1. Introduction
Cattle production systems generally differ regarding production conditions, breed structures, market orientation, decision process-determining parameters, and many other features. Cluster analysis, which originated from application areas such as biology and is regarded as a very useful data-mining tool, allows for the assessment of many aspects of cattle farming [
1]. Generally speaking, it sorts objects into groups (clusters) based on their similarity [
1].
This instrument has been widely implemented in recent studies evaluating cattle farming, mainly for herd classification and animal breeding and selection. Cluster analysis was carried out to establish the typology and basic characteristics of suckler farm systems, evaluating their viability and sustainability by considering various production and economic determinants [
2]. Similarly, clustering was applied to provide a novel classification of small farms in Europe, taking into account their typology and regional-level role for further policy intervention [
3]. A phenotype evaluation of both pure- and crossbred Charolais cows was provided to observe variance within varieties, find phenotypically different types within these groups, and create an appropriate ranking for selection purposes [
4]. Multi-algorithm automatic milking system data clustering aimed to assess cow productivity by group, as well as their stability over time for selection purposes [
5]. Clustering was applied in the genetic evaluation of beef cattle herd weaning weights in order to consider genotype–environment interactions and identify variables more precisely describing individual herd conditions [
6]. Similarly, clustering strategies were implemented to improve genetic evaluation accuracy based on the social–ecological and herd characteristics of small dairy cattle farms in alternative husbandry systems [
7]. Farms using automatic milking systems were clustered into groups with unique management styles, challenges, and production characteristics [
8].
Beef cattle systems in the Czech Republic cover more than 220 thousand suckler cows of 25 breeds located across more than 8 thousand farm units [
9] with variable conditions; half of these are natural constraint areas (formerly less favored areas [
10]). Farms may be located at altitudes from 300 to 700 m (74%) or over 700 m (21%) above sea level [
11]; up to 50 cows is the most common number of animals (88%) [
9]. About 11% of all suckler cows are included in routine beef performance records [
9], which are key in practical breeding and selection. Local beef cattle populations can be enhanced through breeding programs in which values for over twenty traits are routinely estimated [
12]. Some simple selection indices have been suggested for examining calving performance and calf growth [
13]. Nevertheless, in recent times, the breeding program continues to be enriched through the incorporation of new functional traits into breeding value (BV) estimation [
14], the application of genomic data [
15,
16], and the calculation of economic values [
17]. To more comprehensively define breeding strategies and construct selection indices in a more practically applicable way, further details of breeding system characteristics are needed. They should reflect, i.e., the management, marketing, and breeding strategies; breed structure; and herd size. At the same time, farmers’ preferences for breeding objective traits should be respected. Both parameters are currently unknown and need to be defined for the local population. Moreover, they are necessary for appropriately setting input parameters to calculate the trait economic values using the bio-economic approach, as well as for the construction of customized breeding programs.
In this sense, we hypothesized that the survey brings recognition of the overall breeding system characteristics and farmers’ preferences in breeding objective traits, and secondly, the clustering approach enables us to define their specific patterns. Therefore, the main aim of this study was to define the overall and cluster-specific characteristics of breeding systems and evaluate preferences in breeding objective traits from the online survey to inform tailored breeding programs for Czech beef cattle conditions in the future.
4. Discussion
Our study connects the overall and cluster-specific parameters of Czech beef cattle farms gathered through the online questionnaire. Valuable patterns could be identified from such a dataset source and size. It covers the evaluation and determination of the basic parameters of beef breeding systems, as well as farmers’ preferences in terms of breeding objectives. In the following, we will discuss these aspects in view of their practical application in animal breeding.
The ratio of conventional to ecological management (44:49, i.e., without mixed farms and in transition), as practiced in the surveyed beef cattle farms, was close to the 45:55 previously published regarding beef meat production structure [
28]. Since 1990, ecological farming has generally expanded across Europe, aligning with the official strategy of “Farm to Fork”, whereby the share of ecological farms is expected to reach 25% by 2030 [
29]. In terms of agricultural land area, ecological farming makes up 16% of the Czech Republic [
30]. Nevertheless, beef farms are primarily located in more elevated areas [
11] and border regions in the upper proportion of permanent grasslands [
30]. The ratio of ecological areas is considerably higher in these regions (mainly ranking from 30% to 80%), with cattle as the most frequent livestock species [
30].
