Published December 5, 2014
Genetic diversity and pedigree analysis of the Finnsheep breed1
M.-H. Li,2 I. Strandén, and J. Kantanen3
Biotechnology and Food Research, MTT Agrifood Research Finland, FI-31600 Jokioinen, Finland
ABSTRACT: Genetic diversity in the Finnsheep
breed was analyzed by quantifying the demographic
trends, the depth of known pedigree, effective population size, and the amount of inbreeding, as well as identifying candidate rams within the current population
for future breeding and conservation purposes. Pedigree
records of 148,833 animals with a pedigree completeness coefficient ≥0.60 and born from 1989 to 2006 were
used to estimate the parameters. Mean inbreeding coefficient increased by 0.10% (P < 0.001) and 0.15% (P
< 0.001) per annum in all animals and breeding (i.e.,
reproducing) animals, respectively. Average relationship coefficients among rams, among ewes, and between
rams and ewes in breeding animals increased over time
and reached 1.67, 1.45, and 1.46% in the 2005 cohort,
respectively. The average for breeding rams was above
the other 2 averages in almost all birth years. The observed generally low average relationship coefficients
between rams and ewes indicate that no extra restrictions on the use of the breeding animals are needed in
the near future. Average generation interval was 2.85
yr in the studied period, and the effective population
size was estimated to be 119 and 122 using different
methods. Relationship coefficients of rams with other
breeding rams and rams with breeding ewes are suggested to aid in situ and ex situ conservation decisions
on maintaining genetic diversity of Finnsheep.
Key words: effective population size, Finnsheep, genetic diversity, inbreeding, pedigree analysis
©2009 American Society of Animal Science. All rights reserved.
INTRODUCTION
The Finnish native sheep, Finnsheep, is an extremely
prolific breed, exhibiting several components of fertility
such as early sexual maturity, high ovulation rate, outof-season lambing, and large litter size (Maijala and
Österberg, 1977; Maijala, 1984, 1988, 1997). In addition, a considerable proportion of the animals produce
good quality wool in a variety of natural colors with desirable characteristics (Maijala, 1988, 1996). Thus, the
Finnsheep has been exported to more than 40 countries
for experiments on prolificacy and for creating new
breeds (Fahmy, 1996).
1
The authors thank the ProAgria Association of Rural Advisory
Centres in Finland for the data used in this study. Theo Meuwissen
at the Department of Animal and Aquacultural Sciences, Norwegian
University of Life Sciences, Ås, Norway, and 2 anonymous reviewers
are acknowledged for critical and useful comments on an earlier version of the manuscript.
2
Present address: Ecological Genetics Research Unit, Department
of Biological and Environmental Sciences, PO Box 65, FI-00014 University of Helsinki, Finland.
3
Corresponding author: [email protected]
Received January 7, 2008.
Accepted December 22, 2008.
J. Anim. Sci. 2009. 87:1598–1605
doi:10.2527/jas.2008-0848
Originally, Finnsheep were used mainly for serving
domestic needs for wool and fur, but since the 1950s
the main use has gradually shifted to meat production, whence prolificacy is highly appreciated. Since the
1980s, multi-purpose use has been considered important for the Finnsheep in Finland (Puntila and Maijala,
1987). Population size of the Finnsheep has varied principally according to human needs and product prices.
Their numbers declined dramatically during the period
of 1950 to 1970. Currently, there are fewer than 15,000
ewes and 1,000 breeding rams in Finland.
Keeping a limited number of breeding animals will inevitably lead to increased inbreeding in a closed population, and thus to reduction in additive genetic variance
and possibly to inbreeding depression (Carolino and
Gama, 2008). Earlier studies evaluated genetic variation within Finnsheep using molecular genetic markers (Tapio et al., 2003, 2005), but no genetic diversity
analyses based on pedigree data have been presented.
The objectives of this study were to explore the demographic trends and the status of genetic diversity
in the Finnsheep population in terms of the amount
of inbreeding, effective population size, and coefficients
of relationship, estimate average generation intervals,
and secure baseline information to advance conservation strategies aimed at maintaining genetic diversity
of this sheep breed in the future.
1598
1599
Pedigree analysis of Finnsheep
MATERIALS AND METHODS
Animal Care and Use Committee approval was not
obtained for this study because only pedigree records of
animals were used.
