www.elsevier.com / locate / livprodsci
Selection strategies in sire referencing schemes in sheep
*
R.M. Lewis , G. Simm
Animal Biology Division, SAC, King’s Buildings, Edinburgh EH9 3JG, UK
Received 23 August 1999; received in revised form 4 February 2000; accepted 9 February 2000
Abstract
In sire referencing, genetic links are created among flocks by the mutual use of some rams (reference sires). These connections allow for across-flock genetic evaluations offering a larger pool of candidates for selection. Using stochastic simulation, the effect of three characteristics of the design of such schemes on rates of genetic response and inbreeding were investigated. We considered (i) the selection intensity for reference sires (highest ranking, or from the top sixth or top third of available candidates), (ii) the criteria on which reference sires were chosen (BLUP breeding value or phenotypic performance), and (iii) the extent to which the reference sires were used. For the latter, the number of reference sires used (1, 2 or 3) and the number of ewes mated to each reference sire (a total of 10, 15 or 30 ewes per flock or |15, 30 and 45% of
the population) was assessed. Fifteen flocks of different sizes (ranging from 40 to 140 ewes) were simulated. Reference sires were picked from a team of six rams of which half were replaced each year. Surplus ewes were mated to rams born within the flock and unrelated rams born outside the scheme. The mating of full and half-sibs was avoided. When selection was most intensive (highest ranking) the rate of genetic progress per annum was 1.51 to 1.73 as great as when it was least intensive (from top sixth or top third). Selection on BLUP breeding values achieved 1.25 to 1.31 times the genetic response of phenotypic selection. When more ewes (30) were mated to reference sires, progress was as much as 1.14 times as large that when fewer ewes were mated (20 and less). The average inbreeding coefficient after 15 years of selection was at most doubled in schemes where genetic improvement was more rapid. Even so, the rate of inbreeding was always lower than 0.3% per annum (less than 1% per generation). By optimising the selection strategy for a sire referencing scheme, genetic progress can be substantially improved with acceptable levels of inbreeding. 2000 Elsevier Science B.V. All rights reserved.
Keywords: Sire referencing schemes; Sheep; Genetic gain; Inbreeding; Simulation
1. Introduction
In many countries, the average size of pedigree sheep flocks is small with little scope for intensive
*Corresponding author, Animal Biology Division, SAC, Sir within-flock selection. Historically it has not been Stephen Watson Building, Bush Estate, Penicuik, Midlothian
simple to select animals from outside flocks to
EH26 OPH, Scotland, UK. Tel.: 144-131-535-3227; fax: 1
44-overcome the constraint of small flock size. Since
131-535-3121.
E-mail address: [email protected] (R.M. Lewis). flocks differ in their husbandry, the performance
records of animals in separate flocks and born in 100 females) linked by the same reference sires. The
different years could not be fairly compared. intensity and criteria used for selecting reference
With the introduction of best linear unbiased sires and the extent of their use within the scheme
prediction (BLUP) methodologies to sheep breeding was not explicitly considered. Nimbkar and Wray
programmes, across-flock genetic evaluations are (1991) considered some of these selection strategies
possible. But for BLUP to disentangle genetic from but their combined effect on response in sire
refer-environmental sources of variation in performance, encing schemes has yet to be tested.
genetic relationships or links among animals are Our objective was to investigate the effects of
needed across flocks (Garrick, 1991; Kennedy and specific operational characteristics of sire referencing
Trus, 1993). If the degree of linkage is adequate, the schemes in flocks of small size on rates of genetic
size of an individual flock is effectively enlarged, progress and inbreeding for a trait of moderate
since the genetic merit of animals in separate flocks heritability (0.25). This was undertaken using
sto-and born in different years can be directly sto-and chastic simulation. We consider (i) the selection
accurately compared (Kinghorn and Shepherd, intensity for reference sires, (ii) the criteria by which
1990). This allows more intense selection and there- reference sires are chosen and (iii) the extent to
fore quicker rates of genetic progress. which reference sires are used. For the latter,
differ-Sire referencing schemes are used to establish ent combinations of the number of reference sires
genetic links across flocks. In these co-operative used and the number of ewes mated to reference
breeding programmes a team of rams (or reference sires were assessed.
sires) is selected, typically from among member flocks. Each member of the scheme then uses some,
although not necessarily the same, rams from this 2. Methods
team to mate to a proportion of ewes within their
own flock. Stochastic simulation was used to investigate
Several studies have focused on how reference design alternatives for sire referencing schemes. The
sires may be used to link dispersed flocks or herds to population simulated was that of terminal sire sheep
improve the accuracy of genetic evaluations of in the United Kingdom, which have the common
young male progeny tested in a sample of them goal to improve lean meat production (Guy and
(Foulley and Clerget-Darpoux, 1978; Hudson et al., Croston, 1994). This was done to model realistic
1980; Foulley et al., 1983; Miraei Ashtiani and schemes in practice. The growth and carcass traits
James, 1991, 1992). However, besides this role, that dominate in such programmes are moderately
reference sires themselves are a means to genetic heritable.
