Herd clustering strategies and corresponding genetic evaluations based on social–ecological characteristics for a local endangered cattle breed
2021
Abstract. The accuracy of breeding values strongly depends on the
population and herd structure, i.e., the number of animals considered in
genetic evaluations and the size of contemporary groups (CGs). Local breeds
are usually kept in small-sized family farms under alternative husbandry
conditions. For such herd structure, consideration of classical herd or
herd-test-day effects in CG modeling approaches implies only a few records
per effect level. In consequence, the present study aimed on methodological
evaluations of different herd clustering strategies, considering
social–ecological and herd characteristics. In this regard, we considered 19 herds keeping cows from the small local population of German Black Pied cattle (Deutsches Schwarzbuntes Niederungsrind; DSN), 10 herds
keeping Holstein Friesian (HF) cows and one mixed herd with HF and DSN
cows. Herds were characterized for 106 variables, reflecting farm
conditions, husbandry practices, feeding regime, herd management, herd
fertility status, herd health status and breeding strategies as well as
social–ecological descriptors. The variables were input data for different
clustering approaches including agglomerative hierarchical clustering (AHC),
partition around medoids (PAM), fuzzy clustering (FZC) and a clustering of
variables combined with agglomerative hierarchical clustering (CoVAHC). The
evaluation criterion was the average silhouette width (ASW), suggesting a
CoVAHC application and consideration of four herd clusters (HCs) for herd
allocation (ASW of 0.510). HC1 comprised the larger, half organic and half
conventional DSN family farms, which generate their main income from milk
production. HC2 consisted of small organic DSN family farms where cows are
kept in tie stables. HC3 included the DSN sub-population from former East
Germany, reflecting the large-scale farm types. The specialized HF herds
were well separated and allocated to HC4. Generalized linear mixed models
with appropriate link functions were applied to compare test-day and female
fertility traits of 5538 cows (2341 DSN and 3197 HF) from the first three
lactations among the four HCs. Least squares means for milk, fat and protein
yield (Mkg, Fkg and Pkg) significantly differed between HC. The significant
differences among the four HCs clearly indicate the influence of varying herd
conditions on cow traits. The similarities of herds within HC suggested the
application of HCs in statistical models for genetic evaluations for DSN. In
this regard, we found an increase of accuracies of estimated breeding values
of cows and sires and of heritabilities for milk yield when applying models
with herd-cluster-test-day or herd-cluster-test-month effects compared to
classical herd-test-day models. The identified increase for the number of
cows and cow records in CG due to HC effects may be the major explanation
for the identified superiority.
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