Divergent Rumen Metabolic Profiles Underlying Breed-Specific Variations in Slaughter Performance and Visceral Organ Development in Beef Cattle

Abstract

Slaughter performance is a critical economic trait that varies across breeds, yet the rumen metabolic mechanisms driving these phenotypic differences remain unclear. The study involved 30 healthy 12-month-old beef cattle, with 10 animals from each of the three breeds: Chinese Simmental (ST), Taihang Yun (TY), and Charolais (CL). The cattle were randomly assigned into three groups using a completely randomized design, and the average initial body weight was 549.78 ± 59.45 kg. A 130-day feeding trial (10-day pre-feeding period, 120-day main trial period) was conducted. By comparing the slaughter performance, relative organ weight, and rumen fluid metabolomic profiles, the study investigated breed-specific differences in meat quality and potential underlying metabolic patterns. The results showed that CL exhibited a superior carcass yield, with a significantly higher dressing percentage (62.38%, p = 0.013) and net meat percentage (56.54%, p = 0.028) than ST and TY, and a significantly lower backfat thickness (p = 0.006); ST had the highest proportion of premium cuts, relative to carcass weight (72.97%, p = 0.014), with prominent economic value, while TY had significantly higher weights of visceral organs, such as liver, kidney, small intestine and omasum, than CL (p < 0.05). Metabolomic analysis revealed that CL and ST had elevated levels of purine metabolism, nucleotide synthesis and cofactor biosynthesis compared to TY. In conclusion, CL and ST possess advantages in carcass yield supported by upregulated anabolic metabolism in the rumen, whereas TY prioritizes visceral organ development. These findings provide valuable insights into the physiological and metabolic divergences regulating the slaughter performance and regional adaptability across cattle breeds.

1. Introduction

Beef plays a significant part in global meat consumption [1] and serves as a vital source of protein, trace elements, and amino acids [2]. As consumer demand for high-quality protein rises, the optimization of beef production systems has become a priority [3,4]. The production efficiency of beef cattle is influenced by many factors, including environmental conditions, nutritional management, and genetics [5]. Among these, breed is a primary determinant of slaughter performance and terminal market value [6,7]. Therefore, identifying breeds with superior adaptability and production potential is crucial for the sustainable development of the beef industry [8,9]; developing breeding programs to meet the growing demand for beef and enhance energy efficiency is an urgent priority [10,11].

Although China possesses rich germplasm resources with 55 identified indigenous cattle breeds [12], these breeds generally exhibit a smaller body size, slower growth rates, and lower slaughter yields compared to commercial lines [13]. Consequently, crossbreeding indigenous cattle with specialized commercial breeds has been widely adopted to upgrade local herds [14,15]. Thus, exploiting heterosis to enhance the growth performance is considered an effective strategy for the genetic improvement of beef cattle populations [16]. In recent decades, researchers have focused on selecting early maturing cattle breeds and performing interbred crosses to improve carcass growth performance [17]. Simmental cattle (ST) and Charolais cattle (CL) are among the most widely distributed beef breeds globally. Excellent foreign breeds of cattle have been introduced to China since the 1960s [18]. The ST, a dual-purpose breed, is characterized by rapid growth and strong adaptability [19], while the CL is renowned for its high weight gain rates and large body size [20]. Furthermore, the CL breed is widely favored for its rapid growth, high meat yield and ability to thrive on coarse feed [3,21]. Comparative studies indicate that CL exhibit superior carcass characteristics and meat yield performance compared with other cultivated beef cattle breeds such as Simmental and Angus [19,22]. In addition, CL exhibit exceptional growth performance that is comparable to other specialized beef breeds, particularly in intensive systems [23]. The Taihang Yun cattle (TY) is a specialized beef breed developed in Shanxi Province, China, derived from crossbreeding Jinnan cattle with Simmental and Hereford strains. Although TY exhibits rapid growth and high feed conversion efficiency, comparative data regarding the slaughter performance of TY remains insufficient.

