Rapid Method for Computing the Inverse of a
Relationship Matrix
ABSTRACT
The accuracy of prediction of breeding
values can be improved by utilizing all
relationships among animals to be evalu-
ated. The inverse of the numerator rela-
tionship matrix is required for best pre-
diction but is usually much too large to
be computed by conventional inversion
routines. A simple and rapid technique
for finding this inverse directly from a list
of sires and dams, bypassing computation
of the matrix whose inverse is wanted, is
presented.
INTRODUCTION
The use of best linear unbiased prediction
(BLUP) methods for predicting breeding values
has been described by Henderson (1, 2, 3). The
matrix of relationships of animals to be evalu-
ated could be incorporated in these methods,
but as presented in these papers it was neces-
sary either to invert the relationship matrix or
to transform involving extensive matrix multi-
plications. The former was prohibitive compu-
rationally if the matrix was too large to store in
the memory of the computer, and the latter
destroys the customary sparseness of the co-
efficient matrix and thereby reduces efficiency
of an iterative method of solution. A simple
method for inverting the relationship matrix
has the unusual feature that the inverse can
be written without having to compute the
matrix to be inverted. In a noninbred popula-
tion, the inverse can be computed by using only
a list of parents. An inbred population requires
in addition that a triangular matrix be gener-
ated, but still no conventional matrix inversion
is required. This paper presents the method
with examples. The derivation has been re-
ported (4).
Received October 17, 1974.
1727
C. R. HENDERSON
Department of Animal Science
Cornell University, Ithaca, NY 14850
We wish to predict additive genetic merits of
many animals from a set of records with
unknown fixed effects and random variables in
addition to breeding values. Let a general mixed
model for such prediction be
y = X/3 + Z l u + Z 2 a + e [1]
where y is the vector of records, X is a known
matrix, (3 is an unknown fixed vector, Z1 is a
known matrix, u is a nonobservable random
vector, Z2 is a known matrix, a is a nonobser-
vable random vector representing additive
genetic merits, and e is a nonobservable random
vector of "errors." We assume that u, a, and
e all have null means and that Var(u) = Ga 2,
Var(a) = kAo 2 where k is a scalar, and Var(e) =
Io 2. G and A are known and nonsingular, and
A is the numerator relationship matrix de-
fined below. It is assumed that u, a, and e are
mutually uncorrelated. The scalar cr2 is possibly
unknown.
Henderson (1) has shown that BLUP of a is
~, any solution to
_1 . . . . . .
t ~ tI
tX Iz~zl+~ I Z'~Z2 = 't .[21
~X Z~Zl I Z~Z2 + k-1 ^ Lz' ,J
The solution to ~ is not necessarily unique, but
and ~ are unique regardless of the solution to
because of the addition of G-1 and k-1 A-1 to
the usual least squares matrix of coefficients.
In some important applications, either
[~' ~ ~'] has relatively few elements or
x XZll
ix zlz,.
has a large submatrix that is easy to invert (is
1728 HENDERSON
diagonal, for example), and consequently m o s t
"f A P
or all of the elements of [3 : u ] can be ab-
sorbed easily. F o r example, in the Cornel1
m e t h o d o f sire evaluation used in the Northeast
(3), 3 represents a few groups and a large num-
ber of fixed herd-year-season effects. There is
no u in the model. Herd-year-seasons are ab-
sorbed easily, leaving a set o f equations with a
few fixed groups and a large n u m b e r of sires
( a p p r o x i m a t e l y 1,500 Holsteins). Presently, the
relationships among sires are ignored. T h a t is,
A is regarded as having the value I. T h e re-
sulting equations are well suited to an iterative
solution because o f m a n y zero coefficients and
in particular because the diagonal coefficients
are large relative to the off-diagonal ones.
The prohibitive cost o f inverting A has dic-
tated in the past that the r e d u c t i o n in predic-
tion error variance by using A-1 not be utilized.
The ease with which A -1 c a n be written, as
described in this paper, n o w makes feasible in-
c o r p o r a t i o n of relationships in sire evaluation.
The relationship m a t r i x could also be used in
intraherd evaluation of females.
C O M P U T A T I O N OF A T R I A N G U L A R M A T R I X
NEEDED FOR I N B R E D P O P U L A T I O N S
Let A be the n u m e r a t o r relationship m a t r i x
for n animals. The first t < n of these are de-
fined as the " b a s e " population. T h a t is, these
animals are regarded as noninbred, unrelated,
and with unspecified parents. A lower triangu-
lar matrix, say L, exists such t h a t LL ~ = A. If
we can c o m p u t e L, we can use this to c o m p u t e
A. In fact, L is easy to c o m p u t e recursively, and
its c o m p u t a t i o n is well adapted to computeriza-
tion in contrast to the path coefficient m e t h o d .
A simple c o m p u t i n g algorithm follows:
1) N u m b e r the animals 1, 2 , . . . , n, ordered
such that parents precede their progeny.
2) The upper t 2 submatrix of L is I.
3) Given that p < q are the parents of i,
£ij = (l~pj + ~qj)/2 f o r j = 1 . . . . . p
= ~qj/2 f o r j = p + 1 . . . . . q
= 0 for] = q + 1..... i- 1, provided
q<i-1;
P q
E E ~.2vs
~ii = (1 + .5:1j= ~pj~qj q,
Journal of Dairy Science Vol. 58, No. 11
4) If only one parent is k n o w n , say p,
~ij = 9.pj/2 for j = 1 . . . . . p
= 0 f o r j = p + l . . . . . i--1, provided
p<i-1.
~i~ = (1 - ~ ~2).s
j=l ~1
5) If neither parent is known,
n
~ij = 0 f o r ~ . . . . , i - 1 ;
j=l
~ii = 1.
To illustrate, suppose we have the following
animals, with 1 and 2 being defined as the base
population:
Indi~dual Parents
1 Unknown
2 Unknown
3 1 and unknown
4 1 and 2
5 3 and 4
6 1 and 4
7 5 and 6
T h e n L has the value in [3]. Starting with the
third row, the first two elements are (1 + 0)/2
and 0 which is [.5 0]. The third e l e m e n t is
(1 - . 5 2 ) .5 = .866025. The first three elements
o f the f o u r t h row are (1 + 0)/2, (0 + 1)/2,
and 0 which is [.5 .5 0]. The f o u r t h e l e m e n t
of this ,row is 11 + [(1)(0) + ( 0 ) ( 1 ) ] / 2 -- (.5) 2
_ (.5)2t .s = (.5).5. The first f o u r elements
of row five are (.5 + .5)/2, (0 + .5)/2, (.866025
+ 0)2, and .707107/2 which is [.5 .25 .43301c3
. 3 5 3 5 5 3 ] . The diagonal e l e m e n t o f row 5 is 41
+ [(.5)(.5) + (0)(.5) + ( . 8 6 6 0 2 5 ) ( 0 ) 1 / 2 ~ (.5) 2
_ (.25)2 _ (.433013)~ _ (.353553)2I .s =
(.5) "5. The last two rows are generated in a
similar manner.
N o w if we m u l t i p l y matrix [3] b y its trans-
pose, we obtain the A m a t r i x in [4] which is
inverted to d e m o n s t r a t e t h a t the same result
can be obtained by the simple m e t h o d of this
paper. Since this is a matrix of small order, it is
easy to invert by conventional methods. A-1 is
tabulated in [5] so we can check this result
with our simpler m e t h o d . A m u c h easier
m e t h o d for obtaining this inverse is in the n e x t
section.
 TECHNICAL NOTE 1 729

