynomials to develop our indices.
Point gain index to achieve the desired gains at the specific times in fattening process with minimum selection intensity
The point gain index (Ip) is described as
where bj is the index weight for the jth order of Legendre polynomial coefficient, GEBVj is GEBV of the jth order of Legendre polynomial coefficient, and k is the order of Legendre polynomial function. In matrix notation, Ip = b′GEBVαL, where b is a (k+1) vector of index weights and GEBVαL is a (k+1) column vector containing GEBVj(j = 0,1,..,k) for RR coefficients (αL). Hereafter Ip refers to the point gain index.
Desired genetic gains (ΔGs) at s specific times in the fattening process are described as
and
ΔGs=[ΔGt1ΔGt2..ΔGts], where ΔGti is the desired genetic gain for the ith specific time during growth, S is a s×(k+1) matrix, s is the total number of restrictions in the fattening process, ti is the age standardized for the ith specific time in fattening process for the desired gains (i = 1,..,s), ϕj(ti) is the jth order of Legendre polynomial (j = 0,..,k) evaluated at age ti standardized, and ΔαL = (ΔαL0, ΔαL1, .., ΔαLk)′, where ΔαLi is the difference in ith Legendre polynomial coefficient (αLi) before and after selection, i.e., ΔαLi = αLi after selection and −αLibefore selection.
The vector of difference in Legendre polynomial coefficients after and before selection (Δ
αL) can be described according to BLUP properties [
20] as
where αL is a [(k+1)×1] vector of true genetic Legendre coefficients, VGEBVαL is the (co)variance matrix of GEBVαL, ῑ is the intensity of selection, and σIp is the standard deviation of the point gain index (Ip). The selection intensity (ῑ) required to achieve ΔαL can be obtained by setting ῑ = σIp. Therefore,
and
The covariance GEBV between traits i and j was derived by assuming that sufficient data were used to estimate marker effects [
21,
22], such that
where
rGEBV_αLi2 is the reliability of the GEBV for the ith order of Legendre coefficient;
σg_αLi2 is the genetic variance for the ith order of Legendre coefficient; and σg–αLi,j is the genetic covariance for the ith order and jth order of Legendre coefficients.
We used a Lagrange multiplier to choose a vector ΔαL so that the index constructed based on ΔGs has a minimum variance, with the restriction that the vector of expected genetic gains at specific s points during the fattening process (
ΔGs*) is equal to the vector of desired genetic gains (
ΔGs*=(ΔGt1ΔGt2..ΔGts)).
The function to be minimized is
where λ = [λ1 λ2 ….. λs] is a vector of Lagrange multipliers.
Setting the partial derivatives of f with respect to ΔαL equal to zero leads to
Setting the partial derivatives of f with respect to λ equal to zero leads to
According to the principle of Lagrange multipliers, the solution vector Δ
αL in
equation (4) would lead to the minimum selection intensity and satisfy the constraints of the expected genetic gains being equal to the desired genetic gains.
The inverse of the coefficient matrix of
equation (4) can be obtained through inversion by partitioning [
23]. Therefore, the solution to
equation (4) is
The first set of equations is equal to
Conversely, Δ
αL in (
5) has to satisfy the pre-specified gains as shown in (
1), i.e.,
SΔ
αL = Δ
Gs. It can be proved as
Index coefficients (b) for the selection index based on Legendre polynomial coefficients are shown as
Finally, the point gain index based on Legendre polynomial coefficients that would achieve the pre-specified gains with the least selection intensity is
This is a general case when the number (s) of some specific points for desired gains is less than or equal to that of fitted Legendre coefficients (k+1), i.e., s≤k+1.
In particular, when k+1 = s, S is a square matrix, such that
then
Therefore, Δ
αL in (
5) achieves the desired gains at minimum selection intensity.
Note that many possible growth curves could satisfy the desired weight gains at the targeted times in the fattening process. The various indices derived from different sets of ΔαL that satisfy the same vector of desired gains would have different selection intensities. This indicates that given a set of desired genetic gains, the solution to achieve the fixed set of genetic gains is not unique.
Eigenvector index to achieve desired gains at specific time points in the fattening process by using the minimum selection intensity
The eigenvector index (Ie) using n eigenvectors of the additive genetic RR covariance matrix is described as
In matrix notation,
where
En×1=[ɛ1′GEBVαLɛ2′GEBVαL..ɛn′GEBVαL], ɛi is a ith eigenvector of the additive genetic RR covariance matrix, i.e., covariance matrix of the additive genetic Legendre polynomial coefficients (i = 1,2,.., n), and the elements of ɛi are shown as
ɛi′=[ei0ei1ei2…eik], where eij is the jth element of ɛi.
The variance of the eigenvector index is shown as
where VE is a (n×n) matrix and is shown as
The genetic gains at specific times (ΔGs) during the fattening process are described as
where
Gs is a (
s×1) vector of the true genetic values at s specific times during the fattening process, Δ
Gti is the genetic gain at the ith time point in the fattening process, and
σIe is the standard deviation of the eigenvector index (
Ie). In addition,
cov(
Gs,
Ie) can be described according to BLUP properties [
20] as
The selection intensity (ῑ) required to achieve ΔGs can be obtained by setting ῑ = σIe. Therefore,
We used a Lagrange multiplier (λ) to choose a vector b so that the index constructed based on ΔGs has a minimum variance, with the restriction that the vector of expected genetic gains is equal to the vector of desired genetic gains. The function to be minimized is
Setting the partial derivatives of f with respect to b equal to zero leads to
Setting the partial derivatives of f with respect to λ equal to zero leads to
These equations can be written jointly as
Through inversion by partitioning [
23], eigenvector index weights (
b) are shown as
In addition,
b in (
7) has to satisfy the desired gains as shown in (
6), i.e.,
This can be proved as
Stage gain index to achieve the desired gains at specific stages during the fattening process by using the minimum selection intensity
We developed the stage gain index (Is) based on RR coefficients to achieve the desired genetic gains at specific growth stages by using the lowest possible selection intensity. The stage gain index (Is) is described in the same way as the point gain index (Ip), that is
In the previous section regarding the point gain index (Ip), SΔαL= ΔGs.