The rumen microbiome and its metabolome are pivotal in ruminant digestion, influencing the feed efficiency, nutrient absorption, and overall growth performance, which in turn affect slaughter traits such as carcass weight and yield [24]. For instance, rumen metabolites including branched-chain amino acids (e.g., valine, leucine, isoleucine) and volatile fatty acids have been associated with enhanced muscle protein synthesis and energy metabolism in beef cattle, leading to improved liveweight gain and carcass quality [25]. Studies on crossbred steers have shown that variations in rumen metabolic profiles, such as those involving linoleic acid derivatives and glycerophospholipids, correlate with differences in body weight and feed conversion ratios, underscoring the role of metabolomics in elucidating breed-specific production advantages [26]. However, the underlying mechanisms linking breed-specific rumen metabolic profiles to slaughter performance remain largely unexplored.

Therefore, this study aimed to evaluate the slaughter performance and relative organ weights of CL, ST, and TY, while concurrently utilizing non-targeted rumen metabolomics to elucidate the underlying metabolic mechanisms and breed-specific metabolic signatures associated with these production traits. We hypothesized that the divergence in slaughter performance among these breeds is driven by distinct rumen metabolic signatures, particularly through specific pathways governing nutrient absorption and energy partitioning.

2. Materials and Methods

2.1. Ethics Statement

This study was approved by the Shanxi Agricultural University Laboratory Animal Ethics Committee (Approval No.: SXAU-EAW-2024B.QU.004026288). All experimental animals, design, and management were conducted in compliance with the “Animal Research: Reporting of In Vivo Experiments” (ARRIVE) guidelines (https://arriveguidelines.org). All efforts were made to minimize animal suffering, including the use of humane endpoints and standardized housing conditions. Animal experiments were conducted from July to November 2023 at Lvhe Ecological Animal Husbandry Development Co., Ltd. in Heshun County, Jinzhong City, China.

2.2. Experimental Design and Feeding Management

Thirty healthy, aged 12-month-old beef cattle were utilized in the present experiment, with initial body weights of 552.36 ± 48.92 kg for Chinese Simmental (ST), 545.62 ± 65.38 kg for Taihang Yun (TY), and 551.36 ± 58.15 kg for Charolais (CL) (n = 10 per breed). Using a completely randomized design, the cattle were randomly assigned to three groups, based on breed. The experiment lasted for 130 d, consisting of a 10 d adaptation period and 120 d with a finishing period. The adaptation phase was designed for acclimation to both the housing facilities and the experimental diets. During this period, all cattle were offered the same finishing ration as the formal trial (

Table 1. Nutrient levels of base rations (%DM).

Ingredients	Content	Nutrient Levels (2)	Content
Corn	28.10	Ash	4.61
Soybean meal	5.00	NDF	35.65
Cotton meal	3.70	ADF	19.22
Soya bean skin	3.20	CP	10.49
Nacl	0.42	EE	1.84
NaHCO3	0.43	Ca	0.54
Premix (1)	2.15	P	0.35
Dry straw	13.00	NEmf/(MJ/kg)	5.49
Whole-plant corn silage	44.00
Total	100.00

⁽¹⁾ One kilogram of the premix contained the following: VA 500,000 IU, VD 150,000 IU, VE 2400 IU, Fe 500 mg, Cu 1000 mg, Zn 2400 mg, Mn 1500 mg, Se 45 mg, and Co 15 mg. The composition of the premix was verified by laboratory detection, and the deviation between the actual content of each nutrient and the labeled value was ≤5%, which was in line with the Quality Standard for Feed Additives (GB 7291-2017). ⁽²⁾ NEmf was calculated according to the Feeding Standard of Beef Cattle (NY/T 815-2004) [28], while the others were measured values.

) on an ad libitum basis to ensure physiological and behavioral stabilization prior to data collection. Prior to the experiment, all animals received a broad-spectrum anthelmintic treatment to ensure they were free from parasites. Furthermore, the animal pens were thoroughly sanitized with a 2% glutaraldehyde solution to reduce microbial contamination. Fecal matter was removed from the pens daily throughout the study to maintain a hygienic environment and mitigate potential health risks to the animals. All group diets were formulated according to the Feeding Standard of Beef Cattle (NY/T 815-2004) [27] and presented in Table 1.