improvement. This is particularly important where
flock (or herd) sizes are small with reference sires 2.1. Genetic model
mated to a substantial proportion of the available
females. In such situations, the optimal use of the The lean growth trait to be improved (the goal
reference sires to accelerate genetic gain and the trait) was recorded in both sexes at around 150 days
consequence of their use on inbreeding has not been of age. An additive infinitesimal model was assumed.
investigated. For a base population of unrelated animals, the true
Rates of genetic gain and inbreeding have been breeding values were obtained from a normal
dis-compared when flocks were independent or linked tribution with mean zero and an initial additive
2
though reference sires both by prediction (Morris et variance (s ) of 0.25. The number of base males
a0
al., 1980) and by simulation (Hanocq et al., 1996; and females created depended on the size of each
Roden, 1996). With sire referencing, genetic progress flock.
was increased by over 30% and inbreeding level was The trait litter size was also simulated to model
more than halved. However, these studies tested a reproductive rate within flocks. It was assumed that
single design for a sire referencing scheme with litter size was uncorrelated with the goal trait and
litter size were drawn from a normal distribution each litter size category. Since extra variation was
2
with mean zero and s of 0.10. Permanent en- introduced by flock and year, the variance of the
a0
2
liability (s ) was greater than one. This additional
vironmental variation for the trait was assumed to be
2
flock and year variation (s 21) had a non-linear
negligible.
effect on the proportion of ewes placed in each litter For each trait, the true breeding values of
off-size category. Depending on the location of a
spring were simulated as TBV5(1 / 2)(TBV 1
i s
threshold, a change of equal size in threshold value
TBV )1m , where TBV , TBV and TBV are the true
d i i s d
defined a different proportion of the liability (or area breeding value of the offspring (i ), its sire (s) and its
of the standard normal density). To account for this dam (d ), respectively. The Mendelian sampling term
*
non-linearity, an adjusted threshold value (t ) was
(m ) was taken from a distribution with mean zeroi i
2
used to assign ewes to litter size categories. The
and variance (1 / 2) 1f 2(F 1F ) / 2gs , where F
s d a0 s
*
value t was found using a search algorithm that
and F are the inbreeding coefficients of the sire andd i
minimised the function dam, respectively. Inbreeding coefficients were
ob-tained using the algorithm of Meuwissen and Luo `
2 * 2(t 2t )
1 i i
(1992). The animal’s sex was assigned at random, ]]]] ]]]]
pi2
S
]]]D
E
q(t )expiS
2D
dti 2with equal probability of being male or female.
œ
2p(s 21) 2(s 21)2`
where q(t ) is the value of the integral of the standardi
normal distribution between t and infinity (Amer,
2.2. Phenotypic model i
personal communication). Litter size changes sys-tematically with age. Therefore the proportion of For the goal trait, fixed environmental effects of
ewes in each litter size category, and thus the flock, year, dam age, lamb sex and rearing type
adjusted threshold values, were different for 2, 3 and (single or multiple) were generated. Flock and year
4-year and older ewes. The prescribed (input) aver-effects were obtained by taking a random number
age litter size values were equal to those obtained in from a normal distribution with mean zero and
the simulation and are shown in Table 1 by age variance 0.20 for flock and 0.05 for record year.
category. On average, ewes that lambed produced Offspring of ewes 3 years old and older had an
litters of 1.75 lambs. advantage of 0.20 units in performance. Female
offspring, and those reared in multiple litters, had
0.85 and 0.35 unit disadvantages, respectively, in 2.3. Reproductive and mortality parameters
performance for this trait. The size of these effects
was based on evaluations of industry sire referencing 2.3.1. Conception rate
schemes as described by Mercer et al. (1994). For Rams and ewes were considered reproductively
litter size, environmental influences of flock and year mature at 6 and 15 months of age, respectively.
were simulated as for the goal trait. There was one mating season per year that lasted for
The phenotypic value for each trait (the goal trait three oestrous cycles (a total of 51 days) and all ewes
and litter size) was generated as the sum of the fixed were assumed to be cycling at the start of season. In
environmental effects, the residual value (obtained at each of the oestrous cycles one and two, 65% of the
random from a normal distribution with mean zero
2
and variance 12s ), and the true breeding value.
a Table 1
Litter size was assumed to have a continuous, Percentage of ewes within a lambing category
normal underlying distribution (liability). Variation
Ewe age (years) Percentage of ewes within a lambing
on this liability scale was both genetic and
en-category
vironmental (flock, year and residual values) in
Single Twin Triplet
origin. When a ewe’s liability exceeded specific
2 39.2 59.1 1.7
threshold values (t ) on the liability scale, she gavei
3 25.4 69.3 5.3
birth to one, two or three lambs. The thresholds
4 and older 31.6 61.8 6.6
ewes conceived; at cycle three, of the remaining tion was then carried out for 15 years with genetic
open ewes, 20% conceived. Ewes mated to reference evaluation of all animals once each year. In all
sires (RS) had a 65% chance of conceiving to a scenarios a team of six rams were made available as
single artificial insemination (AI). Ewes that failed to reference sires (RS). RS were always chosen from
AI were then mated naturally to a ram from their among rams born in the member flocks of the
respective flock over the final two oestrous cycles of scheme.
