Partitioning International Genetic Trends by Origin in Holstein bulls

G. Gorjanc1, F.S. Hely

2 & P.R. Amer

2

1

University of Ljubljana, Biotechnical Faculty, Animal Science Department, Groblje 3, 1230,

Domzale, Slovenia 2

AbacusBio Limited, PO Box 5585, Dunedin, New Zealand

Abstract

Dairy cattle breeding is globalized to a large extent, in particular in the Holstein breed.

Assessing the impact of different sources of genetic gain in such a setting is important to

strategically allocate limited resources. Such an assessment can be achieved by partitioning

breeding values by the origin of Mendelian sampling terms. In order to capture the whole

global Holstein breeding population, InterBull pedigree and associated breeding values were

used. Analysis was focused on the total merit indexes (TMI) from four countries: Great

Britain (GBR), Ireland (IRL), New Zealand (NZL), and USA. Partitioning was performed on

the global and local population scale. Global trends in the TMI of each respective country

reflect the changes in merit of all bulls from all countries included in Interbull analyses. In

contrast, local trends are achieved by weighting the global partitions of each bull by the

number of daughters in the local country, and are therefore not dominated by countries which

progeny test large numbers of animals. Analysis of global trends showed the dominating role

of selection performed in USA on all four TMI. The contribution of USA origin had a large

positive effect on the global GBR TMI trend, a modest positive effect on the global NZL TMI

trend, and a large negative effect on the global IRL TMI trend, but with improvement in

recent years. Analysis of local GBR TMI trend showed a large positive contribution of USA

followed by Canada and approximately equal positive contributions from GBR and The

Netherlands. The local IRL TMI trend showed a dominating negative effect of the USA and

fluctuating positive contributions from The Netherlands, NZL, and GBR. The local NZL TMI

trend showed dominating positive effect of NZL and minor positive contribution from USA

followed by The Netherlands. Overall, results showed the dominating positive and negative

effect of USA on the global TMI trends, while local TMI trends can deviate considerably

from global trends due to country specific breeding practices.

Keywords: Holstein, genetic trends, partitioning, origin

Introduction

The history of the Holstein(-Friesian) breed was written by breeders from different countries

(Felius, 2007). Today this breed is a prime example of globalized breeding (e.g. Brotherstone

& Goddard, 2005). Reproductive techniques enable the easy dissemination of germplasm

from one country to another. Many countries are improving local populations of black and

white cattle with the importation of the top global Holstein germplasm.

Assessing the impact of different countries in such a setting is important to strategically

allocate limited breeding resources. Since experimental assessment is logistically and

financially impossible, Gorjanc et al. (2011) proposed to use the method of partitioning

breeding values by the origin of Mendelian sampling terms (García-Cortés et al., 2008) to

quantify the marginal contributions of different countries to the global genetic trend. Their

application in the global Brown-Swiss breeding population showed that selection in a single

country has had a major positive contribution to genetic trend for production traits, but an

almost exclusive contribution to negative genetics trend for fertility.

The aim of this work was to apply the method of Gorjanc et al. (2011) to assess the

contribution of different countries to global (world-wide) genetic trends in Holstein bulls and

to project these contributions to local genetic trends for a contrasting subset of countries.

Materials and Methods

Data on the global Holstein breeding population were obtained from the Interbull database.

For each bull evaluated at Interbull a sire-dam pedigree and associated breeding values from

the multiple across country evaluation (MACE) system (Jakobsen & Dürr, 2012) were

collected. All available pedigrees and breeding values for animals born between years 1960

and 2003 were used. Analysis was focused on four countries: Great Britain (GBR), Ireland

(IRL), New Zealand (NZL), and USA. For each country considered, MACE results (April

2012 routine run) for all evaluated traits on country specific scale were obtained. From these

data, current country specific total merit indices (TMI) were computed: the profitable lifetime

index (PLI) for GBR, the economic breeding index (EBI) for IRL, the breeding worth index

(BW) for NZL, and the net merit index (NM) for USA. In order to enlarge the number of bulls

in the analysis missing breeding values that are components of TMI were set to the average of

bulls from the same country in the same birth year. Only the TMI values were used in the

partitioning analysis. In addition to global (Interbull) data, total numbers of daughters per bull

up until present were obtained from each country. This information was used to project the

global partitioning analysis to local level as described in more detail below.