Prior to the experiment, all animals were housed in individual stalls and underwent routine deworming. The TMR was offered twice daily at 08:00 and 16:00 in equal portions to ensure ad libitum access to feed and water. The feed offered was adjusted daily to allow for approximately 5% to 10% refusals. All experimental cattle in this study were from the same breeding base, adopted the same basic feeding and management mode before the start of the experiment, and were assigned to each group by a completely randomized design. There were no significant differences in initial body condition, health status and age (p > 0.05), which excluded the confounding effect of animal pre-existing conditions on the experimental results, ensured that the experimental treatment (breed) was the only variable, and improved the credibility and repeatability of the study results.

2.3. Sample Collection and Chemical Analyses

2.3.1. Slaughtering Methods

On day 130 of the trial, all animals were subjected to a 24 h fasting period and were weighed prior to slaughter to determine their final live weight. Subsequently, following the slaughter procedures established by Galvani et al. [29], throughout the slaughter process, strict adherence to cattle welfare standards was maintained [30]. Immediately post-mortem, the hot carcass weight was recorded, and carcass morphometric traits, including carcass length, depth, and backfat thickness, were measured. The weight of the external offal (head, feet, and hide) were also recorded. To determine the visceral organ weight and relative organ weight at slaughter, the heart, liver, spleen, lungs, and kidneys were separated and weighed individually. Additionally, the compartments of the gastrointestinal tract (reticulum, omasum, abomasum, small intestine, and large intestine) were separated, stripped of mesenteric fat, emptied of digesta, rinsed with physiological saline, and weighed to determine their absolute mass.

Following slaughter, carcasses were chilled at 4 °C for 24 h. The cold carcass weight was then recorded. The left half-carcass of each animal was fabricated into primal and sub-primal cuts in accordance with the Beef Carcass and Cuts Standard (GB/T 27643-2011) [28]. These cuts were subsequently classified into three quality grades: high-grade cuts (comprising chuck eye, eye round, striploin, and tenderloin), premium cuts (comprising knuckle, rump, silverside, topside, shank, and chuck tender), and standard cuts (comprising flank, brisket, neck, and shin). Any remaining meat trimmings were categorized as “other cuts.” Finally, the dressing percentage, net meat percentage, and meat-to-bone ratio were calculated based on the recorded carcass and bone weights.

2.3.2. Calculation Methods for Slaughter Performance and Organ Indicators

The slaughter performance and organ index indicators are calculated as follows.

Carcass weight (kg): The weight of the bovine remaining after slaughter and bleeding, with the following parts removed: skin, head, hooves (including joints and bones below the carpal bones), tail (including the tailbone connection), internal organs (excluding kidneys and perirenal fat), reproductive organs, and abdominal fat.

Slaughter yield (%): (carcass weight/live weight) × 100.

Net meat weight (kg): The weight of the carcass after deboning, including the kidneys and the fat surrounding them.

Carcass bone weight (kg): The weight of the bones remaining after removing the meat from the carcass.

Net meat yield (%): (net meat weight/pre-slaughter live weight) × 100.

Backfat thickness (cm): Measure the thickness of subcutaneous fat at the 12th to 13th intercostal space using a vernier caliper (Shanghai Tool Factory Co., Ltd., Shanghai, China), excluding the skin.

Meat-to-bone ratio = net meat weight/bone weight.

Proportion of gastric retention = weight of each gastric compartment/total weight of the whole stomach × 100%.

Reticulo-rumen index = reticulo-rumen weight/pre-slaughter live weight × 100%.

Omasum index = omasum weight/pre-slaughter live weight × 100%.

Abomasum index = abomasum weight/pre-slaughter live weight × 100%.

Gastrointestinal index = total gastrointestinal weight/pre-slaughter live weight × 100%.

Relative organ weight = calculated as total organ weight/pre-slaughter live weight × 100%.