the mating season. Overall, about 90% of the ewes Depending on the scenario tested, the specified
mated lambed. number of RS used within a flock was chosen at
random from the team of six rams. When more than
2.3.2. Mortality and culling one RS were used in each flock, only one of these
The rate of mortality from birth to recording of the RS was re-used in the following year. On average
goal trait was 13% for singletons, 13.6% for twins the generation interval for reference sires and natural
and 15.6% for triplets. Between recording and first service sires was 2.7 years.
mating 3% of the animals died. Thereafter, an annual
mortality rate of 2.5% was assumed. All rams chosen 2.5.1. Selection intensity
as sires were culled at 4 years of age. Ewes could The intensity at which rams were selected was
lamb a maximum of four times and thus were culled varied. This applied to both RS and rams chosen
at about 6 years of age. The average generation from within flocks for home use. Three selection
interval for ewes was 3.5 years. intensities were considered. Firstly, rams with the
highest ranking (best) for the selection criteria were
2.4. Establishing flocks selected. For the RS team, the rams chosen were
within the top 0.5% of the candidates available.
Fifteen flocks with sizes between 40 and 140 Rams were also selected at random from among the
breeding ewes (average size of 70 with standard top sixth and top third once ranked on the selection
deviation 30) were evaluated. Before the start of sire criteria. No more than one ram from a full-sib family
referencing, each flock underwent 10 years of ran- (in a birth year) was chosen. Enough ewes were
dom selection. One half of these flocks used only chosen each year to maintain a constant flock size;
unrelated rams from outside the scheme. The remain- around 26% of the breeding ewes in a flock were
ing flocks used a mix of outside and homebred rams. replaced annually.
The mean genetic value for outside rams was equal
to that of contemporary animals born within the 2.5.2. Selection criteria
flocks under evaluation. That is, the true breeding Rams and ewes were chosen on either of two
value of outside rams was obtained from a normal selection criteria: their estimated breeding value
distribution with mean and additive variance ger- (EBV) or their phenotype (mass selection) for the
mane to the year of evaluation. Each flock used a goal trait. BLUP EBVs were obtained by using an
minimum of two rams, with each ram mated to about individual animal model with genetic groups and
20 ewes. Rams were first used as sires at about 18 fitting flock, year, dam age, lamb sex and rearing
months of age and at most for two mating seasons type as fixed terms. Animals with unknown ancestors
within a flock. born during the years preceding sire referencing were
Mate assignment was based on a strategy that assigned to one genetic group. Thereafter, all outside
avoided mating relatives. This involved two levels of rams born in a year were assigned to a separate
priority. Firstly, son–dam, daughter–sire and full-sib genetic group. With mass selection, no pre-correction
matings were avoided. Secondly, where possible, for the influence of environmental factors was made.
half-sib matings were avoided. However, since selection decisions were made within
year and sex, the noise introduced by these fixed
2.5. Sire referencing scheme effects was necessarily accounted for. For
replace-ment decisions made within-flock (the selection of
Following the period of random selection, the 15 homebred rams and ewes), flock effects were also
2.5.3. Reference sire usage For animals born each year, the within-flock and
Scenarios in which 0, 1, 2 or 3 RS were used were between-flock additive variance and the accuracy of
considered. Since the specified number of RS needed selection (the correlation between the true breeding
was chosen at random by each flock from the RS value for the goal trait and the selection criteria)
team of six rams, individual flocks did not necessari- were computed. The selection differential was
calcu-ly use the same RS. When no RS were chosen, lated as the average superiority of the selected
selection was strictly within-flock. A RS was mated parents for the selection criteria weighted by progeny
to 5, 10, 15, 20 or 30 ewes. Since the smallest flock number. This statistic was computed separately for
had 40 ewes, only some combinations of the number RS (across flocks), and for homebred sires and ewes
of RS used and the number of ewes mated were (within flocks). All scenarios evaluated were
repli-considered (Table 2). Within a flock, in total 10, 20 cated 100 times and the results averaged across the
or 30 ewes were mated to RS; this corresponds with replicates and, where appropriate, flocks.
|15%, 30% and 45% of the ewe population being
mated to RS. If excess ewes were available within a
flock above those mated to RS, these were mated to 3. Results
outside or homebred rams as described earlier.