Regarding marketing strategies, a third of farms’ incomes came from breeding animals, which corresponded well with the main objective of our survey focused on animal breeding and selection. Secondly, farms have diversified sources of revenue: breeding animals (bulls for AI/natural mating, heifers), weaned calves, and/or fatteners (29%). Diversified production could bring many benefits to beef farmers, reducing the risks associated with the farm business in terms of stable income [
31], overall output value, investment return, and farm sustainability [
32]. In accordance with the aforementioned, the breeding strategies of the surveyed farms mostly combined both pure- and crossbreeding in one herd (56%). Generally, a higher supply variability on the market (breeding and carcass animals), crossbred meat quality and yield, and the possibility of practical production applications could play important roles in these strategies.
The breed structures reported in our survey corresponded to the official cow numbers recorded by [
9], in that Limousine, Charolais, Aberdeen Angus, and Beef Simmental were the most common. In terms of cows included in the 2024 performance testing, the list of the most popular breeds was similar; numbers of Charolais, Aberdeen Angus, Beef Simmental, and Limousine (based on own calculations from the database provided by the CBCA) have remained stable over the last decades [
10]. The proportion of surveyed herds predominantly farming one breed (80%) was close to the 86% calculated from the CBCA database (relevant for herds with the most frequent breeds, according to our own calculations).
The herd size structure of the survey participants was relatively balanced (37% had up to 60 cows, 44% up to 210 cows, and 19% had larger farms, as shown in
Table 1). This is in accordance with the authors of [
33], who reported corresponding beef herd size ratios of 25%, 35%, and 40%, respectively. This balanced herd structure also aligned with the authors of [
3], who stated that although farm sizes have decreased in recent decades, large-scale farms still prevail in Czech agriculture. Nevertheless, according to the central animal recording databases [
9], small-scale farms dominated (53% up to 10 cows) and only 10% of farms had over 200 cows in 2024. This difference could possibly be due to the different data sources; the central database covered all farms, i.e., those owning one-cow herds as a hobby or as a secondary income activity. Such farms would probably have a minor emphasis on animal breeding and selection, although they would still receive practical benefits from enhanced breeding programs.
The most common farmer age calculated using our survey (75% up to 49 years) corresponded to the overall agriculture employee structure published by [
30], where the majority (i.e., 58%) was up to 49 years old. However, the proportion of the following age category (over 50 years) is obviously lower in our survey (22%) than in the cited study (nearly 42%). The possible reason for this is the natural generational change in beef cattle farmers, which may have taken place with a slightly higher intensity (especially in terms of the position of farm owner/manager) compared to all other agriculture workers. In this context, the authors of [
30] noted that generational change has been significantly disrupted in the last decades; the proportion of workers in older age categories has gradually increased, and this problem is common across agriculture in most EU countries. The online form of the survey, perhaps making it more accessible and easy to use for younger breeders, could have partially impacted the age structure found.
Farmers who participated in the survey mostly selected animals according to both BVs and performance (73%). This result seems to be positive from a breeding and practical point of view, showing that farmers have confidence in BVs, complementing it with or assessing it against measured performance. This attitude helps in building a valuable foundation for further breeding program enhancements.
The identified overall farmer preferences correspond to the top traits considered in the genetic evaluation of local beef cattle populations [
12]. The scores assigned to calving performance and growth positioned them amongst the four most important traits (
Figure 1), followed by exterior or linear scoring traits (such as body capacity and productive type), which have long occupied a stable place in genetic evaluation across the globe [
6,
24,
34]. Further traits that were highly preferred by farmers were cow temperament and calf viability, calving performance, and maternal fertility and longevity. These trait groups have recently been incorporated into local performance testing and evaluation [
15,
26] and feature in the evaluation of other beef populations [
35,
36]. As such, they would probably play an important role in further breeding program enhancements.
The same is true of the relatively high-scoring metrics of polledness and animal health, as directly suggested by farmers (
Figure 1). Generally, polled cattle breeding brings farmers many benefits in terms of management, injury prevention, overall animal welfare, and public attitude. Polledness also has measurable economic benefits in terms of reducing dehorning costs (labor, material, veterinary treatment) and increasing the market value of genetically polled animals [
37]. This trait is therefore a suitable candidate for animal breeding and selection. In this context, some specifics of the genetically polled Aberdeen Angus breed should be mentioned. Therefore, some farmers (mainly of Limousine, Beef Simmental, and Charolais) added this breeding objective when filling out the survey. In current breeding practices, calf survival is evaluated for animal health in local beef populations, with limb assessment to be used as an indicator of beef cattle resistance. Moreover, some specific diseases such as Charolais ataxia (mentioned by one of the survey respondents), diarrhea (causing calf loss), and cow respiratory diseases [
11] could be considered here. In terms of the optional traits, gestation length, feed conversion, and body condition were also mentioned by farmers. Based on very low frequency (added by four farmers in total), they were omitted from further evaluation. Nevertheless, they should be kept in mind as possible breeding goals to avoid potentially overlooking emerging priorities.