2.3.3. Non-Targeted Metabolomics of Rumen Fluid

Rumen fluid was collected from six experimental cattle of all groups within 30 min after slaughter. The contents of the rumen ventral sac were collected, homogenized and filtered through four layers of gauze. Then, the rumen fluid was immediately aliquoted into 1.5 mL cryotubes, quickly frozen in liquid nitrogen for 15 min, and then transferred to a −80 °C ultra-low temperature refrigerator (Haier Biomedical Co., Ltd., Qingdao, China) for further metabolomic analysis. The metabolomic profiling of rumen fluid was performed by Majorbio Bio-Pharm Technology Co., Ltd. (Shanghai, China). Briefly, 100 µL of rumen fluid was mixed with 400 µL of extraction solvent (acetonitrile:methanol = 1:1, v/v) containing internal standards (L-2-chlorophenylalanine, 0.02 mg/mL). The mixture was vortexed for 30 s, sonicated at 5 °C (40 kHz) for 30 min and incubated at −20 °C for 30 min to precipitate proteins. Following centrifugation at 13,000× g for 15 min at 4 °C, the supernatant was evaporated to dryness under a stream of nitrogen and reconstituted in 100 µL of acetonitrile:water (1:1, v/v). The reconstituted solution was sonicated and centrifuged again under the same conditions, and the supernatant was transferred to vials for LC-MS analysis. Chromatographic separation was achieved on an HSS T3 column (100 mm × 2.1 mm, 1.8 µm) maintained at 40 °C. The mobile phases consisted of 0.1% formic acid in water:acetonitrile (95:5, v/v; Phase A) and 0.1% formic acid in acetonitrile:isopropanol:water (47.5:47.5:5, v/v/v; Phase B), delivered at a flow rate of 0.40 mL/min. Mass spectrometry data were acquired in both positive and negative ionization modes scanning from m/z 70 to 1050, with ion source voltages set at 3500 V (+) and −3000 V (−).

2.3.4. Metabolome Sequencing Data Processing and Analysis

Raw data were processed using Progenesis QI software (Version 2.0, Waters Corporation, Milford, MA, USA) for baseline filtering, peak alignment, and integration. Metabolite identification was performed by matching MS and MS/MS spectra against the HMDB and METLIN databases. The resulting data matrix was uploaded to the Majorbio Cloud Platform for statistical analysis. Preprocessing included the removal of variables with missing values in >20% of samples (80% rule) and imputation of the remaining missing values using minimum detection limits. Data were normalized by sum normalization and log10-transformed. Variables with a relative standard deviation (RSD) > 30% in quality control (QC) samples were excluded to ensure data quality. Rumen fluid metabolites were identified by the Human Metabolome Database (HMDB) [31]. The final dataset containing information such as peak number, sample name, and normalized peak area was imported into the SIMCA 16.0.2 software package (Sartorius Stedim Data Analytics AB, Umea, Sweden) for multivariate analysis [32]. Significantly changed metabolites (SCMs) were identified based on variable importance (VIP) scores > 1 and p-values < 0.05 from the orthogonal projections to the latent structures–discriminate analysis (OPLS-DA) model [33]. The metabolic pathway enrichment of SCMs was performed using the Kyoto Encyclopedia of Genes and Genomes (KEGG) (http://www.genome.jp/kegg/ accessed on 16 May 2024) and MetaboAnalyst (http://www.metaboanalyst.ca/ accessed on 17 May 2024), elucidating pathways related to the experimental conditions.

2.4. Data Analysis

Data regarding the slaughter performance, relative organ weight, and carcass traits were analyzed using the general linear model procedure of SAS (Version 9.4, SAS Institute Inc., Cary, NC, USA). The normality of residual distributions was assessed using the UNIVARIATE program in SAS software, with both the NORMAL and PLOT options enabled. Meanwhile, the homogeneity of variances was verified through Levene’s test. The statistical model used was as follows:

$$Y_{ij}=\mu +B_i+e_{ij}$$

(1)

$Y_{ij}$ is the dependent variable, $\mu$ is the general average, $B_i$ is the fixed effect of breed (Charolais, Chinese Simmental, Taihang Yun); and $e_{ij}$ is the experimental error.

The differences among the treatments were compared using a multiple comparison test, following the Tukey method. p ≤ 0.05 indicated a significant difference and 0.05 < p ≤ 0.10 indicated a tendency.

3. Results

3.1. Slaughter Performance

In this study, the average pre-slaughter weights at 16 months of age (12 months of age + 4 months of finishing) for the three breeds were 618.83 kg for Simmental cattle, 655.00 kg for Taihang Yun cattle, and 635.00 kg for Charolais cattle. This weight range aligns with the physiological growth norms for the finishing beef cattle of these three breeds, which is consistent with the inherent growth characteristics of each breed.