The total number of bulls with the available TMI on a global scale was equal to

145,611. However, only a subset of these bulls had daughters in the countries under

consideration for this analysis. The total number of bulls ranged from 1,537 with daughters in

IRL to 21,261 with daughters in the USA (Table 1). The use of foreign bulls from different

countries (origins) was quite dispersed for GBR, IRL, and USA, but highly limited for NZL

(Table 1). The latter can be explained by the pastoral nature of dairy production in NZL, and

the long history of NZL based breeding program targeting the NZL production environment.

Nonetheless, some foreign bulls were used as bull sires in all countries (data not shown).

Table 1. Number of bulls with daughters and TMI data in countries of interest by selected

origins.

Focal country

Origin GBR IRL NZL USA

CAN 1,088 87 / 1,638

DEU 166 70 / 67

DNK 79 6 / 14

FRA 318 157 / 113

GBR 2,652 270 / 83

IRL / 180 / 1

ITA 135 31 / 183

NLD 726 457 / 306

NZL 98 46 4,672 37

USA 1,252 224 1 18,700

Total1 6,529 1,537 4,849 21,261

1 Includes also bulls of other origins

Partitioning of breeding values by origin is performed by allocating an animal’s Mendelian

sampling term to the country of origin and accumulating these terms along the whole pedigree

(for details see García-Cortés et al., 2008 and Gorjanc et al., 2011). At the end of this process

the breeding value of each individual animal is partitioned in origin specific partitions

.

Country specific TMI were partitioned according to the Interbull global sire-dam

Holstein pedigree and country of origin of an animal. Before partitioning, breeding values

were adjusted such that the mean breeding values in year 1960 was zero and scaled by the

standard deviation of breeding values. Total breeding value partitions for TMI for each

country of interest were averaged by bull’s birth year to quantify the contributions of all

countries to the global (world-wide) breeding population of the Holstein breed. These trends,

on each of the 4 different TMI scales, show changes in the global breeding population due to

selection performed in different countries (origins). The same method was applied also for the

analysis of proportion of genes by origin, where breeding values for all animals are equal to

one (Gorjanc et al., 2011).

In order to consider the global impacts on the genetic trend in the local TMI for each

of the four countries, bull breeding values and partitions were weighted by the number of

daughters in a country and again averaged by birth year. This effectively removed bulls with

no daughters in the local country and provided total and origin specific genetic trend for TMI

for each local population. In all plots only origins with the largest contributions were

presented to avoid clutter. While analysis included all the available data since 1960, results

are presented only for the period after 1980.

Results and Discussion

Gene proportion analysis of global Holstein breeding population based on the Interbull sire-

dam pedigree of bulls showed the increasing proportion of genes of USA origin from 1965

onwards (Figure 1). The increase was from about 30% to almost 90% and is levelling off in

more recent years. In these more recent years, the remaining non trivial proportions of genes

in the global Holstein breeding population originate from Canada (between 5 and 7%), New

Zealand (~1.5%), The Netherlands (~1%). These results match with the history of upgrading

populations of black and white cattle with the USA Holstein breed in many countries (e.g.,

Felius, 2007).

Overall the global trend for the USA TMI (NM) was positive (Figure 2); +1.75 TMI

standard deviations in the period between 1980 and 2003. Partitioning analysis showed that

USA dominated the global trend until 1990 when its influence began to gradually reduce to

about 60% of the total global genetic trend in the last years. Other origins that had measurable

contribution to the global trend for the USA TMI were Canada, The Netherlands, Germany,

and France. The importance of these origins has been increasing since 1990. The projection of

global trend to a local trend for USA TMI showed an expected increase of North American

(USA and Canada) contribution and decreased contribution of other countries.

