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Optimum truncation points for independent culling level
selection on a multivariate normal distribution, with an
application to dairy cattle selection
V. Ducrocq, J.J. Colleau
To cite this version:
Original
article
Optimum
truncation
points
for
independent culling
level
selection
on a
multivariate normal
distribution,
with
an
application
to
dairy
cattle selection
V.
Ducrocq
J.J. Colleau
Institut National de la Recherche
Agronomique,
Station deGénétique
Quantitative etAppliquée,
Centre de Recherches de
Jouy-en-Josas,
78350Jouy-en-Josas,
France(received
1 March 1988,accepted
19September 1988)
Summary — Independent culling
level selection is oftenpracticed
inbreeding
programs because extreme animals for someparticular
traits arerejected by
breeders or because records on whichgenetic
evaluation is based are collectedsequentially. Optimizing
these selectionprocedures
for agiven
overallbreeding objective
isequivalent
tofinding
the combination of truncation thresholds orculling
levels which maximizes theexpected
value of the overallgenetic
value for selected animals. Ageneral Newton-type algorithm
has been derived toperform
this maximization for any number ofnormally
distributed traits and when the overallprobability
ofbeing
selected is fixed.Using
apower-ful method for the
computation
of multivariate normalprobability integrals,
it has beenpossible
to undertake the numerical calculation of theoptimal
truncationpoints
when up to 6 correlated traits orstages of selection are considered
simultaneously.
The extension of thisalgorithm
to the morecom-plex
situation ofmaximizing
annualgenetic
responsesubject
to nonlinear constraints is demonstra-tedusing
adairy
cattle modelinvolving
milkproduction
and asecondary
trait such as type. Conside-ration isgiven
to three of the fourpathways
of selection: dams of bulls; sires of bulls; and sires ofcows.
Independent culling
level selection -dairy
cattle -multistage
selection -genetic galn
-multivariate normal distrlbutionRésumé — Seuils de troncature
optimaux
lors d’une sélection à niveauxIndépendants
sur une distribution multlnormale, avec uneapplication
à la sélection chez les bovins laitiers. Une sélection à niveauxindépendants
est souventpratiquée
dans les programmesgénétiques,
parce que les animaux extrèmes pour certains caractères sont
rejetés,
ou parce que les donnéesqui
servent à l’évaluationgénétique
des animaux sont recueilliesséquentiellement. L’optimisation,
pour unobjectif
donné, de cesrègles
de sélectionéquivaut
à la recherche des seuils de troncaturequi
maximisentl’espérance
deI objectif
de sélection pour les animaux retenus. Unalgorithme
géné-ral de type Newton est établi pour effectuer cette maximisation pour un nombrequelconque
de caractères distribués selon une loi mulünormale etlorsque
laprobabilité
finale d’être retenu est bxée. Apartir
d’une méthodepuissante
de calculd’intégrales
de lois multinormales, il a étépossible
d’entreprendre numériquement
le calcul des seuils de troncaturequand
jusqu’à
6 caractères ouétapes
de sélection corrélés sont considérés simultanément. L’extension de cetalgorithme
à des situationsplus complexes,
comme la maximisation duprogrès génétique
annuel sousplusieurs
contraintes non linéaires, est illustrée à travers le calcul de
règles optimales
de sélection des mères à taureau, pères à taureau etpères
de service pour laproduction
laitière et pour un caractère secondaire tel que lepointage
laitier dans un schéma de sélectiontypique
des bovins laitiers. sélection à niveauxIndépendants -
bovins laltlers - sélectlonpar
étapes - progrès
Introduction
It is often
possible
to describe selectionobjectives through
linear combinations -aggre-gate genotype -
ofbreeding
values on several(m)
traits. Then theoptimal
selectionpro-cedure consists of
using
a selection index which combines observed values for several(n)
sources of information(Hazel
andLush,
1942).