Once sire referencing began, it required several
2.5.4. Standard scheme years for the system to adjust to the selection
A standard scheme was used as the benchmark for strategy imposed. Since selected animals were
gradu-comparing genetic response and inbreeding in alter- ally introduced into a flock, the selection differential
native scenarios. In this scheme the best animals for males and females and the rate of genetic gain
were selected on EBV, three RS chosen at random was more variable in early (year 1 to 5) than later
from the RS team and each RS was mated to 10 years (year 5 to 15).
ewes (in total, 30 ewes mated). The average inbreeding coefficient was 2.2% at
the start of sire referencing. In early years, it
2.6. Statistics obtained remained largely unchanged or even declined (when
30 ewes were mated to RS) because the RS used
Average true breeding values (G ) and inbreedingi within a flock usually originated from other
mem-coefficients (F ) were obtained for all animals born ini bers’ flocks which were unrelated. After 5 years,
the ith year, and for rams chosen as RS in that year. once genetic relationships among animals had been
The annual rate of response between years j and i established, inbreeding levels accumulated at a
rela-was calculated as DG 5(G 2G ) /( j2i ), where tively constant rate within a scenario.
i2j j i
j.i. Rates of inbreeding were calculated for each
year as DF 5(F2F ) /(12F ). The rate of 3.1. Selection intensity
i i i21 i21
inbreeding between year i and j (DF ) was obtained
i2j
by taking the average of annual rates. Results were Genetic response and inbreeding coefficients
ob-summarised for the early (1–5) and late (5–15) tained per year when selection intensity was varied is
years of selection. shown in Fig. 1. Selection was based on BLUP EBV
with three RS each mated to 10 ewes. For com-parison, the response from within-flock selection
Table 2 when the best animals were chosen as replacements
Scenarios considered for reference sire usage
based on BLUP EBV is also presented.
Number of Total number of ewes mated to When the selection intensity was decreased, the reference sires reference sires
rate of genetic response was 0.58 to 0.69 times that
0 10 20 30 when selection was most intensive (the standard
scheme), and the rate of inbreeding was only 0.17 to
0 ✓
1 ✓ ✓ ✓ 0.33 times as large. (The same trends were observed
2 ✓ ✓ ✓ for mass selection although the decrease in the rate
3 ✓
Fig. 1. Change in genetic mean (phenotypic standard deviation units) and inbreeding coefficient (%) over years with different selection intensities. Selection was based on BLUP breeding value in all cases with, for sire referencing, three reference sires each mated to 10 ewes. Selections made from:j, best;m, top 1 / 6;^, top 1 / 3;h, best but within-flock selection only.
use of the best animals within-flock achieved slightly variance was 0.86 as great as that at the start
within-higher rates of genetic progress than sire referencing flock. In the first year of sire referencing, this
within-with less intensive selection (top sixth or top third ) flock variance increased (Table 3). Linkage
dis-but inbreeding was substantially higher. equilibrium is expected to reduce within-flock
Table 3 genetic gain and inbreeding coefficient at the end of Pooled within- and between-flock additive variance for different selection (G ; F ) are shown in Tables 4 and 5 for
a 15 15
selection intensities by year of selection
different selection criteria. Selection intensity and
Additive Year Selection intensity ram usage is also varied. variance of selection
Best Top 1 / 6 Top 1 / 3 With mass selection, the annual and cumulative
b genetic response were between 0.75 to 0.82 times
Within-flock 0 0.216 0.216 0.216
that from selection on EBV for equivalent ram usage
1 0.246 0.228 0.226
5 0.235 0.207 0.205 and selection intensity (Table 4). However, if the
10 0.226 0.205 0.204 best animals were selected on performance records,
15 0.227 0.210 0.207
higher gains were achieved than with less intensive
Max S.E. 0.001 0.001 0.001
selection based on EBV.
Min S.E. 0.002 0.002 0.002
The rate of inbreeding with mass selection was at
b
Between-flock 0 0.204 0.204 0.204 most 0.67 of that from selection on EBV and, at year
1 0.178 0.169 0.175 15 of selection, the inbreeding coefficient was no
5 0.207 0.178 0.171
more than 0.80 times as large (Table 5). In fact, with
10 0.228 0.191 0.174
selection based on performance alone, the average
15 0.230 0.190 0.177
level of inbreeding remained largely unchanged
Max S.E. 0.004 0.004 0.003
Min S.E. 0.005 0.005 0.004 (under 0.1% per annum) throughout selection; when
a 20 or more ewes were mated to RS, the average
The standard scheme but with the selection intensity varied
2
(a050.25). inbreeding coefficient was of similar or smaller size
b
The average within- or between-flock additive variance at the than that at the start of selection (F 52.2). With 0
start of sire referencing. Additive variances were adjusted for selection withflock on EBV or performance, in-small differences in initial values between selection intensities.
breeding levels were substantially higher.
At the start of sire referencing, the accuracy of
However, the use of RS from other scheme mem- selection on EBV was 0.61 and the accuracy of
bers’ flocks caused an increase in that variation. selection on performance record was 0.45. When the
When selection was most intense (the best strategy), best animals were chosen on EBV, the accuracy of
the additive variance approached its initial size evaluation was 1.15 to 1.25 times as great as with
(0.246). This was because the genetic superiority of less intensive selection by year 15 of selection. If
the progeny of RS relative to those from homebred selection was less intensive or based on performance,
and outside rams was larger when the RS themselves any improvement in accuracy over the years of
were intensely selected thus introducing more addi- selection was less.
