Download Pedigree Analysis of Holstein Dairy Cattle Populations

Pedigree Analysis of Holstein Dairy Cattle Populations
C.Maltecca1, F.Canavesi2, G.Gandini1, A.Bagnato1.
1
Department VSA, University of Milan, Italy
2
ANAFI, Cremona, Italy
Summary
A pedigree analysis on the Holstein populations of France, Germany, Italy, and The Netherlands
was performed. Generation interval, number of founders and Country-Gene origin contribution to
populations were calculated from the complete pedigree of each population. Generation intervals
averaged 6 years in all populations. Founders are mostly indigenous but a proportion of 60% to
80% of gene contribution to the living populations comes from USA founder population , while
10% from Canadian one.
Table 1. Pedigree size.
Introduction
Project PROTEJE aims to develop an
international evaluation system for bulls and cows
(Canavesi, 2001). Four countries participate to the
project: France, Germany, Italy and The
Netherlands. Each partner of the group has
specific tasks to address. One of the Italian group
goals is to define the structure of the Phantom
groups.
Country
FRA
DEU
ITA
NLD
N° of individuals
9,602,174
5,693,176
2,841,979
3,338,103
For each pedigree the following descriptive
statistics were calculated: i) population size across
years (calculated as number of recorded animals
per year); ii) generation interval, calculated for
each of the four selection pathways using part of
the Pedig software package (Boichard, 1997); iii)
number of founders per origin, calculated per year
assuming as founder each individual with
unknown parents.
Because global market of bull semen, gene
migration has been active in the four populations
for years. Gene migration occurs especially from
USA and Canada, but some exchange occurs also
across the UE populations.
In a study on Italian Haflinger horse Gandini
et al. (1997) showed the proportionate gene
contribution of founder breeds, due to migration,
to herd book recorded population.
Eight different founder populations (gene
origins) were defined: Italy, France, Germany,
The Netherlands, USA, Canada, Europe
(including, Austria, Belgium, Czech Republic,
Denmark, Spain, UK, Israel, Sweden, Slovakia,
Hungary, Ireland, Norway, Portugal), and Other.
For each pedigree the genetic contribution of
founder breeds to each population was calculated.
A founder population origin (gene origin) was
assigned to each founder individual according to
its Country of birthplace. For individuals with
only one known parent, the origin of the unknown
parent was assumed as the Country of birthplace
of the animal itself. Gene origin contribution of
each parent animal was then halved in each
generation and tracked along the pedigree.
Founder
populations
contributions
were
successively averaged by birth year and sex.
Aim of this work is to perform a preliminary
analysis on the complete pedigrees of the four
countries in order to understand the dynamics of
genes migration.
Material and Methods
Complete pedigree data base from France,
Germany, Italy and The Netherlands were
available for the analysis. Consistencies of the
four populations are reported in Table 1.
168
Generation intervals are similar in all the
populations. Italian population shows a larger
generation interval for SB during the period from
1970 to 1980 which is related to the fact that
before 1986 no genetic improvement programs
were in place in the Holstein population. The
average generation interval is close to 6 years for
all the populations. The reduced generation
interval in age ‘60-‘70 in Figure 4 (German
pedigree) is due to missing information of animals
birth year.
Results and Discussion
Figures 1 and 2 show the population size by year
of the four males and females populations
respectively. All the populations show an increase
in size since 1975 and until 1990, when each
population reach a plateau in the number of
recorded individuals. The situation is similar for
all four male and female populations.
Figures 3 to 6 show generation intervals by 5years periods in the four populations for the four
pathways of selection: sires of bull (SB), sires of
cow (SC), dams of bull (DB), dams of cow (DC).
In this figures is also reported the average
generation interval per year.
Figure 3. Generation Interval for France.
FRANCE
12
10
ye 8
ar 6
Figure 1. Size of female population per year.
4
2
700000
600000
500000
400000
300000
200000
100000
0
0
60-64 65-70 71-75
76-80 81-85 86-90 91-95
period
SB
SC
DB
DC
AVG
1965
1967
1969
1971
1973
1975
1977
1979
1981
1983
1985
1987
1989
1991
1993
1995
Frequency
FEMALES
birth year
Figure 4. Generation Interval for Italy.
ITA
FRA
ITALY
12
NLD
DEU
10
year
8
Figure 2. Size of male populations per year.
4
MALES
2
0
6000
60-64 65-70 71-75 76-80 81-85 86-90 91-95
period
5000
Frequency
6
4000
3000
SB
2000
1000
1995
1992
1989
1986
1983
1980
1977
1974
1971
1968
1965
0
birth year
ITA
FRA
DEU
NLD
169
SC
DB
DC
AVG
Figure 5. Generation interval for Germany.
ITA
30
GERMANY
77
90
96
57
FRA
DEU
10
20
NLD
8
15
EUR
6
USA
10
CAN
4
5
2
OTHER
0
0
ITA
60-64 65-70 71-75 76-80 81-85 86-90 91-95
period
THE NETHERLANDS
12
10
6
4
2
0
60-64 65-70 71-75 76-80 81-85 86-90 91-95
period
Figure 9. Males populations – Proportion of
founders by birth year.
Figure 7 and 8 show the percentage of
founders by origin in the four male and female
populations respectively. The Italian male
population shows a large founder contribution
from foreign countries, especially from USA. The
other populations show to have the largest
proportion of genes from indigenous founders
and, regarding foreign founder animals, a
prevalence of USA and Canadian ones.