On the contrary, bull fertility and meat quality ranked quite low in terms of importance. A relatively new trait in local evaluation [
14], bull fertility aims to improve reproduction potential and, secondly, growth ability (as mentioned by [
38]). Scores assigned to meat quality possibly consider meat as sold by body weight rather than the quality of the meat itself. Such a payment system could explain the low economic value of this trait in both beef and dairy cattle production systems [
17,
39,
40].
In our study, we applied ASW, WSS, and gap statistics as criteria for assessing clustering methods and determining cluster numbers. ASW or WSS were solely used for clustering herds of beef [
6], dairy cattle [
7], and sheep [
41] for breeding purposes. Nevertheless, to the best of our knowledge, a combination of the various criteria for evaluating the performance of clustering approaches used in our study (ASW, WSS, and gap statistics) was applied in another study examining the general typology of small farms across Europe [
3]. The authors considered ASW, connectivity, and the Dunn index to choose the most suitable algorithms for data clustering and gap statistics to define an optimal number of clusters. Contrary to previously mentioned papers, in our study, the ASW evaluation criteria showed separation efficiency similarity among clustering approaches and clearly did not prioritize one approach over another. The AHC method showed slight superiority with three clusters, which could fit our data. This presumption was confirmed when considering all evaluation criteria (ASW, WSS, and gap statistics, as indicated in the Results section). In our study, regarding the clustering method and number of clusters, a combination of various clustering criteria seems to be beneficial for finding the solution.
The separation similarity among the evaluated methods in Czech beef farms is supported by the fact that, when using the AHC and k-means as a function of three clusters, similar clusters were created. The only difference was farms switching between individual clusters (16/8/17 vs. 16/17/8 in cluster 1/2/3, respectively; see the plots in
Supplementary Figure S1). Regarding the AHC and PAM approaches, the clustering results were identical for 76% of Czech beef farms. Such results also partly confirmed the general statement that these methods (mainly those of the partitioning group) work well for finding clusters in small- to medium-sized databases [
1]. This was the case in our study (consisting of seven characteristics of 41 farms), as well as in that of [
4], which evaluated about 300 animals with various Charolais gene ratios according to six variables. Likewise, 15 determinants were applied by the authors of [
41] to cluster 25 sheep farms, and the AHC method was found to be the most suitable approach. Nonetheless, this approach seems to be suitable for evaluating larger datasets as well. The k-means approach was applied for clustering nearly 73 thousand beef calves based on their weaning weight and pedigree data [
6]. Similarly, 22 production and economic variables in most small European territorial units were analyzed by the authors of [
3], who found that the PAM approach is the most suitable solution for such data. It is worth noting that this method outperformed the centroid-based CLARA approach specified for large datasets. Generally speaking, centroid-based partitioning and hierarchical methods have successfully been used for clustering the various structures of farm data.
Regarding the overall and cluster-specific characteristics applied as determinants of Czech beef farms (breed, herd size, management and marketing strategy, farmer age), most of them were shared with other studies that clustered farms for breeding purposes by population level (e.g., [
7,
41]). More specific determinants (cow age, live weight, and body measurements) were considered to provide a phenotypic evaluation of beef herds [
4]. Similarly, after herd size, some environmental factors (average temperature and rainfall) were also considered during clustering to investigate genotype–environment interactions [
6]. Likewise, various production and economic determinants were taken into account to establish the basic typology and characteristics of suckler farm systems and evaluate their viability and economic perspectives [
2]. In addition to classical characteristics, such as herd size and pasture area, they evaluated the degree of intensity, labor efficiency, housing system, and infrastructure level. In this context, some specific determinants, such as breeding strategy (pure/crossbreeding or mixed) and selection decision (based on BVs, performance, or both), that were incorporated into our survey aimed to define the overall Czech beef breeding system, specifically to further breeding goals and enhance indexes (indices).
Based on the overall characteristics and preferences of farmers participating in the survey (both discussed above), they proved to be representative of Czech production conditions, supporting some of the top traits currently included in genetic evaluation and identifying some novel traits. Moreover, clustering could allow us to gain a more precise understanding of beef farms and breeding objectives from a breeding and selection point of view. As previously mentioned, production (breeding) system characteristics significantly influenced breeding goals and farm economics; secondly, farmer requirements regarding breeding animals may differ significantly according to their breeding objective [
13].