The pre-slaughter live weight, hot carcass weight, net meat weight and carcass length did not differ among breeds (p > 0.05,

Table 2. Comparison of slaughter performance of different breeds of beef cattle.

Items	Chinese Simmental Cattle	Taihang Yun Cattle	Charolais Cattle	SEM	p-Value
Live weight/kg	618.83	655.00	635.00	8.122	0.281
Carcass weight kg	366.00	386.83	389.40	6.684	0.359
Dressing percentage/%	59.20 b	59.41 b	62.38 a	0.598	0.013
Lean meat weight/kg	321.00	351.50	353.29	6.923	0.117
Lean meat percentage/%	52.82 b	53.64 b	56.54 a	0.681	0.028
Bone weight/kg	37.00 a	25.33 b	26.81 b	1.651	0.0005
Meat bone ratio/%	8.70 b	13.95 a	13.21 a	0.721	0.0001
Torso length/cm	204.75	198.00	203.20	1.616	0.288
Backfat thickness/cm	1.92 a	1.93 a	1.42 b	0.090	0.006

^a and ^b represent different groups. There was a significant difference in the different letters between groups (p < 0.05). The same letters between groups showed no significant differences (p > 0.05).

). Charolais cattle showed a significantly higher dressing percentage (p = 0.013) and net meat percentage than ST and TY, alongside reduced backfat thickness (p = 0.028). In terms of bone content, ST presented a significantly higher bone weight than the other two breeds (p < 0.01). Moreover, ST and TY displayed greater backfat thickness than CL (p = 0.006).

3.2. Cut Weight

The weights of the tenderloin, striploin, eye round, round, rump, top sirloin, bottom sirloin, plate, chuck, brisket, flank, chuck flap, shoulder, and total premium cuts did not differ among the three breeds (p > 0.05,

Table 3. Comparison of meat weights of parts of beef cattle of different breeds.

Items	Chinese Simmental Cattle	Taihang Yun Cattle	Charolais Cattle	SEM	p-Value
Tenderlion/kg	7.42	6.65	6.75	0.207	0.337
Striplion/kg	11.11	10.97	11.10	0.340	0.987
Ribey/kg	13.03	11.83	14.12	0.513	0.186
High rib/kg	22.74 b	22.33 b	26.79 a	0.859	0.023
Top side/kg	22.14	23.92	22.35	0.562	0.470
Kunckle/kg	14.21	15.35	15.40	0.316	0.278
Rump/kg	12.83	14.57	14.15	0.390	0.250
Outside flat/kg	15.70	17.13	16.38	0.473	0.587
Eyeround/kg	7.14	6.67	6.71	0.265	0.794
Sinew/kg	7.55	8.38	7.82	0.246	0.489
Pre-tendon/kg	11.41	10.60	10.77	0.280	0.570
Shank/kg	10.66	12.22	11.58	0.290	0.130
Abdominal meat/kg	38.58	39.63	39.08	1.175	0.957
Chuck tender/kg	4.32	4.18	4.25	0.116	0.923
Neck meat/kg	24.96 b	28.60 ab	32.45 a	1.242	0.018
Shoulder meat/kg	16.22	17.67	18.55	0.590	0.289
Human chest/kg	32.63	32.63	30.62	0.828	0.531
Total weight of quality meat blocks/kg	267.04	262.47	268.93	4.722	0.877
Quality meat blocks as a percentage of carcass weight/%	72.97 a	67.81 b	69.07 b	0.786	0.014
Gross weight of high-grade cuts of meat/kg	53.40	51.78	58.76	1.571	0.132
Percentage of carcass weight of high-grade meat blocks/%	13.80 b	13.42 b	15.08 a	0.281	0.007

^a and ^b represent different groups. There was a significant difference in the different letters between groups (p < 0.05). The same letters between groups showed no significant differences (p > 0.05).

). In contrast, CL exhibited significantly higher weights for the neck meat compared to ST and (p = 0.018). ST cattle possessed a significantly higher proportion of premium cuts relative to the carcass weight compared to the other breeds (p = 0.014). However, the proportion of high-grade cuts was significantly greater in CL than in ST and TY (p = 0.007).

3.3. Organ and Tissue Weight

The weights and relative organ weight did not differ among the breeds (p > 0.05,

Table 4. Comparison of visceral organ weights and proportion of pre-slaughter live weight in different breeds of beef cattle.