However,
thisapproach
isoccasionally
not used for two main reasons:a)
Practitioners sometimesemphasize
the need to cull extreme animals(deviants
forsome
traits)
becausethey
are deemed undesirable.Then,
the selectionobjective
isimpli-citly recognized
asbeing
nonlinear. The cost of such apractice
withrespect
to a strictapplication
of theoptimal
linear index may not bejustifiable
when thisnonlinearity
isunimportant
orquestionable.
b)
The recordsrequired
tocompute
the selection index are notalways
availablesimul-taneously
and/or their cost does notjustify
their collection for all the candidates for selec-tion. Therefore selection schemes involve differentstages
whichcorrespond
totrunca-tions on the
joint
distribution of allpossible
records.Within these
constraints,
it ispotentially interesting
to evaluate andimprove
theeffi-ciency
ofpractical
selectionprocedures by determining
optimal
conditions ofapplication
of
independent
culling
level selection. As far as weknow,
thepublished
works on thistopic
have beengreatly
limitedby
the number of variables considered.Generally
speaking,
studies on thealgebraic
derivation ofoptimum
truncation thresholds withcor-responding
numericalcomputation
have dealt with no more than 2 variables(Namkoong,
1970;
Evans, 1980;
Cotterill and James, 1981; Smith and Quaas,1982). Recently,
Ducrocq
and Colleau(1986)
treatedexamples
with 3 variables to illustratepotential
usesof a numerical method to
compute
multivariate normalprobabilities.
Inpractice, though,
the number of traits or selection
stages involved may be
significantly
larger.
Moreover,
thealgorithms previously
considered have beenspecifically
developed
for agiven
num-ber n of variables and their extension to any n is not obvious
though
algebraic
conditions which must be verified at theoptimum
have beenreported (Jain
andAmble, 1962;
Smith andQuaas, 1982).
Indeed,
as aconsequence
of the limitation of the number of variablesconsidered,
theoptimization problem
has been restricted to rathersimple
types
ofobjective
functions,
which may notadequately
summarize the overallefficiency
of selection schemes. Inpar-ticular,
authors have not considered functions such as the annualgenetic
gain
of theselection
objective - computed using
Rendel and Robertson’s(1950)
formula - inrela-tively complex
situations(e.g. involving
the 4paths
of transmission ofgenetic progress).
This paper
presents
basicyet
general,
i.e. for any nalgorithms
which can be used for thecomputation
ofoptimal
truncationpoints
for a broad class ofobjective
functions withone or more constraints.
Theory
isdeveloped
andapplications
arepresented
for thegeneral
multivariateproblem
consideredby
Smith and Quaas(1982).
Apractical
example
ofapplication
in thedairy
cattle context is described.Corresponding
numericalSolution of Smith and Quaas’
problem
in thegeneral
caseStatement of the
problem
Let u, xl, ....x,, be n+1 random variables with
joint
multivariate normal distribution:u is the
breeding
objective
and the xis are the observed variables.The
problem
is to find cl, Cn&dquo;&dquo;C2so as to maximizeEp
(u)
subject
to:where P is
given
andrepresents
the overall fraction of candidates selected.Notations
Let
!&dquo;
(x; R
n
)
be the standard multivariate normaldensity
of dimension n with variance covariance matrixR
n
.
Let
We need the
following
recursive definitions for distributions conditioned onq::;;n-1
Solution
Using
thegeneral
result of Jain and Amble(1962)
we have:Since
Q(c
1
,... c
n
)
is to beequal
to a constantP,
the maximization ofEp
(u)
is tanta-mount to the maximization ofN(c
l
,..., c
n
).
The constraintQ(c,,... c
n
)
= P isincorporated
using
the method ofLagrange multipliers (Bass,
1961, p. 928;
Smith andQuaas,
1982):
the
optimal
truncationpoints
are those for which thepartial
derivatives of the functionf
(w)
=N(c
1’
&dquo; e
n
)
+X(Q(c,... c
n
) - P)
withrespect
to w’=(
C1’
&dquo;
’’
cn,X)
are 0. Â. is called aLagrange
multiplier.
The
resulting
system
of nonlinearequations
in w’= (
C1’
... cn.X)
is solvediteratively
using
the multidimensional Newton’s method(Dennis
andSchnabel,
1983).
Denote aswct> the
approximate
solution at iteration t(w(o)
is agiven starting value).
A better estimate w(t+1)is
computed
from:The final solution wIt) = w* is obtained when
is
sufficiently
small,
whereI I
h I I denotes any
norm.As
long
as thestarting
value w(o) is not too far from w*(generally,
w(o) = 0 seems to bea robust initial
value),
convergence is very fast(quadratic
convergence: Dennis andSchnabel,
1983).
c* is a local maximum for E(u), provided
’is
positive
definite,
butnothing
guarantees
that w* is aglobal
maximum for f(w).