The clustering provided in our study indicated three breeding systems in the Czech beef population, organized in terms of herd size, management, breeding strategy, breed structure, and farmer age. The same was true for the respective cluster preferences of breeding goal traits. BV and performance were the joint primary information sources in all three breeding systems. Cow temperament and calf viability, along with maternal fertility and longevity, were found to be among the most important mandatory cluster-specific traits. Although these are relatively novel traits in local genetic evaluation, they fully correspond to breeders’ overall interest in achieving sustainability and efficiency. Calf production per cow life, as a result of maternal fertility, calf viability, maternal temperament, and cow longevity, most likely plays a leading role in this case. Similarly, cow productivity was found to be one of the core economic parameters of Greek beef farms [
2]. The authors further recognized that this was also connected to the level of veterinary and zootechnical support on pastures. In accordance with this statement, animal health was found to be a further high-scoring trait in all Czech beef clusters, ranging from 4.0 in clusters 2 and 3 to 5.0 in cluster 1 (as shown in
Figure 5). Such a score difference between clusters was reported as large in terms of Cohen’s d value (
Table S3) and indicated the practical trait importance for cluster 1. Health was not considered a mandatory trait in our survey, as it has not yet been incorporated into the ongoing genetic evaluation. Nevertheless, it was suggested as a new breeding goal directly by survey participants. The way it could contribute to further breeding was briefly discussed above (in the context of overall trait preferences); health should probably be validated when enhancing beef breeding goals for individual breeding systems. Nevertheless, the position of animal health as an important breeding objective was generally confirmed among livestock species [
7,
41,
42].
In terms of breeding strategy, pure-breeding dominated in the farms of cluster 1; nonetheless, a combination of pure- and crossbreeding strategies was typical for the rest of the farm clusters. This parameter would probably be the first distinctive feature to define particular breeding systems and goals. Pure-breeding farms have specialized in producing breeding animals and, in part, other beef categories (such as weaned calves and/or fatteners (as by-products)). This breeding system seems to be fully compatible with two selection strategies focused on production sires as foundation bulls (sires of dams) and sires for beef herds, both formerly defined for Czech beef conditions [
13]. In this study, breeding goals were further specified to gain heifers for replacement (with good maternal traits) and weaned/slaughter calves with excellent growth ability. In accordance with this intention, calving performance and growth were found to be among the top-scoring traits (3.94,
Figure 5) in cluster 1 in our study. Across all three clusters, farmers paid higher attention to production traits (13% vs. 11% in cluster 2) and only placed growth among the top four breeding goal traits. Likewise, health received the highest score (5.0) when considering all trait preferences across clusters. Exterior, legs, body capacity, and production type were further high-scoring traits (3.75 to 3.88). The second characteristic of cluster 1 was a predominance of smaller herds, running conventionally and managed by younger farmers. The farmers’ age category and a lower herd size might partially align with conventional management and pure-breeding strategies, as these are appropriate in relation to their practical experiences and farm scales. Nevertheless, in some cases, the pure-breeding strategy would be based more on personal conviction than the farmer’s age.
Farms in clusters 2 and 3 combined pure- and crossbreeding strategies (100% and 88%, respectively). Incomes from breeding animals were characteristic of one-third of all farms (38% and 24% in clusters 2 and 3, respectively, as shown in
Figure 4). The ratio of respondents focused on other beef categories was two to three times higher in comparison to purebred farms (e.g., 25% vs. 6% on weaned calves in cluster 2 vs. cluster 1). Therefore, overall production could be defined as partially (cluster 2) and fully (cluster 3) diversified, focusing on selling both breeding animals and other beef categories while using pure- and crossbreeding strategies. In view of the above findings, these farm clusters were also specific in terms of management strategy. Higher production differentiation was likely possible due to herd size (large and medium in clusters 2 and 3, respectively), whereby a portion of cows could be included in a crossbreeding strategy to produce other beef categories. One common characteristic was a predominance of ecological management (in contrast to the conventional farms prevailing in cluster 1), which probably carried certain limitations (e.g., in terms of land management and animal treatment). Such diversified production and specific production conditions are in agreement with the findings of study [
2], where farmers genetically improved the production parameters of animals and final product quality. Nonetheless, this was all in accordance with the production conditions.