Data
In the present analyses we considered the Finnsheep
population in Finland. The database kept by ProAgria
Association of Rural Advisory Centres in Finland has
pedigree records for 319,119 Finnsheep individuals. The
records contain information on individual identification
code, sex, dam and sire identification codes, flock of
origin, and birth date.
Pedigree Analysis
A breeding population changes through selection decisions. This may affect numbers of animals in time,
and therefore changes in the number of animals by
birth year were studied. Further pedigree analysis included calculation of pedigree completeness, inbreeding coefficients, estimation of effective population size,
and average relationship coefficients between groups of
animals.
Pedigree Completeness. As the quality of available pedigree information is of great importance in assessing inbreeding and trends in inbreeding, a coefficient for pedigree completeness (PEC) was computed,
and the degree of completeness of pedigree was assessed
using the index proposed by MacCluer et al. (1983):
PECanimal =
2Csire Cdam
,
Csire + Cdam
where Csire and Cdam are contributions from the paternal and maternal lines, respectively. The contributions
are computed as
4 section pathways were obtained from records of birth
dates of breeding animals in each year and the birth
dates of their sires and dams. The average generation
interval (l ) was subsequently computed from
1 d
C = å gi ,
d i=1
where gi is the proportion of ancestors present in generation i and d is the total number of generations taken
into account. In this study, 5 ancestor generations were
considered (d = 5). The average pedigree completeness
index for the 5 generations was calculated according to
the birth year. Only animals with PEC values of 0.6
or more (PEC ≥ 0.6) were included in further analyses. The analyses sometimes involved all animals with
(PEC ≥ 0.6), and at other times they were restricted to
the subset of animals that comprised just the breeding
(i.e., reproducing) animals.
Generation Intervals. The generation intervals
(l) were calculated along the 4 gametic pathways: ram
to son (lmm), ram to daughter (lmf ), ewe to son (lfm), and
ewe to daughter (lff; Rendel and Robertson, 1950). The
l =
lmm + lmf + lfm + lff
.
4
Inbreeding Coefficient. Inbreeding coefficients
(F) for all animals and breeding animals (i.e., all with
PEC ≥ 0.6) were computed using the RelaX2 program
(Strandén and Vuori, 2006). The average inbreeding coefficients were then calculated to monitor the changes
in the level of inbreeding by year. A linear regression
line was fitted to these values to estimate annual average increase in inbreeding within the 2 animal groups.
Effective Population Size. The effective population size is the number of breeding animals that would
lead to the observed increase in inbreeding if they contributed equally to the next generation (Gutiérrez et
al., 2003). The effective population size (Ne) was estimated as
Ne =
1
2DF
(Wright, 1931), where ΔF is the rate of inbreeding
per generation. The rate of inbreeding was estimated
by 2 methods described in Gutiérrez et al. (2003) and
Gutiérrez et al. (2008). The earlier method assumes
discrete generations, and the latter allows overlapping
generations.
Rate of inbreeding is estimated in Gutiérrez et al.
(2003) by
DF =
l ´b
,
1 - [Flast - (l ´b)]
where l is the average generation interval, b is the average annual increase in inbreeding coefficient, estimated
by regressing F on birth year, and Flast is the inbreeding
coefficient in the last year studied.
The other estimate for rate of inbreeding is the average individual increase in inbreeding values (Gutiérrez
et al., 2008). Increase in inbreeding for individual i is
defined as
t
DFi = 1 - i 1 - Fi ,
where Fi is inbreeding of individual i, and ti is equivalent
complete generations (Maignel et al., 1996). Equivalent
complete generations for animal i is
ti =
æ 1 ö÷n j
å ççççè 2 ÷÷÷ø ,
k
i
j=1
1600
Li et al.