Overall, the global trend for the GBR TMI (PLI) was also positive (Figure 3); +1.86

TMI standard deviations in the period between 1980 and 2003. Partitioning analysis showed

very similar results as for the USA TMI. The majority of influence has come from the USA

with Canada and The Netherlands and to a lesser extent Germany contributing most of the

remainder. Projection to the local trend shows the reduced influence of the USA in

comparison to other origins. On average the local trend is higher for bulls used in GBR, than

the average trend for the global population. This implies that the breeding goal in GBR has

been different from the weighted average of the global population breeding goal (dominated

by selection in the USA), and that bulls imported into the GBR have been selected based on

GBR TMI. GBR partition is also rising in importance in the last years.

Figure 1. Proportion of genes by origin in global Holstein breeding population.

Figure 2. Partitioning of the global (left) and local (right) genetic trend by origin for the USA

TMI – NM (in standard deviation units).

Figure 3. Partitioning of global (left) and local (right) genetic trend by origin for GBR TMI -

PLI (in standard deviation units).

In contrast to global USA and GBR TMI trends, the global trend for IRL TMI (EBI) is

strongly negative (Figure 4). In recent years the average trend is -1.5 TMI standard

deviations. This implies that the direction of selection in the global population is not at all

suitable for production systems in IRL. Partitioning analysis showed that the major

contribution to this negative trend is due to genetic changes attributed to USA and to a smaller

extent to Canada. Negative global trend is driven by the changes of non-production traits in

IRL TMI (calving interval, longevity, and somatic cell scores - data not shown). A recent

improvement in these traits in the North American bulls appears to be negating this negative

trend. Projection to local trend showed an overall improvement after 1990 that can be

attributed to the choice of better than average bulls from North America for use in Ireland.

The positive influence on local IRL TMI trend is due to The Netherlands, New Zealand, and

Great Britain. Selection of bulls within Ireland is also starting to make a favourable

contribution to the local genetic trend in Ireland.

Figure 4. Partitioning of global (left) and local (right) genetic trend by origin for IRL TMI –

EBI (in standard deviation units).

Figure 5. Partitioning of global (left) and local (right) genetic trend by origin for NZL TMI –

BW (in standard deviation units).

Overall, the global trend for the NZL TMI (BW) is positive (Figure 5); +1.25 TMI

standard deviations in the period between 1980 and 2000. Partitioning analysis showed a

sizeable contribution of USA followed by The Netherlands, New Zealand, and Canada.

Projection to local population showed that the local trend is on average much higher than the

global trend. In addition the majority of genetic change since 1980 can be attributed to

selection activities performed in New Zealand. A modest contribution from USA and

Netherlands was evident at approximately 2002, although this contribution does not appear to

be an on-going upward contribution. The contribution from Canadian bulls is slightly

negative over the whole analysed period.

Conclusions

The partitioning analysis of the global Holstein breeding population has shown a major

influence of the USA when considered on a global scale, although this overall dominance of

the USA appears to have been declining. For GBR, having global bulls evaluated on the GBR

TMI index scale through a combination of domestic data recording and participation in

Interbull appears to have allowed faster improvement in the local index than could be

achieved by following the global trend in genetic merit. For countries like Ireland and New

Zealand whose pasture based systems require different trait emphasis compared to other

countries, the existence of domestic sire improvement infrastructure in New Zealand has been

of significant benefit, while in Ireland the historic absence of domestic infrastructure has been

a major lost opportunity.

Acknowledgement

Authors would like to acknowledge the contribution of Jette Jakobsen (Interbull) for

preparation of global Holstein data and for representatives of USA, GBR, IRL, and NZL for

permission to access data, undertake the analyses, and make the results publicly available.

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