USA
5
CAN
0
OTHER
ITA
FRA
DEU
NLD
170
EUR
10
NLD
15
DEU
FRA
20
ITA
25
3HUFHQWDJH
62
)(0$/ (6
74
Figure 10. Female populations – Proportion of
founders by birth year.
69
Figure 7. Male population - Percentage of
founders by origin.
49
3HUFHQWDJH
0$/ (6
year
8
30
NLD
Figures 9 and 10 show the proportion of
founders on recorded population by birth year for
the four male and female populations respectively.
In the male populations a large proportion of
founders is shown in the older recorded
individuals, while in recent registered animals the
percentage of founders comes close to zero. The
Italian female population shows a different trend
with respect to other females populations: the
proportion of founder individuals on recorded
population vary from 60% to 80% until age ‘80.
This is due to the openness of Italian genealogical
herd book where cows are registered on a herd
basis. In the Dutch population the percentage of
females founders is always close to zero. This is
probably due to the fact that recorded animals
have at least one known parent.
The
for
Interval
DEU
Figure 8. Female population – Percentage of
founders by origin.
AVG
Generation
DC
Figure 6.
Netherlands.
DB
SC
SB
FRA
year
12
25
The high proportion of USA genes and
Canadian ones does not imply that same genes
were equally sampled and bred in the four
different populations. Different selection criteria
and different selection objectives produced
different crosses across populations and this result
in the different characteristics that the living male
and female populations do maintain across
countries.
Figures 11 to 18 show the contribution by
year, of each of the eight founder populations
(gene origin) to the composition of the four male
and female populations. All the graphics show a
similar trend. While animals recorded in older
periods (1950 to 1970) own a large native
population gene contribution, individuals of the
living population (1995 to present) exhibit a large
proportion of genes from foreign populations.
Because of gene migration, the native population
contributions were gradually substituted by USA
genes and, at a smaller rate, by Canadian ones.
Animals of the four populations born in the most
recent years own a percentage of USA genes that
vary from 70% up to 80% in the male populations
and from 60% up to 80% in the female
populations. Canadian genes are present in a
proportion close to 10% in all populations.
There is some evidence of a larger European gene
migration across France Germany and the
Netherlands respect to Italy even if the proportion
of genes coming from the four EU populations is
very small.
References
Boichard, D., Maignel, L. & Verrier, E. 1997. The
value of using probabilities of gene origin to
measure genetic variability in a population.
Genet. Sel. Evol. 29, 5-23.
Canavesi, F., Boichard, D., Ducrocq, V., Gengler,
N., De Jong, G. & Liu, Z. 2001. PROduction
traits European Joint Evaluation (PROTEJE).
Interbull Bulletin 27, 32-34.
Gandini, G.C., Samorè, A.B. & Pagnacco, G.
1997. Genetic contribution of the Arabian to
the Italian Haflinger horse. J. Anim. Breed.
Genet. 114, 457-464.
Conclusions
Italian and German populations seems to maintain
a larger proportion of native genes in living
female populations. In all populations the largest
contribution comes from USA population and, in
smaller proportion, from Canada.
Acknowledgements
The partners of PROTEJE project are gratefully
acknowledged for providing the pedigree data and
for the useful comments.
171
Figure 11. Proportion of gene origin in France
male population.
Figure 15. Proportion of gene origin in Italian
male population.
FRANCE - MALES
ITALY - MALES
1
1
0.9
0.9
0.8
ITA
FRA
DEU
NLD
EU
USA
CAN
OTHER
0.7
0.6
0.5
0.4
0.3
0.2
ITA
FRA
DEU
NLD
EU
USA
CAN
OTHERS
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0.1
0
0
1970 1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994 1996
1970 1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992
birth year
birth year
Figure 12. Proportion of gene origin in France
female population.
Figure 16. Proportion of gene origin in Italian
female population.
FRANCE - FEMALES
ITALY - FEMALES
1
1
0.9
0.9
0.8
ITA
0.7
0.8
FRA
0.5
NLD
0.6
EU
0.5
0.4
USA
0.3
CAN
0.4
OTHER
0.3
0.2
ITA
FRA
DEU
NLD
EU
USA
CAN
OTHERS
0.7
DEU
0.6
0.1
0.2
0
0.1
0
1970 1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994 1996
1970 1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994
birth year
birth year
Figure 17. Proportion of gene origin in Dutch
male population.
Figure 13. Proportion of gene origin in German
male population.
THE NETHERLANDS - MALES
GERMANY - MALES
1
1
0.9
0.9
0.8
0.8
ITA
FRA
DEU
NLD
EU
USA
CAN
OTHERS
0.7
0.6
0.5
0.4
0.3
0.2
ITA
FRA
DEU
NLD
EU
USA
CAN
OTHER
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0.1
0
0
1970 1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994
1970 1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994
birth year
birth year
Figure 18. Proportion of gene origin in Dutch
female population.
Figure 14. Proportion of gene origin in German
female population.
THE NETHERLANDS - FEMALES
GERMANY - FEMALES
1
1
0.9
0.9
0.8
0.7
0.6
DEU
NLD
EU
USA
CAN
OTHERS
0.6
0.5
0.4
0.3
0.2
ITA
FRA
DEU
NLD
EU
USA
CAN
OTHERS
0.8
ITA
FRA
0.7
0.5
0.4
0.3
0.2
0.1
0.1
0
0
19701972 1974 197619781980 198219841986 198819901992 1994 1996
19701972 19741976 1978 19801982 19841986 198819901992 19941996
birth year
birth year
172