tive variation. This advantage remained throughout
selection. In all scenarios, the within-flock additive 3.3. Reference sire usage
variance then declined through year 5 of selection
and remained relatively constant thereafter. 3.3.1. Number of ewes mated to reference sires
At the start of sire referencing, flock genetic Genetic progress was highest when the most ewes
means differed due to random drift. The between- (30) were mated to reference sires as long as the best
flock additive variance declined in the first year of rams were selected for the RS team. The rate of
sire referencing as RS were shared across flocks. As genetic gain was 0.94 as great when 20 ewes were
selection continued, the genetic means of individual mated to RS and 0.88 as great when 10 ewes were
flocks diverged particularly if selection was more mated to RS, as compared with 30 ewes mated to RS
intense (best or top sixth). (Table 4). When selection was less intense or based
on performance record, genetic progress was not
3.2. Selection criteria increased by mating RS to more than 10 ewes.
The greater cumulative gain achieved when 30
Average rates of genetic gain and inbreeding from ewes were mated to the best RS partly reflects higher
year 5 to 15 (DG ; DF ) and the cumulative gains early in selection. Annual genetic gain between
Table 4
Rate of genetic progress (phenotypic standard deviation units) for different selection intensities, selection criteria and usage of reference
a
sires (RS)
Selection No. ewes Number EBV Mass
intensity mated to RS RS used D
G5 – 15 G15 DG5 – 15 G15
Best 0 0 0.095 1.44 0.078 1.17
10 1 0.112 1.67 0.089 1.32
2 0.112 1.68 0.087 1.29
20 1 0.121 1.82 0.092 1.39
2 0.121 1.83 0.091 1.36
30 1 0.129 1.97 0.099 1.51
2 0.127 1.92 0.097 1.49
3 0.128 1.95 0.100 1.51
Top 1 / 6 0 0 0.079 1.18 0.065 0.97
10 1 0.087 1.31 0.068 1.02
2 0.087 1.33 0.069 1.03
20 1 0.086 1.32 0.070 1.05
2 0.088 1.33 0.070 1.04
30 1 0.090 1.38 0.071 1.08
2 0.087 1.34 0.069 1.04
3 0.088 1.36 0.068 1.05
Top 1 / 3 0 0 0.068 1.04 0.056 0.84
10 1 0.074 1.12 0.060 0.89
2 0.073 1.10 0.059 0.88
20 1 0.074 1.13 0.060 0.89
2 0.072 1.11 0.059 0.89
30 1 0.075 1.16 0.060 0.90
2 0.074 1.14 0.060 0.91
3 0.074 1.13 0.060 0.91
Min S.E. 0.001 0.01 0.001 0.01
Max S.E. 0.001 0.02 0.001 0.02
a
The standard scheme is shown in bold.
years 5 and 15 was 0.95 of that between years 1 to 5. mated to RS, the ratio of within to between flock
This reduction corresponds with a larger fall in the additive variance remained at one after 10 years of
within- and between-flock additive variance in the selection. This suggests that once a sufficient
propor-early years of selection in this scenario where more tion of ewes in all member flocks are mated to RS
ewes were mated to RS. When 20 or fewer ewes (over 20%), a scheme effectively operates as a large
were mated to RS, annual rates of genetic gain panmictic population allowing a more reliable
ge-remained relatively constant throughout selection. netic evaluation of animals across-flock. That was
This greater gain also reflects the structure of the less the case when fewer ewes were mated to RS.
scheme when more ewes were mated to RS. In Fig. 2 The annual rate of inbreeding, and the inbreeding
the ratio of between- to within-flock additive vari- coefficient at year 15, was in general smaller when
ance is shown at specific years of selection when more ewes were mated to RS (Table 5). The
different numbers of ewes were mated to the best RS exception was when selection decisions were based
selected on EBV. As selection continued, the genetic on EBV and the best animals were chosen — as
merit of individual flocks diverged and the between more ewes were mated to RS, the annual rate of
flock additive variance increased toward and then inbreeding increased. With intense selection on EBV,
Table 5
a
Rate of inbreeding (%) for different selection intensities, selection criteria and usage of reference sires (RS)
Selection No. ewes Number EBV Mass
intensity mated to RS RS used D
F5 – 15 F15 DF5 – 15 F15
Best 0 0 0.627 10.66 0.348 7.13
10 1 0.206 4.97 0.090 3.68
2 0.223 5.14 0.099 3.77
20 1 0.220 4.46 0.043 2.49
2 0.234 4.61 0.036 2.45
30 1 0.285 4.85 0.039 1.98
2 0.278 4.71 0.036 1.91
3 0.260 4.41 0.032 1.91
Top 1 / 6 0 0 0.489 9.04 0.334 7.01
10 1 0.172 4.95 0.097 3.85
2 0.216 5.35 0.125 3.90
20 1 0.105 3.50 0.021 2.35
2 0.132 3.72 0.024 2.35
30 1 0.103 2.94 20.002 1.66
2 0.105 3.00 0.004 1.68
3 0.086 2.77 20.005 1.64
Top 1 / 3 0 0 0.469 8.84 0.315 6.79
10 1 0.164 4.83 0.102 3.85
2 0.181 4.90 0.095 3.69
20 1 0.070 3.09 0.010 2.25
2 0.075 3.23 0.007 2.18
30 1 0.062 2.51 0.000 1.69
2 0.064 2.53 20.002 1.63
3 0.043 2.28 20.007 1.54
Min S.E. 0.004 0.07 0.003 0.05
Max S.E. 0.017 0.27 0.003 0.06
a
The standard scheme is shown in bold.