Table 1. Summary of the Finnsheep pedigree records, the data used in the pedigree analysis, and the annual estimates of pedigree completeness and average inbreeding coefficient for all of the selected and breeding animals
Birth year
No. of animals
No. of animals with
PEC ≥ 0.6
No. of breeding animals
with PEC ≥ 0.6
1972–1978
1979–1981
1982–1983
1984
1985
1986
1987
1988
1989
1990
1991
1992
1993
1994
1995
1996
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
In total
1–20
30–600
1,500–2,200
2,170
15,949
15,654
14,235
12,472
12,792
14,675
15,339
16,988
17,906
20,105
20,269
16,630
14,152
11,623
10,215
8,621
8,527
10,563
11,750
12,853
11,916
14,123
5,216
319,119
0
0
0
1
82
98
153
531
1,877
3,924
5,314
8,000
10,415
12,976
13,251
10,627
9,659
7,859
7,230
6,316
6,080
6,974
7,985
9,360
9,240
11,746
4,759
154,457
0
0
0
1
11
7
9
88
327
644
933
1,432
2,076
2,435
1,804
1,284
1,086
896
913
965
945
1,333
1,319
1,485
1,113
386
0
21,492
PEC
1
0
0
0
0.6061
0.6319
0.6401
0.6438
0.6454
0.6602
0.6800
0.7016
0.7183
0.7416
0.7740
0.7975
0.8125
0.8249
0.8421
0.8533
0.8714
0.8824
0.8960
0.8976
0.8998
0.8985
0.9033
0.9237
—
Fall2
Fbreeding3
0
0
0
0
0.0284
0.0440
0.0476
0.0326
0.0110
0.0147
0.0186
0.0140
0.0121
0.0116
0.0115
0.0191
0.0179
0.0232
0.0194
0.0228
0.0208
0.0245
0.0241
0.0295
0.0273
0.0292
0.0231
—
0
0
0
0
0.0156
0.0045
0.0263
0.0131
0.0063
0.0057
0.0089
0.0061
0.0085
0.0086
0.0097
0.0134
0.0175
0.0211
0.0212
0.0248
0.0229
0.0208
0.0206
0.0295
0.0257
0.0215
0
—
1
PEC = pedigree completeness (only animals with PEC ≥ 0.6 considered).
Fall = average inbreeding coefficient for all the selected animals with PEC ≥ 0.6.
3
Fbreeding = average inbreeding coefficient for the breeding animals with PEC ≥ 0.6.
2
where ki is the number of ancestors for animal i, and nj
is the number of generations between animal i and its
ancestor j.
The Coefficients of Relationship. The average
coefficient of relationship (R) between breeding animals
predicts the future level of the inbreeding coefficient.
We calculated average coefficients of relationship between groups of rams and ewes by birth year, as well
as among rams and among ewes, using the RelaX2 program of Strandén and Vuori (2006).
A further analysis was conducted using the scatter plot of average relationship coefficients of a ram
to other rams and of the ram to ewes, with the aim
of identifying rams with a low relationship coefficient
to the current Finnsheep ram and ewe populations.
These rams may be of value in monitoring the annual
increase of the average relationship in a closed purebred
Finnsheep population (in situ conservation of the living
Finnsheep population), but could also be donors of genetic material for long-term conservation of Finnsheep
genetic resources (ex situ conservation of frozen semen;
Meuwissen, 1999). Only the breeding rams and ewes
born in 2000 or later were considered for this analysis.
Data for 651 breeding rams and 6,897 breeding ewes
were included in the calculations.
RESULTS
Demographics
Basic statistics for the total pedigree records and for
the data used for the pedigree analysis (animals with
PEC ≥ 0.6) are in Table 1. Numbers of recorded Finnsheep with PEC ≥ 0.6 were small from 1972 (n = 0) to
1988 (n = 531), but in 1989 there were more records (n
= 1,877) than for all of the previous years combined.
In addition, the animal registrations in 2007 were incomplete. Thus, 148,833 animals with PEC ≥ 0.6 that
were born in 1989 through 2006 were those used for
subsequent analyses. During the last 16 yr, variation in
the number of animals has been considerable. A rapid
increase in the number from 1,877 to 13,251 annually
was recorded up until its maximum in 1995. This was
followed by a substantial drop of 55% over the subsequent 6 yr, and after 2001 it increased again. By 2006
there were 11,746 Finnsheep with PEC ≥ 0.6.