However, in the current section regarding the stage gain index (Is), the vector ΔGs is the desired genetic gains for s stages, and
where ΔGsj is the desired genetic gain for the jth stage in the fattening process. Note that ΔGsj is not the jth specific time point during growth but the jth specific stage during the fattening process. Therefore, S does not correspond to a specific point but to a specific stage during the fattening process. That is, S is described as
where ϕi(t) is the ith order of Legendre polynomial evaluated at week t standardized, and mj and nj are the first and last week of age of the jth stage, respectively. In this study, the fattening process was measured in units of weeks of age; accordingly stage was divided into units of weeks of age. Note that the only difference between the point gain and stage gain indices is the definition of S. The point gain index and stage gain index correspond to the genetic gains for specific points and specific stages, respectively; all other equations are completely the same between these two indices. Therefore, as in the previous section on the point gain index (Ip), the difference in Legendre polynomial coefficients (ΔαL) (α after selection – α before selection) in the stage gain index (Is) can be described as
Then the stage gain index (Is) is shown as
As mentioned previously about the point gain index, we can choose an ideal unique stage gain index to achieve the desired gains at specific stages by using a minimum selection intensity when the number (s) of restrictions or desired gains is less than the number of Legendre polynomial coefficients (k+1), i.e., s≤k+1.
Numerical example
We assumed the genetic covariance matrix of Legendre polynomial coefficients (
Table 1) given the fattening process in Japanese Black steers [
24,
25] (
Supplementary file). In the current study, quartic Legendre polynomials (
k = 4) were assumed as done previously [
26,
27,
13]. Japanese Black steers are slaughtered at approximately 30 months of age [
28], so we fitted a growth curve to 130 weeks of age, corresponding to 30 months of age. We assumed that the growth curve before selection was similar to the curve from [
24], who fitted a Gompertz growth curve. Instead, we fitted a RR model for that curve to develop a selection index based on RR coefficients. Gompertz growth curve depends on three parameters, i.e., A, B, and K are the asymptotic weight, growth starting point, and maturity rate of the growth curve, respectively. The three parameters, A, B, and K are used from [
24] such as 768, 3.4, and 0.03, respectively. Weekly body weights from birth through 130 weeks of age were estimated from Gompertz growth curve by using the three parameters [
24]. Covariates for Legendre RR curve are shown as
ϕ in
Supplementary file. RR coefficients before selection are estimated from weekly body weights from birth through 130 weeks of age and covariates for Legendre RR curve. The desired curve was derived according to the breeding goal that the birth weight was less than before selection and that the 130-week-old weight was achieved earlier than before selection. Birth weight; body weight at 5, 81, 127, 128, and 130 weeks of age during the fattening process; and the Legendre coefficients before selection and those of the desired curve are shown (
Table 2).
The desired gain at a specific point or a stage can be any value that satisfies the breeder’s purpose. However, we assumed a desired curve as a criterion, to compare the point gain, stage gain, and eigenvector indices and to show that the procedures we developed in this study are correct. We set four break points at weeks of age during the fattening process from birth to 130 weeks of age and used four combinations of break points, such that combination 1 = 0, 40, 120, and 130 weeks; combination 2 = 0, 26, 106, and 130 weeks; combination 3 = 0, 26, 120, and 130 weeks; and combination 4 = 0, 42, 86, and 130 weeks. The specific weeks of age chosen for combination 4 roughly divide the entire 130-week growth period into thirds. The time points of 40 and 120 weeks were derived from the inflection points of the growth curve before selection (
Table 2). The times of 26 and 106 weeks were derived from the inflection points of the first eigenvector function for the covariance matrix of the genetic Legendre coefficients (
Table 1).
The desired gains at selected specific points and stages were computed from the difference between the body weight from the desired growth curve and that before selection (i.e., BW in desired growth curve – BW before selection) (
Table 2). The desired growth curve was chosen such that the body weight at 130 weeks of age before selection could be achieved approximately 2 weeks earlier. Similarly, the desired growth curve was chosen such that body weight at birth was approximately 2.5 kg less than that before selection. The genetic gain during the targeted stage was computed from the difference between the desired curve and that before selection. For example, during the specific stage from birth through 41 weeks of age, the desired stage gain
=∑i=0i=41BWi in the desired curve
-∑i=0i=41BWi before selection.
Regarding the eigenvector index, we had five eigenvectors because the order of matrix of Legendre coefficients is k+1, i.e., 5. We could provide a maximum of 5 index traits as products between the eigenvector and Legendre coefficients expressed in GEBV, that is,
We compared two, three, four, and five index traits in the eigenvector index, i.e.,
We examined the effects of point gain selection on body weights throughout the entire fattening process by comparing the point gain index with the stage gain index when the number of stages was 1, i.e., the target period was the entire process. The reliability of GEBVj (j = 0, 1,.., k) for the jth order of Legendre polynomial coefficients was assumed to be 0.7. From the point that inaccurate estimation of population parameters could bias estimates of theoretical gains, in addition to the reliability of 0.7, we also added reliability of 0.5 and 0.6 to the point gain selection index in which the four target ages were 0, 42, 86, and 130 weeks and the respective desired gains were −2.5, 15.7, 16.6, and 5.4 kg.