often being sons of former RS. When mated to more criteria and usage of RS. As the total number of
ewes within each flock, the level of inbreeding ewes mated to RS decreased, the increase in
accura-increased. When selection was less intense or based cy with each year of selection was larger. This was
on less accurate criteria, the ancestral relationship most pronounced when selection was intense and
among the members of the RS team was substantial- based on EBV. When fewer ewes were mated to RS,
ly less. Mating more ewes to rams from such a team the number of offspring per homebred or outside ram
increased rather than decreased the effective size of increased within a flock. With intense selection on
the scheme. EBV, homebred rams were chosen from fewer
Although the annual rate of inbreeding was higher families increasing co-ancestry within-flock. These
when more ewes were mated to RS with the best factors increased the information drawn from
rela-EBV, the average inbreeding coefficients at year 15 tives managed in the same flock improving the
were of similar or smaller size. This was because of average accuracy of evaluation. These higher
‘with-a l‘with-arger reduction in inbreeding ‘with-at the st‘with-art of sire in-flock’ accuracies correspond with less accurate
referencing when more ewes were mated to ge- comparisons of animals across flocks contributing to
netically unrelated RS. the slower genetic response observed in scenarios
The average accuracy of selection at year 15 is where RS usage was less.
Fig. 2. Ratio of between- to within-flock additive variance at specific years of selection when different numbers of ewes were mated to reference sires.&, 0 ewes;h, 10 ewes;9, 20 ewes;j, 30 ewes.
Table 6
Accuracy and coefficient of variation (CV%) between replicate of mean breeding value at year 15 for different selection intensities, selection
a
criteria and usage of reference sires (RS)
No. ewes Number Best Top 1 / 6 Top 1 / 3
mated RS used
EBV Mass EBV Mass EBV Mass
to RS
Accuracy
0 0 0.719 0.488 0.640 0.478 0.605 0.458
10 1 0.734 0.481 0.676 0.455 0.629 0.446
2 0.727 0.481 0.664 0.462 0.630 0.451
20 1 0.714 0.476 0.650 0.453 0.622 0.442
2 0.714 0.470 0.657 0.453 0.630 0.448
30 1 0.699 0.460 0.634 0.439 0.608 0.443
2 0.702 0.466 0.642 0.446 0.622 0.444
3 0.699 0.461 0.645 0.442 0.624 0.434
CV%
0 0 13.06 13.87 13.52 13.31 10.40 13.24
10 1 10.13 12.21 11.15 12.97 11.57 12.96
2 10.91 12.37 9.28 14.25 12.21 13.12
20 1 9.49 11.23 11.15 11.76 11.00 11.54
2 8.89 10.59 10.61 12.01 10.95 12.80
30 1 9.34 9.64 11.52 13.16 10.04 13.78
2 8.77 10.00 9.42 11.24 10.71 11.13
3 8.25 9.62 10.60 12.51 10.80 13.44
a
100 replicates of the simulation for true breeding medium (1.13 to 1.24 times) and small (1.44 to 1.65)
value at year 15 of selection is also shown. With sized flocks. The same trends were observed for the
intensive selection, particularly on EBV, variation other selection strategies considered, although
differ-between replicates was less when more ewes were ences were smaller.
mated to RS with less risk as to the outcome of the These results correspond to the proportion of ewes
selection programme (Meuwissen, 1991; Woolliams mated to RS within flocks of different size. As flock
and Meuwissen, 1993). size decreases, proportionally more ewes were mated
to RS. Although these RS were genetically superior
3.3.2. Number of reference sires used and caused quicker genetic progress, their use
re-For a set number of ewes mated, there was little duced the number of ewes mated to outside rams
difference in genetic progress and selection accuracy leading to more inbreeding.
when different numbers of RS were used. However, when the best rams were selected on EBV for the RS
team, using more RS reduced variability in genetic 4. Discussion
response. This probably reflects sampling when
choosing RS at random from a team of fixed size Committing more ewes to reference sire matings
where all members have similar genetic merit. When (30 versus 20 or fewer) increased rates of genetic
more RS were used within each flock, it was more gain with less variation in selection response. This
likely the RS chosen overlap between flocks. This was particularly the case when rams with the highest
ensures that progeny of the entire RS team were EBV were chosen for the reference sire team and
more equitably represented in all flocks. when three RS (from the team of six) were used
within each flock. This increase in genetic progress
3.4. Flock size was due to more offspring of the elite reference sires
born in each flock and stronger across-flock genetic
In Table 7 the cumulative genetic gain and the links when more rams were used in common among
average inbreeding coefficient at year 15 are shown flocks. Nimbkar and Wray (1991) also showed that
for small (40–50 ewes), medium (60–90 ewes) and with heavier use of highly selected reference sires
large (100–120 ewes) sized flocks for the standard (50 versus 20% of females mated to reference sires)
scheme. RS usage was varied. Cumulative genetic rates of gain were accelerated and to a similar extent
gain was as much as 1.04 times as great in medium as observed in this study.