Now,
note that:where:
Another method exists for the derivation of these
expressions,
firstreasoning
onderi-vatives of
integrals
and thenusing
Jain and Amble’s(1962)
formula on conditionalconsidera-tions on several u
(general problem
with several constraints on severalobjectives) (see
Appendix).
Expressions
(3)
to(11)
include all the elementsrequired
for thecomputation
of thevector
8f(w)/Bw
and the matrix(8
2
f(w)/Bw
Sw
*
)
in(1).
Inparticular,
It can be observed that the
equations (6f(w)/6c
i
)
= 0 in(12)
for 1 !i!n are linear in X.The size of the
system
ofequations
to be solved can beeasily
reducedby absorption
of theLagrange
multiplier.
Forexample,
we have:is equivalent to:
Derivatives with
respect
to the cis of theequations
in(17)
arerequired
for theapplica-tion of Newton’s method as in
(2).
They
arereadily
derivedusing (6)
to(8).
Numerical
applications
Studies on
independent
culling
level selection have beenmainly
limited to 2-trait selec-tionprobably
becausegeneral
and efficient programs tocompute
the multivariate normalprobability integrals
in Jain and Amble’s formula were not available for dimensions > 2.and Soms
(1976) proposed
ageneral
method characterizedby good precision
whencor-relation coefficients and truncation
points
are nottoo
extreme. For more details on thismethod,
itsprecision
andcomputation
times,
seeDucrocq
and Colleau(1986).
Dutt’s .technique
is well suited for numericalapplications
of theoptimization algorithm
presented
in this paper when up to 6 selection
stages
or traits are considered.In this
particular
case,expressions (7)
to(11)
aresimpler,
sinceQ
jj
= 1 andQ
ijk
= 0.Algebraic
and numerical results areequivalent
to thosegiven
by
Smith and Quaas(1982).
In
(9),
Q;ik
= 1. Thealgorithm
described here leads to the same results as thosepre-sented in
Ducrocq
and Colleau(1986).
3) . n = 4 to 6.
Consider for
example,
n traits withr;
i
=(-1
(j/20i)
for1 <_i<_j<_n
and with economicweight
mi= 1+i/20 1!i!n.Table
I presents
the truncationpoints
qs on these traits which maximizeEp (u
I c1,... c&dquo;)
when the overall selected fraction is P =0.25, 0.025,
0.001. At iteration 0,the cis were taken
equal
to 0. Thestopping
criterion for the Newton’s iteration was:where
E
i
was the i th left hand side ofsystem
(17).
Convergence
was fast anddepended
on how far the initial value of the truncationpoints
was from the solution.Note, however,
that in theexamples presented
in Table I,correlations between variables are not very
high
Q
r;! !
1 S 0.3)
and theweights
of thediffe-rent traits are of the same
magnitude.
When this is not the case, theoptimal
selectionprocedure
may involve no selection at all on one or several of these traits. The sameobservation
applies
to small overall selectionintensity (Young,
1961;
Namkoong,
1970;
Smith andQuaas, 1982; Tibau I Font and
Ollivier, 1984;
Ducrocq
andColleau,
1986).
Inlimiting
cases(with
very low or veryhigh
selectionintensity
on one or several traits orwhen correlations are
extreme),
it should be remembered that theprecision
of Dutt’salgorithm
forcomputation
of multivariateprobability integrals
may beunsatisfactory
(Ducrocq
andColleau,
1986).
Then alternative methods may have to be used(e.g.,
Rus-sell et
al.,
1985).
An
application
in thedairy
cattle contextAssumptions
Dairy
cattle selection isperformed through
a sequence ofstages
which characterizes thetransition from one
generation
(g)
to the next(g+1 ).
In the additive
polygenic
situation which is assumed for most of the traits selected in domesticanimals,
it ispossible
to describe thesestages
through
truncation selectionThese first include selection criteria
corresponding
to the transition betweengenera-tions g and
g+1
(reproductive stage),
followed in the course of timeby
those criteria usedduring generation
g+1,
before the nextreproductive cycle.
Ourapproach
for theoptimiza-tion of these successive selecoptimiza-tion
stages
relies on theassumption
of multivariatenorma-lity
for these 2 criteria when candidates for selection are born. Such anassumption
isplausible
in the additivepolygenic
context,especially
whenheritability
values are low(Bulmer,
1980, p.
154;
see also Smith andHammond, 1987,
for a discussion on thispoint).