The mean generation interval (l ) for animals born
over the 1989 to 2006 interval was 2.85 yr. The generation intervals for the 4 pathways were lmm = 2.96, lmf =
3.15, lfm = 2.65, and lff = 2.49 yr. The generation interval of the pathway from ram to progeny was 2.97 yr,
1601
Pedigree analysis of Finnsheep
Figure 1. Average inbreeding coefficient by birth year for all animals over the period 1989 to 2006 (dotted line), and for breeding animals
between 1989 and 2005 (thick solid line). The straight thinner lines are regression lines on the annual average inbreeding coefficient lines.
which is longer than the pathway from ewe to progeny
of 2.72 yr.
Pedigree Completeness and Trend
in Inbreeding
The pedigree completeness by birth year is given in
Table 1 for animals with PEC ≥ 0.6. Pedigree filling
improved over time, with the most recent cohort of
Finnsheep born in 2006 having pedigrees with up to
5 generations of known ancestors (PEC ≥ 0.9). The
pedigrees were quite complete, with PEC ≥ 0.8, from
1995 onwards, whereas PEC ranged from 0.66 to 0.77
for animals born in 1994 or before.
Average inbreeding coefficients by birth year are given in Figure 1 for all animals and for all breeding animals born between 1989 and 2005. The indices of both
groups of animals increased, although they fluctuated.
They reached their greatest levels in 2004, ranging from
1.1% in 1989 to 2.95% in 2004 for all animals, and
from 0.63% in 1989 to 2.95% in 2004 for the breeding
animals. During most of the time frame of this study
the average level of inbreeding was less in the group of
breeding animals than for all animals. From the linear
regressions estimated, the average increase in inbreeding was 0.10% (P < 0.001) per annum in all animals,
and 0.15% (P < 0.001) per annum in breeding animals.
Relationship Coefficients
Average relationship coefficients in breeding animals
among rams, among ewes, and between rams and ewes,
were plotted by birth year from 1989 to 2006 (Figure 2).
The average relationship coefficient among rams was invariably greater than that for the other 2 relationships.
In general, all 3 average relationships increased over
the period studied. Variance (not shown) in average
relationship coefficient was greater among rams than
among ewes and than between rams and ewes. The 3
average coefficients varied slightly during 1989 to 1996,
after which they increased at greater rates and reached
1.67, 1.45, and 1.46% in the 2005 cohort, respectively.
The scatter plot of average relationship coefficients of
rams against those between rams and ewes is presented
in Figure 3. With this analysis, we aimed at identifying
rams with a low relationship coefficient to the current
ram and ewe populations, which would be of value in
conserving genetic diversity of Finnsheep. All of the
average coefficients of both relationships were less than
0.03. A total of 137 rams were identified as having a
relatively low relationship coefficient (R ≤ 0.01), both
with other rams and with ewes, whereas 60 rams had
values between 0.02 and 0.03.
Effective Population Size
The rate of increase in inbreeding was 0.148% (derived from Table 1). Based on this value (b = 0.148%)
and 2.85 yr for l , an effective population size of Ne =
119 animals was estimated for the Finnsheep population using the method of Gutiérrez et al. (2003). This
estimate does not, however, account for overlapping
generations. The other method of Gutiérrez et al. (2008)
accounts for overlapping generations and gave an effective population size of 122.
DISCUSSION
There have been numerous previous studies on pedigree analysis of domesticated animal species, including
cattle (Kearney et al., 2004; Sørensen et al., 2005; Mc
Parland et al., 2007), pigs (Fernández et al., 2002; Toro
et al., 2002), dogs (Hamann et al., 2003; Cole et al.,
2004), and horses (MacCluer et al., 1983; Sevinga et al.,
2004), as well as in other species, such as blue fox (Peu-
1602
Li et al.
Figure 2. Average relationship coefficient by birth year in breeding animals calculated among rams (thick solid line), among ewes (dashed
line), and between rams and ewes (thick solid line with dots).
ra et al., 2007; Strandén and Peura, 2007), and a few
such studies on sheep population pedigrees have also
been published (Goyache et al., 2003; Huby et al., 2003;
Maiwashe and Blackburn, 2004; Norberg and Sørensen,
2007; Álvarez et al., 2008). Our analyses provide comprehensive information on the Finnsheep breed during
the past 2 decades.