flocks and as much as 1.07 times as great in small Reference sires serve two roles. Firstly they create
flocks as compared with large flocks. The inbreeding genetic links between flocks. The strength of genetic
coefficient, however, was considerably larger in the links depends on progeny numbers. When a small
Table 7
Cumulative genetic progress (phenotypic standard deviation units) and average inbreeding coefficient (%) at year 15 for different flock sizes
a
and numbers of ewes mated to reference sires (RS)
No. ewes Flock size mated
Small Medium Large
to RS
(40–50 ewes) (60–90 ewes) (100–140 ewes)
G15 F15 G15 F15 G15 F15
0 1.34 17.74 1.45 9.55 1.49 6.42
10 1.69 6.23 1.68 4.86 1.65 4.31
20 1.87 5.76 1.81 4.48 1.77 3.71
30 2.03 6.14 1.96 4.61 1.89 3.72
Min S.D. 0.02 0.13 0.02 0.28 0.02 0.25
Max S.D. 0.04 1.45 0.05 0.50 0.05 0.87
a
number of ewes were mated to reference sires, each avoiding the mating of close relatives; (ii) the overall
had few progeny in a flock. More ewes were then size of the scheme (over 1000 breeding ewes); and,
mated to each homebred and outside ram and that (iii) the use of outside rams. The outside rams used
increased the accuracy of their evaluation (Hudson et in this study were unrelated to contemporaries born
al., 1980). However, such gains in accuracy were within the scheme yet of the same average genetic
counteracted by losses in genetic links between merit as them. If outside rams are related to animals
flocks and, where reference sires were themselves of born in the scheme or are genetically inferior to them
high merit, substantially slower genetic progress. — undoubtedly the case as selection progresses —
Where the goal of a scheme is to accelerate gain their contribution to the control of inbreeding would
within its members’ flocks, the extent to which be lessened. When no outside rams were used, the
reference sires are used may differ from that to rate of inbreeding was at least three times as large in
maximise the accuracy of the evaluation of indi- comparable scenarios of sire reference schemes
vidual rams (Foulley et al., 1983). In this study, (Nimbkar and Wray, 1991; Roden, 1996). Although
genetic gain was highest when about 45% of the the use of outside rams may reduce inbreeding, the
ewes (30 per flock) were mated to reference sires. If genetic merit of these rams is not comparable to that
flock sizes allowed, this likely could be increased of rams born within the scheme; that, at the least,
further if more ewes were mated to reference sires. increases risk.
Miraei Ashtiani and James (1991, 1992) show that An alternative to sire referencing is an open
over a range of scenarios, however, the accuracy of nucleus breeding scheme. Roden (1996) compared
breeding value estimation is maximised when ap- rates of genetic gain and inbreeding in such schemes.
proximately one third of progeny are from reference With unrestricted migration of rams and ewes
be-sires. tween the nucleus and member flocks, the rate of
The second role for reference sires, the focus of genetic gain was the same, while the rate of
inbreed-this study, is to bring about genetic improvement. ing was 1.20 times that with sire referencing. With an
This clearly requires that reference sires are them- additional stage of selection that ensured animals
selves genetically superior. Only when the selection with highest EBV were mated within the nucleus
of reference sires was intensive and based on EBV flock each year, the nucleus scheme achieved 1.09 to
was genetic progress increased appreciably over that 1.14 times the rate of genetic progress but with 1.75
from within-flock selection. An exception was inten- to 1.97 times the inbreeding rate as that of sire
sive (best) mass selection. With that selection referencing. In practice, such a strategy would also
strategy, genetic gains from sire referencing were require movement of rams and ewes between the
substantial and higher than in otherwise comparable nucleus and members’ flocks with associated animal
scenarios based on less intensive selection (top 1 / 6 health and organisational considerations.
and less) with BLUP breeding values. This result in An alternative would be to combine attributes of
part reflects the extent environment influenced per- sire referencing and nucleus schemes. Roden (1996)
formance. In this study, within a year and sex, compared responses in a conventional sire
referenc-husbandry and rearing effects defined about 20% of ing scheme with that obtained when such a scheme
the phenotypic variance. If these effects were larger, was augmented with a dispersed nucleus. The
addi-the accuracy of mass selection, and addi-the progress tion of the dispersed nucleus involved mating the top
achieved with it, would be less. 10% of ewes from across the scheme to the
highest-The strategies that increased rates of genetic gain ranking rams available other than the reference sires.
also led to higher rates of inbreeding. This expected The rate of genetic progress was 1.13 times that of
link between response and inbreeding has been conventional sire referencing with 1.33 to 1.52 times
´
reported elsewhere (Toro and Silio, 1990; Villanueva the rate of inbreeding. The same improvement in
et al., 1995). Even so, inbreeding levels were still genetic gain was achieved in this study by altering
low — under 0.3% per annum or less than 1% per reference sire usage with a smaller increase in
Garrick, D.J., 1991. Best linear unbiased prediction for across
complimented by some assortative mating
within-flock / year breeding values. Proc. NZ Soc. Anim. Prod. 51,
flock, could allow even higher rates of genetic gains
411–416.
to be achieved with acceptable rates of inbreeding. Guy, D.R., Croston, D., 1994. UK experience and progress with
sire referencing schemes. In: Proceedings 5th World Congress on Genetics Applied to Livestock Production, Vol. 18, pp. 55–58.