A more stridentassumption
is that thedispersion
parameters
of thejoint
multiva-riate distribution remain constantthrough
the different selectioncycles.
Breeding objective
and selectionstages
Assume that the selection
objective
in adairy
cattle breed is a linear combination of 2traits: &dquo;milk
production&dquo;
and asecondary
trait such as&dquo;type&dquo;
(both
of these traits may be themselves linear combinations of morespecific characters).
Apossible
sequence of selectionstages
whichapproximates
what is often done inpractice
is thefollowing
(Figure 1):
1)
Dams of bulls(DB)
ofgeneration
g are selected based on their estimatedbreeding
values X1
(for milk)
and X2(for type),
withrespective
thresholds C1 and c2on the standar-dized variables. These dams of bulls are mated to sires of bulls(SB)
ofgeneration
g.2)
The sons of these cows are progeny tested. Sires of cows(SC)
and sires of bulls ofmilk)
and X4(for type).
Truncation thresholds on these 2 variables are different for SCand SB
(c
3
,
c4and c5 c6,respectively).
Selection of DB can be modelled as if it were
performed
at birth of the male calves. This is essential in order to be able to invoke therestoring
of multivariatenormality
ateach
generation.
Let RP be theregistered (with
knownpedigree)
and recordedpopula-tion of cows and let y denote the
proportion
of these cowswhich
can bepotential
dams of bulls(e.g.
!y= 0.53 if Al sons are selected from cows with at least 2 knownlactations).
If it is assumed(as
inDucrocq,
1984)
that an average of nd = 6potential
dams must be selected in order to obtain one male calfentering
progeny test, it can be considered thatDB selection is
performed
by
truncation on the estimatedbreeding
values x, and X2 of the dams of nb=(y RP)/n
d
male calves.The
expression
of the annualgenetic
gain
given by
Rendel and Robertson(1950)
is:Selection on the dam of cow
path
isignored (I!
=0).
Constraints
Three constraints are added here:
1)
The fractionTy
of thepopulation
bred to young sires is considered as constant,since in
practice
this isusually
thelimiting
factor for the extension of progeny test. In thisexample,
the number of recordeddaughters
per young siren
v
y
is also assumedconstant:
then,
the numberny
of young siresprogeny-tested
each year is fixed, as well as theirrepeatablity.
2)
The number of sires of cows selected each year is determinedby
the number of cows(= (T-RP)
+(1-Ty)
RP)
to be bred to proven sires in the wholepopulation (T)
and the total number of dosesproduced by
agiven
sireduring
his lifetime(AI).
- - ,--,
3)
The number of sires of bulls retained each year is constrained to beequal
to nsB, the number below whichproblems
ofinbreeding
and reduction ofgenetic variability
arefeared.
Numerical methods and results
When constraints
(22), (23)
and(24)
aresatisfied,
equations (18)
to(21)
lead to thefollo-wing
result:where
L,
the sum of thegeneration
intervals over the 4paths,
is a constant in our case.The combination of truncation
points
c;,i=1,...
6 which maximizes(25)
with the constraints(22), (23)
and(24)
is obtainedby equating
to 0 the derivatives of f(w)
withrespect
to w’ =(c
l
,..c,,
X,
/.1,v)
where:and
X, p,
v areLagrange
multipliers.
The first and second derivatives of f
(w)
arereadily
obtainedusing
thegeneral
formu-laegiven
in thepreceding
sections. The 3Lagrange
multipliers
are eliminatedthrough
tri-vialabsorption.
The nonlinearsystem
to solve then involves 6 unknowns: the 6trunca-tion thresholds. Solutrunca-tions obtained
using
Newton’s method arepresented
in TableIII,
whereparameters
take the valuesgiven
in Table II. Thestopping
criterion for thewhere
E
i
*
was the ith left hand side of the absorbedsystem
ofequations.
Convergence
was fast -always
less than 8 iterations - aslong
as thestarting
valuec 0) (of c =
{c
;
6
a
,
’
was not too far from the solution. In contrast with the numerical resultspresented
in TableI,
c !o! = 0 does not lead to convergence, because the values of c inthe next iterates are found to be
extremely large
orlow; i.e.,
totally
unrealistic and inregions
where theprecision
of Dutt’s method is notgood.