Several factors caused the dramatic fluctuations observed in the records for the Finnsheep population during 1989 to 2006. Political decisions influence the price
of sheep products (mainly meat) and thus can be regarded as being the principal cause for the changes. The
first turning point in 1995 was due to Finland joining
the European Union. Immediately after the liberation
Figure 3. Average relationship coefficients among rams against average relationship coefficients between rams and ewes in breeding animals
born in 2000 or later.
Pedigree analysis of Finnsheep
of sheep meat import restrictions in 1995, considerable
importation of mutton at decreased prices compared
with other European Union countries and New Zealand
decreased profits in the sheep sector in Finland. Hence,
Finnish farmers scaled down sheep production. The decline continued until the second turning point toward
resurgence in 2001. The policies on farm subsidies and
new market exploration for sheep products contributed
to the restoration of the census size of the Finnsheep
population between 2001 and 2006.
The average generation interval of the Finnsheep
population (2.85 yr) in the current study was somewhat
less than has been observed for some other breeds. Blair
and Garrick (2007) reported generation intervals of 3
to 4 yr in New Zealand breeds, whereas, for Egyptian
breeds, intervals of 4.29 yr (Rahmani) and 4.34 yr (Ossimi; Shaat et al., 2004), and 4.4 yr (Barki; Mansour et
al., 1977) have been reported. One possible explanation
for the shorter generation interval may be the more
extensive use of a few elite breeding animals within the
Finnsheep population, but particularly that the Finnsheep matures earlier (7 to 8 mo; Maijala, 1996). The
slightly shorter intervals of the ewe-progeny pathways
compared with the ram-progeny pathways in this study
are in contrast to reports for French Merino sheep
(Prod’Homme and Lauvergne, 1993), where ewe-progeny generation intervals were longer. In the Finnsheep
population, the slightly increased generation intervals
in the 2 ram pathways are probably attributable to
the fact that the prominent rams, compared with ewes,
have usually been employed for more years to produce
progeny.
Previous studies showed that the completeness of
pedigree information has an effect on the estimates for
inbreeding coefficients within a breed (Sigurdsson and
Jonmundsson, 1995; Lutaaya et al., 1999; Cassell et al.,
2003). A large fraction of missing parents in a pedigree
may cause serious underestimation of the inbreeding
level and the associated losses arising from inbreeding
(Boichard et al., 1997; Lutaaya et al., 1999). Average
PEC of the selected animals in the Finnsheep population is quite acceptable. In the whole population,
PEC seems quite good after 1995, being above 0.6. The
proportion of animals with PEC ≥ 0.6 increased from
14.7% in 1989 to 83.2% in 2006. It was more than 58%
from 1993 onward and was 72.8% in 2004 and 77.5% in
2005. The increase of pedigree quality is due to increasingly complete recording practices, the computerized
animal recording system, and extensive distribution of
breeding animals with good pedigree records, particularly during the most recent years.
In the Finnsheep population, the present inbreeding
coefficients were low. More than 80% of the animals
with PEC greater than 0.6, born in 2000 or later, had
an inbreeding coefficient of less than 3.125%. The proportion of animals having inbreeding coefficients greater than 6.25%, which is the level reached by cousin
mating, was 13.1%. This is also a critical maximum
that is not exceeded when mating principles are applied
1603
on many farms. Similar low levels of inbreeding in the
Finnsheep population were also recorded in previous
studies based on microsatellite and blood protein loci
in the broad context of north European sheep breeds
(Tapio et al., 2003, 2005).
Average inbreeding coefficient in the Finnsheep population can be considered to be below critical levels.
However, in contrast with the current inbreeding coefficient, the rate of inbreeding is an essential population variable. Moreover, as pointed out above, the
inbreeding coefficients for animals are very sensitive
to the quality of available pedigree information, and
thus absolute inbreeding coefficient levels provide less
information for comparative purposes than the average
rate of increase per generation per annum. According
to FAO guidelines (FAO, 1998) and the recommendation by Bijma (2000), a rate of inbreeding of more than
1% per generation should be avoided to maintain fitness in a breed. The rates of inbreeding recorded for the
Finnsheep population (approximately 0.3% per generation for all of the animals and 0.45% per generation for
the breeding animals) are less than this level and less
than the levels reported in Danish populations of Texel
(1.1% per generation), Shropshire (1.1% per generation), and Oxford Down (1.0% per generation; Norberg
and Sørensen, 2007). The low levels indicate maintained
potential for continued genetic gain. The estimated levels and rates of inbreeding for the Finnsheep population, considered alone, do not justify major changes
to current breeding practices. These typically involve
selection decisions done on Finnsheep farms and typically the mating of 1 ram to 10 to 50 ewes. Artificial
insemination is not used, and Finnsheep lack a centralized breeding program.