(1) (2) (3) (4) (5) (6) (7)

(1) ~000000 .000000 .000000 .000000 .000000 .000000 .000000
(2) .000000 1.000000 .000000 .000000 000000 .000000 .000000
(3) .500000 .000000 .866025 .000000 .000000 .000000 .000000
(4) .500000 .500000 .000000 .707107 .000000 .000000 .000000 [31
(5) .500000 .250000 .433013 .353553 .707107 .000000 .000000
(6) .750000 .250000 .000000 .353553 .000000 .707107 .000000
(7) .625000 .250000 .216506 .353553 .353553 .353553 .637378

(1) (2) (3) (4) (5) (6) (7)

(1) ~-.00000 .00000 .50000 .50000 .50000 .75000 .62500-
(2) .00000 1.00000 .00000 .50000 .25000 .25000 .25000
(3) .50000 .00000 1.00000 .25000 .62500 .37500 .50000
(4) .50000 .50000 .25000 1.00000 .62500 .75000 .68750 [41
(5) .50000 .25000 .62500 .62500 1.12500 .56250 .84375
(6) .75000 .25000 .37500 .75000 .56250 1.25000 .90625
(7) .62500 .25000 .50000 .68750 .84375 .90625 1.28125

(1) (2) (3) (4) (5) (6) (7)

(1) 2.333333 .500000 -.666667 -.500000 .000000 -1.000000 .000000
(2) .500000 1.500000 .000000 -1.000000 .000000 .000000 .000000
(3) -.666667 .000000 1.833333 .500000 -1.000000 -1.000000 .000000
(4) -.500000 -1.000000 .500000 3.000000 -1.000000 -1.000000 .000000 151
(5) .000000 .000000 -1.000000 -1.000000 2.615384 .615384 -1.230767
(6) -1.000000 .000000 .000000 -1.000000 .615384 2.615384 -1 230767
(7) .000000 .000000 .000000 .000000 -1.230767 -1.230767 2.461534

INVERSE OF R E L A T I O N S H I P M A T R I X --.5 where the first t e r m arises as a con-