Items	Chinese Simmental Cattle	Taihang Yun Cattle	Charolais Cattle	SEM	p-Value
Heart
Weight/kg	2.54	2.28	2.17	0.073	0.074
Cardiac Index/%	0.39	0.35	0.34	0.118	0.217
Liver
Weight/kg	7.85 ab	8.57 a	7.21 b	0.230	0.044
Liver Function Tests%	1.20 ab	1.31 a	1.09 b	0.035	0.034
Spleen
Weight/kg	1.52	2.30	1.58	0.187	0.313
Spleen Index/%	0.17	0.37	0.27	0.037	0.146
Lung
Weight/kg	3.77	3.55	3.69	0.110	0.798
Lung Index/%	0.56	0.54	0.58	0.010	0.239
Kidney
Weight/kg	1.39 a	1.30 a	1.02 b	0.057	0.001
Kidney Index/%	0.21 a	0.20 a	0.16 b	0.009	0.011
Total Organ Weight/kg	14.73	15.33	13.61	0.369	0.191
Organ Index/%	2.25	2.42	2.16	0.061	0.345

^a and ^b represent different groups. There was a significant difference in the different letters between groups (p < 0.05). The same letters between groups showed no significant differences (p > 0.05).

). However, significant variations were observed in the weight and relative weight of the liver and kidney among the breeds. TY exhibited a significantly higher liver weight (p = 0.044) and liver index (p = 0.034) compared to CL. Furthermore, both ST and TY possessed significantly greater kidney weights (p = 0.001) and kidney indices (p = 0.011) than CL.

The live weights and proportional contributions of the large intestine, omasum, reticulum, and total gastrointestinal tract did not differ among the breeds (p > 0.05,

Table 5. Comparison of gastrointestinal weights and percentage of live weight at slaughter in different breeds of beef cattle.

Items	Chinese Simmental Cattle	Taihang Yun Cattle	Charolais Cattle	SEM	p-Value
Large intestine
Weight/kg	4.51	4.37	4.14	0.100	0.295
Colon index/%	0.69	0.67	0.65	0.021	0.711
Small intestine
Weight/kg	6.79 ab	7.17 a	6.63 b	0.089	0.036
Small intestine index/%	1.04	1.10	1.04	0.026	0.722
Reticulo-rumen
Weight/kg	13.49	12.52	11.80	0.326	0.067
Proportion of gastric retention/%	50.46	48.33	47.35	0.795	0.266
Gastric tumor index/%	2.06	1.91	1.84	0.043	0.069
Omasum
Weight/kg	8.90 b	9.35 a	8.85 b	0.087	0.036
Proportion of gastric retention/%	33.39	34.42	35.62	0.665	0.431
Cervical index/%	1.37	1.36	1.36	0.047	0.996
Abomasum
Weight/kg	4.31	4.47	4.51	0.112	0.773
Proportion of gastric retention/%	16.15	17.26	17.03	0.312	0.319
Wrinkled stomach index/%	0.66	0.68	0.71	0.024	0.693
Total gastrointestinal weight/kg	26.71	25.88	24.62	0.408	0.087
Gastrointestinal index/%	4.09	3.96	3.83	0.094	0.581

^a and ^b represent different groups. There was a significant difference in the different letters between groups (p < 0.05). The same letters between groups showed no significant differences (p > 0.05).

). However, breed-specific differences were identified in tissue masses. TY possessed a significantly heavier small intestine compared to CL (p = 0.036). Moreover, the Omasum weight in TY was significantly greater than that in both ST and CL (p = 0.036). The weights of the head, hide, and hooves did not differ among the breeds (p > 0.05,

Table 6. Comparison of other non-carcass tissue and organ weights and proportion of live weight at slaughter in different breeds of beef cattle.

Items	Chinese Simmental Cattle	Taihang Yun Cattle	Charolais Cattle	SEM	p-Value
Top-heavy/kg	31.15	33.87	31.82	0.562	0.176
Proportion of antemortem Live weight/%	4.77	5.17	5.01	0.099	0.320
Tare weight/kg	49.75	49.87	47.25	0.801	0.319
Proportion of antemortem Live weight/%	7.61	7.61	7.44	0.122	0.830
Hoof weight/kg	13.93	14.22	12.98	0.257	0.102
Proportion of antemortem Live weight/%	2.14	2.18	2.05	0.059	0.692

).