A greater selection intensity in rams than in ewes
may be responsible for the greater average relationship
coefficients among rams than among ewes. The smaller
number of selected rams than ewes could also explain
the greater variation observed in the average relationship coefficients among rams when the population size
has changed in time. A greater increase in rates of the
3 relationships since 1996 could be due to scaling down
of the Finnsheep production during 1996 to 2001. Although the population size has resurged since 2001, no
demographic bottleneck effect has been indicated in the
variations of present average coefficients of the 3 paired
relationships, as shown in Figure 2. This finding could
be due to the fact that the number of elite breeding
ewes and rams remained the same. In addition, a large
amount of molecular variation was observed within the
Finnsheep breed at microsatellite and blood protein
loci (Tapio et al., 2003, 2005), indicating no trace of a
genetic bottleneck.
An effective population size of 50 animals is a critical
level for an animal breeding population according to
FAO (1998). However, a recommendation by Meuwissen
(1999) is to maintain a Ne of at least 50 to 100 to take
into account mutation and drift. He also suggested that
a Ne below 100 animals leads to a decrease in popula-
1604
Li et al.
tion fitness. The estimates of Ne = 119 and 122 for the
Finnsheep population are somewhat above the interval
of 50 to 100. As noted by Sørensen et al. (2005), the
recommendations are by no means magic numbers, but
have been derived from theoretical arguments, where
natural selection counteracts inbreeding depression.
When the variation of selection response due to random genetic drift is used as a criterion, a much larger
effective population size (order of several hundreds) is
required to reduce the variation to an acceptable level
(Nicholas, 1989; Grundy et al., 2000; Nomura et al.,
2001). Our estimate of Ne is comparable with those of
other livestock breeds. For example, most of the estimates for cattle breeds are below 100, and they are
essentially independent of the actual (census) size of
the breed population (Taberlet et al., 2007). However,
if the annual change in mean inbreeding coefficient increases in the Finnsheep population (for example, as
a result of intensive use of a few rams), maintenance
of genetic variability would become more difficult, and
sound action would consequently be needed.
Different interventions can be suggested according to
the demonstrated relationship coefficient information.
Finnsheep is an indigenous sheep breed and forms a
closed population where the management of inbreeding
and genetic variation cannot be based on imports of
genetic material from other breeds. The breeding rams
presently identified with a decreased average relationship coefficient (R ≤ 0.01) may have the greatest potential for future breeding purposes aimed at monitoring
the increase of inbreeding in the Finnsheep population.
Currently, the decreased values for rams could be due
to their limited breeding use in only one or a few flocks.
Given the ownership and flock sizes, an in situ conservation activity may be quite viable for them. In addition, as suggested by Maiwashe and Blackburn (2004),
collection of samples from the pedigreed population for
an animal genebank can be based on the least level
of known genetic relationship. Development of germplasm cryoreserves to reintroduce genetic diversity at a
later juncture could be also adopted to preserve genetic
material of these animals for future utilization. Thus,
the combination of an in situ live and cryoconservation scheme is advisable to reduce genetic drift and allow the population to evolve, and provide animals and
breeding material to farmers over the longer term.
In conclusion, pedigree analysis was useful in monitoring changes in population structure and gathering
key demographic parameters for the Finnsheep population. Average inbreeding coefficient by birth year
in the Finnsheep population has increased over time,
although current estimates of rate of inbreeding and
effective population size are not in the range of critical
levels. It seems that current mating practices to avoid
inbreeding in the Finnsheep population work well and
strategies to minimize inbreeding are not of immediate
concern. For long-term maintenance of genetic diversity
and dynamics of the breed, minimization of genetic relationships between candidate breeding animals is the
most promising approach. Moreover, with the aid of
knowledge from molecular and genealogical analyses,
development of viable conservation programs such as in
situ or ex situ live conservation populations and germplasm cryo-genebanks should be considered.
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