In terms of breed structure, two main groups were indicated. Cluster 2 represented farms that specified four of the most frequent breeds, whereas farms in cluster 3 also covered other breeds (Belgian Blue, Salers, and Galloway, making seven in total). In this context, breeds may differ according to the purpose they will be used for [
13]. The same was true for scores assigned to potential breeding goals in clusters 2 and 3 in our study. After the top traits mentioned above, calving performance, growth, polledness, and udder score were among the most important traits in cluster 2. On the contrary, exterior traits (polledness, body capacity, productive type, muscularity, and legs) were among other most preferred goals in cluster 3. Their scores assigned by farmers in cluster 3 were noticeably or substantially different from scores in cluster 2 (see
Table S3). Partially diversified farms in cluster 2 (38% purely produced breeding animals) paid higher attention to the traits currently defined among the top breeding goals, which are probably most appreciated when selling breeding animals. These criteria are therefore similar to those applied in cluster 1, in that they are entirely oriented to pure-breeding, in accordance with the above-mentioned selection strategy for producing sires for beef herds [
13]. On the contrary, fully diversified farms in cluster 3 (24% having breeding animals as the only product and 12% represented by farms solely oriented to crossbreeding) were intensely focused on phenotype and animal performance. Pure-breeding is probably applied on these farms to produce breeding animals (especially cows) to replace their own herds. Therefore, farms in cluster 2 combined current top breeding traits and exterior traits; this is in contrast with farms in cluster 3, which altogether preferred exterior performance. The dominant position of exterior traits in cluster 3 was supported by the score assigned to the production (breeding) type (4.12), which was significantly higher than in cluster 2 (3.25). Production type has a high genetic correlation with overall animal muscularity and therefore could be used as a representative for exterior traits [
13]. The same was true for the trait preferences when score for production type was moderately (0.56 on average) and significantly correlated to all exterior traits (
Table S2). Regarding the main breeding goal categories, farmers in cluster 2 paid slightly higher attention to functional traits (39% vs. 35% in cluster 3), and farmers in cluster 3 preferred exterior (53% vs. 49% in cluster 1).
In the context of the main production, functional, and exterior trait categories, a slight preference for the latter was indicated by both, as indicated by their relatively high scores (all over 3.1 score; legs in cluster 2) and the highest number of traits (seven in total) involved. On the contrary, the production category covered only two traits (growth and meat quality), and for the second trait, the score was typically very low (1.7 to 2.7 in clusters 2 and 1, respectively). The functional category showed a moderate emphasis, covering five traits in total and four with relatively high scores in all clusters (3.7 for calving performance in cluster 3 to 5.0 for health in cluster 1). These specifics determined the overall superiority of the exterior category (51% on average). On the contrary, in case the trait numbers among these categories were more balanced and health traits were separated from the functional category (e.g., 3:4:3:2 traits in sheep breeding systems [
41]), the individual trait and overall category importance could possibly be understood more clearly (e.g., 22:32:29:17 ratio [
41]). For Czech beef breeding purposes, future studies could reassess traits in the functional (specification of those related to health) and exterior (omitting the body frame due to low preferences, defining the production type as representative (as mentioned above)) categories.
Our survey was predominantly oriented toward breeds in the beef breeding system. Nevertheless, based on recent communication with local breeders, they are also interested in crossbreeding beef bulls with dairy cows (i.e., beef on dairy system). This system has already been mentioned in an earlier Czech study [
13]; however, specific breeding objectives and selection candidates have not been defined, and no practical applications for mating plans have been provided. Nevertheless, the number of Czech Holstein cows included in this breeding strategy increased three times in the last decade (up to nearly three thousand matings in 2023, based on our own calculations from the database provided by the CBCA). To identify beef bulls suitable for such a strategy, breeding objectives (e.g., easy calving, short gestation) should be developed and appropriately validated [
43]. Moreover, some financial benefits of the system indicated by [
43] would probably be linked to diversified production and enhanced sources of revenues, as found in our study (
Figure 4) and others already cited [
31,
32].
Our further investigation will reflect the cluster-specific patterns in breeding systems and breeding objective trait preferences to inform tailored breeding programs for Czech beef cattle conditions. The current breeding program, which is universal and simple, will be modified to consider farm specifics in marketing and breeding strategies (pure/cross breeding, specialization vs. part/fully diversification, beef on dairy), farmed breed(s) with new functional traits among the top breeding objectives, and selecting mostly on performance (growth, calving performance) vs. exterior traits. The trait categories in breeding objectives will be more balanced (e.g., separate health from functional category). Similarly, the economic weights of beef breeding goal traits calculated previously [
17] will be updated to consider cluster-specific characteristics and preferences. Farm characteristics will ensure the appropriate setting of production systems, and preferences for the scope of traits will be economically evaluated in the bio-economic model. The current farmers’ interests in terms of beef on dairy strategy will focus on the genetic and economic evaluation of breeding objective traits for such a breeding system under local conditions (as part of the ongoing project). The production (genetic) and economic benefits of the suggested breeding strategies and considered traits will be evaluated. All features will be discussed with the local beef cattle association and breeders (farmers) to apply them into selection in a practically appropriate way.