This behavioris,
at leastindi-rectly,
a consequence of the verylarge
selectionintensity
of proven sires. To avoid thissituation,
more realisticstarting
values must be chosen. Forexample,
c (0) can becom-puted
as the truncationpoints
for which the conditions(22), (23)
and(24)
are satisfied with agiven
distribution of selection efforts between milk andtype, i.e.,
c (0) is such thatQ
(c!O)
=d,/a,
Q(c,co!! c!<0»
=d!!
Q(c,tot,
c!<o>,
C3
(o))
=d
2
la,
etc... for some a. In mostcases
presented
in TableIII,
a = 0.75. Forstrongly
unbalancedweights
for the 2 traits(5:1),
convergence is obtainedonly
for evenlarger
values of a(e.g.,
a =0.99).
It should be noted that selection on
type
was consideredposterior
to selection on milkproduction.
Thisassumption
has been chosen because thiscorresponds
to what is done inpractice
for dams of bulls in France:only
the best cows for milkproduction
areevalua-ted for
type.
This does not influence the values ofoptimal
thresholds butonly
their useThe results in Table III underline the
sensitivity
of thistype
ofcomputation
to theeco-nomic
weights
assigned
to the 2 traits and theirgenetic
correlation.According
to the rela-tive economicweight
fortype,
theoptimal
situation maycorrespond
to
virtually
no selec-tion ontype
(weights 5:1)
or to aculling
ontype
evaluation of between aquarter
and ahalf of the candidates
(weights 2:1)
on eachpath.
When thegenetic
correlation between milk andtype
varies fromslightly
positive (0.15)
toslighly negative (-0.15) (thus covering
the range of values most often indicated in the
literature) optimum
selection intensities and overallgenetic gain
for theobjective
function are notdramatically
modified. Butthen,
thegenetic
trend fortype
varies from a very favorable increase(for
apositive correlation)
even when no selection ontype
isperformed,
to a notnegligible
decline(for
anegative
correlation and
weights
3:1 or5:1 ).
These features were alsopointed
outby Ducrocq
(1984).
Conclusion
The
previous example clearly
demonstatesthat,
at least in certainsituations, it is
pos-sible toalgebraically
andnumerically develop
algorithms
tocompute
optimal
selectionintensities in
relatively complex multistage breeding
schemes and with several nonlinear constraints.They
are not limitedby
drastic conditions such as2-stage
selection,
uncor-related traits and/or very
simple optimization
criteria.Indeed,
morecomplex
situations than thatpresented
in theexample
can beenvisaged.
Forexample,
theoverlap
ofgene-rations of bulls and cows can be accounted for in the determination of
genetic
in Hill
(1974),
Elsen andMocquot (1974, 1976)
andDucrocq
and Quaas(1988): dividing
each
population
of candidates intohomogeneous
cohorts of animals of same age, sexand
reproductive
role,
intracohort selection differentials can becomputed
under theassumption
that selection isperformed
by retaining
all the individuals whose estimatedgenetic
values are above aunique
set of truncation thresholds for the n traits orstages
considered
(Ducrocq, 1984).
Then,
computation
of elements in(18)
and their derivatives is tedious butperfectly
feasible.However,
beforeundertaking optimization
studies ofcomplex
schemes,
it should be remembered that troublesomeproblems
of convergence may occur such as those found in theapplication
described. In theparticular
case of thedairy
cattle context, convergenceproblems
were also found when we tried to relax theassumption
of fixed number of young siressampled
(ny)
or the number ofdaughters
per young sire(n!),
i.e.,
theirrepeatability
*.Obviously,
further research is needed in awide-ning
field.Finally,
the determination of anoptimal
selectionpolicy,
which is&dquo;optimal&dquo; only
from apurely genetic standpoint,
should be followedby
asensitivity analysis.
It appears that theannual
genetic gain AG,
variesonly slightly
over a wide range of values for somepara-meters. Situations close to the
optimum
may be ofgreater
interest becausethey
aresimple,
morepractical
or lessexpensive
toimplement.
Theknowledge
of the trueopti-mum is nevertheless
required
to assess this&dquo;suboptimality&dquo;.
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Another method for
calculating
the derivatives of N. Besides the notations defined in the text, let us define:R
2
,ij
= square of themultiple
correlation coefficient between u and thepredictors
xi, xj.By
firstdifferentiating
N and thenusing
Jain and Amble’s formula on theresulting
conditionaldis-tributions, it can be shown that:
This