5. Conclusions
Hanocq, E., Boichard, D., Foulley, J.L., 1996. A simulation study of the effect of connectedness on genetic trend. Genet. Sel.
Mating 30 ewes to reference sires produced the Evol. 28, 67–82.
quickest rates of genetic progress, particularly when Hudson, G.F.S., Schaeffer, L.R., Wilton, J.W., 1980. Alternative
three reference sires were used. The intensity at progeny testing programs for weaning weight and ease of
calving in beef cattle. Can. J. Anim. Sci. 60, 609–620.
which rams were selected had an important
conse-Kennedy, B.W., Trus, D., 1993. Considerations on genetic
connec-quence on genetic gain. When selection was most
tedness between management units under an animal model. J.
intensive, the rate of genetic gain was 1.51 to 1.73 as Anim. Sci. 71, 2341–2352.
great as that when least intensive. Although selection Kinghorn, B.P., Shepherd, R.K., 1990. The impact of across-flock
strategies that increased genetic response also in- genetic evaluation on sheep breeding structures. In:
Proceed-ings 4th World Congress on Genetics Applied to Livestock
creased the rate of inbreeding, given the
characteris-Production, Vol. 15, pp. 7–16.
tics of the schemes considered (mating of close
Mercer, J.T., Brotherstone, S., Bradfield, M.J., Guy, D.R., 1994.
relatives avoided; over 1000 breeding ewes; some Estimation of genetic parameters for use in sheep sire
referenc-use of unrelated outside rams) inbreeding was low ing schemes. In: Proceedings 5th World Congress on Genetics
(less than 1% per generation). In conclusion, the Applied to Livestock Production, Vol. 18, pp. 39–42.
Meuwissen, T.H.E., 1991. Expectation and variance of genetic
intensive selection and use of reference sires will
gain in open and closed nucleus and progeny testing schemes.
achieve the highest rates of genetic progress and
Anim. Prod. 53, 133–141.
these gains are sustainable over, at least, a medium Meuwissen, T.H.E., Luo, Z., 1992. Computing inbreeding
co-time horizon. efficients in large populations. Genet. Sel. Evol. 24, 305–313.
Miraei Ashtiani, S.R., James, J.W., 1991. Efficient use of link rams in Merino sire referencing schemes. Proc. Aust. Assoc. Anim. Breed. Genet. 9, 388–391.
Acknowledgements
Miraei Ashtiani, S.R., James, J.W., 1992. Optimum distribution of progeny in sire referencing schemes. Proc. Aust. Assoc. Anim.
The financial support of the Meat and Livestock Breed. Genet. 10, 476–479.
Commission is gratefully acknowledged as are the Morris, C.A., Jones, L.P., Hopkins, I.R., 1980. Relative efficiency
of individual selection and reference sire progeny test schemes
contributions of David Croston and Derrick Guy. We
for beef production. Aust. J. Agric. Res. 31, 601–613.
are also grateful to our colleagues Peter Amer, Ron
Nimbkar, C., Wray, N., 1991. An investigation of the use of sire
Crump, Bill Dingwall, Robin Thompson, and Beatriz referencing in genetic improvement in beef cattle. Anim. Prod.
Villanueva for their suggestions and input into the 52, 567, Abstract.
project. The ongoing interest and support of British Roden, J.A., 1996. A comparison of alternative nucleus breeding
systems and a sire referencing scheme for sheep improvement.
Sire Referencing Scheme members in this research is
Anim. Sci. 62, 265–270.
greatly appreciated.
´
Toro, M.A., Silio, L., 1990. Selection for lean meat production in sheep: a simulation study. In: Proceedings 4th World Congress on Genetics Applied to Livestock Production, Vol. 15, pp.
References 96–99.
Villanueva, B., Simm, G., Woolliams, J.A., 1995. Genetic progress and inbreeding for alternative nucleus schemes for beef cattle. Foulley, J.L., Clerget-Darpoux, F., 1978. Progeny group size for
Anim. Sci. 61, 231–239. evaluating natural service bulls using AI reference sires. Ann.
Woolliams, J.A., Meuwissen, T.H.E., 1993. Decision rules and Genet. Sel. Anim. 10, 541–546.
variance of response in breeding schemes. Anim. Prod. 56, Foulley, J.L., Schaeffer, L.R., Song, H., Wilton, J.W., 1983.
179–186. Progeny group sizes in an organised progeny test programme