BY THE SIMPLE M E T H O D
Let d be a v e c t o r of the inverse of the
squares o f each diagonal e l e m e n t of L. T h a t is,
d i = 1 / ~ i as c o m p u t e d in the previous section.
In our example, matrix [3], d' = [1, 1, 1.333,
2, 2, 2, 2 . 4 6 1 5 3 4 ] .
T h e n the elements of A-1 can be c o m p u t e d
using d and a list of sires and dams. We denote
the i j t h e l e m e n t of A-1 by aij.
1) a ii = d i + .25 ff d k where k refers to the
progeny of the ith sire. In our example,
a 11 = 1 + (.25) (1.33) . . . + 2 + 2) =
2.33 . . . and a 44 = 2 + (.25)(2 + 2)
2) aiJ (i < j) = - . 5 d ] + .25 ~ dk i f j i s a
progeny of i, or = .25 ~ d k f r o m the
mating of i with j. Of course, aJi = alJ
since A-1 is symmetric. For example,
a 12 = (.25)(2) = .5 as a c o n s e q u e n c e of
their c o m m o n progeny, n u m b e r 4;
a 67 = (--.5)(2.461534) = -1.230767
as a consequence of 7 being a progeny
of 6; and a 14 --- ( - . 5 ) ( 2 ) + (.25)(2) =
sequence of 4 being a progeny of 1 and
the second t e r m results f r o m the mating
of 1 and 4 to produce 6.
F U R T H E R S I M P L I F I C A T I O N IN N O N I N B R E D
POPULATIONS
The m o s t laborious aspect of the preceding
section is the c o m p u t a t i o n of L to obtain d.
In a n o n i n b r e d population, however, this com-
p u t a t i o n is not needed since d can be written
immediately. Only three values are possible,
n a m e l y d i = 1 if neither parent o f i is known,
= 3. d i = 4/3 if only one parent o f i is known, or
d i = 2 if b o t h parents of i are known. Thus, in
a n o n i n b r e d population, all o f the elements of
A-1 can be c o m p u t e d directly b y inspection of
the list of parents. Also in such a p o p u l a t i o n
the c o n t r i b u t i o n to aij (i < j) can be either
parent-progeny relationship or c o m m o n prog-
eny, b u t n o t both.
These c o m p u t a t i o n s for a n o n i n b r e d popula-
tion are illustrated with the following list of
parents.

J o u r n a l o f D a i r y S c i e n c e V o l . 58, N o . 1 1
1730 HENDERSON

Individual Parents
1 Unknown
2 Unknown
3 1 and 2
4 1 and 2
5 1 and 2
6 1 and unknown
7 1 and unknown
8 2 and unknown
9 7and8
T h e n d' = [1 1 2 2 2 4/3
PROGRAM FOR C O M P U T I N G A - 1
A F O R T R A N p r o g r a m has b e e n w r i t t e n
t o c o m p u t e A-1. It is e x t r e m e l y fast a n d uses
little m e m o r y . T h e p r o g r a m requires t h a t a list
o f individuals w i t h t h e i r p a r e n t s b e s t o r e d in
m e m o r y . If t h e p o p u l a t i o n is specified n o n -
i n b r e d or if o n e c h o o s e s t o use d o f a n o n i n b r e d
population regardless o f i n b r e e d i n g , t h e pro-
gram computes d and then proceeds to gen-
e r a t e e l e m e n t s o f A -1 . If i n b r e e d i n g is speci-
fied, d m u s t b e s t o r e d in m e m o r y . A n o t h e r
p r o g r a m has b e e n w r i t t e n to c o m p u t e this
4/3 4/3 2]. vector.

19 9 -6 -6 -6 4 -4 0 0
REFERENCES
17 -6 -6 -6 0 0 -4 0
-6 12 0 0 0 0 0 0
1. Henderson, C. R. 1963. Selection index and
- -6 0 12 0 0 0 0 0 expected genetic advance. Page 141 in: Statistical
K I = I/6 -6 o 0 ~2 o o 0 0 genetics and plant breeding. Hanson, W. D. and H.
0 o 0 0 8 0 o o
F. Robinson, eds. NAS--NRC, Pub. 982.
o 0 0 o o I1 3 -6
-~ o 0 o 0 3 11 -6
2. Henderson, C. R. 1973. Sire evaluation and
0 0 0 0 0 -6 -6 12 genetic trends. Page 10 in Proc. of the Anim.
Breeding and Genet. Symp. in Honor of Dr. Jay
L. Lush. ASAS and ADSA, Champaign, IL.
T o illustrate c o m p u t a t i o n of s o m e of the 3. Henderson, C. R. 1974. General flexibility of
e l e m e n t s of this matrix, a 11 = 1 + ( . 2 5 ) ( 2 + linear model techniques for sire evaluation. J.
2 + 2 + 4/3 + 4 / 3 ) = 19/6;a 12 = (.5)(2 + 2 + Dairy Sci. 57:963.
4. Henderson, C.R. 1976. A simple method for
2) = 9/6 since 1 a n d 2 have c o m m o n p r o g e n y computing the inverse of a numerator relationship
3, 4, a n d 5; a n d a ~9 = ( - . 5 ) ( 2 ) = - 1 since 9 is matrix used in prediction of breeding values.
a p r o g e n y o f 7. Biometrics (In press.)

Journal of Dairy Science Vol. 58, No. 11