3.4. Rumen Metabolomics

A total of 1414 metabolites were identified across both ionization modes, primarily belonging to lipids and lipid-like molecules and organic acids and derivatives (Figure 1A). To evaluate the metabolic divergences between the indigenous and introduced breeds, OPLS-DA models were constructed for pairwise comparisons. The score plots demonstrated clear spatial separation between ST vs. TY and CL vs. TY (Figure 1B), with 200-repetition permutation tests confirming the absence of overfitting (Figure 1C). Based on the integration of OPLS-DA VIP values (VIP > 1) and volcano plots, we identified 249 significantly changed metabolites (SCMs) between ST and TY (122 metabolites with higher abundance and 127 metabolites with lower abundance in ST) and 337 SCMs between CL and TY (126 metabolites with higher abundance and 211 metabolites with lower abundance in CL). Notably, the top 30 VIP-ranked metabolites, including N-methylrosmaricine, MG(PGD2/0:0/0:0), pyrilamine, and cirazoline, consistently exhibited lower relative abundances in the TY group. However, the relative abundance of CE(5:0) was higher in the TY group (Figure 2A–C).

KEGG enrichment analysis was employed to elucidate the functional implications of these SCMs (Figure 3). The differentially abundant metabolites were significantly enriched in pathways that were critical for nutrition and energy metabolism, specifically galactose metabolism, fat digestion and absorption, and purine metabolism. Furthermore, significant alterations were identified in amino acid metabolism (tyrosine and tryptophan metabolism) and the biosynthesis of cofactors. The enrichment of pathways such as ABC transporters and dopaminergic synapse further highlights breed-specific variations in nutrient transport and physiological regulation. Collectively, these findings indicate that the observed variations in slaughter performance and organ development among these breeds are driven by distinct rumen metabolic patterns, where CL and ST exhibit more active anabolic pathways related to growth, while TY maintains a metabolic profile that is potentially aligned with regional adaptability and lower metabolic intensity.

4. Discussion

4.1. Breed-Specific Divergence in Slaughter Performance and Carcass Commercial Value

Slaughter performance serves as a primary indicator of animal production efficiency and economic value [22,34]. Moreover, slaughter performance is influenced by factors such as breed, age, sex, feeding level, and environmental conditions [35]. When feeding management conditions are consistent and the nutritional concentration of the diet meets the growth and development requirements of livestock, genetic factors are a key determinant of beef cattle production performance [36,37]. In the current study, CL exhibited significantly lower backfat thickness than the other breeds, suggesting a higher lean meat yield and reduced adipose deposition. These results align with the previous study, which found that backfat thickness is negatively correlated with the lean meat percentage [38]. While no significant difference was observed in the final pre-slaughter live weight among the three breeds, their body compositions exhibited distinct phenotypic divergence. Specifically, Charolais cattle displayed significantly lower backfat thickness and a higher muscle-to-bone ratio compared to Simmental cattle, indicating a nutrient partitioning strategy that preferentially favors myogenesis over adipogenesis and skeletal growth. Conversely, Simmental cattle showed the highest bone mass, yet maintained a high proportion of premium cuts, suggesting a robust skeletal framework supporting substantial muscle deposition. This uniformity in final live weight serves as a standardized baseline, effectively eliminating body size as a confounding factor and demonstrating that the observed variations in tissue accretion are driven by breed-specific genetic programs and metabolic priorities. This result indicated that CL cattle prioritize nutrient partitioning toward muscle accretion. However, the commercial value of a carcass is also dictated by the yield of premium cuts [39]. Genetic foundation is a key factor influencing the production of high-quality beef [36,40]. Interestingly, ST demonstrated a significantly higher proportion of premium cuts (72.97%) relative to carcass weight compared to TY (67.81%) and CL (69.07%). This confirms the superior genetic merit of Simmental cattle for producing high-value primal sections, such as the chuck, striploin, and tenderloin. While CL produced the highest proportion of high-grade cuts (15.08%), the overall economic utilization value was highest in ST due to its superior premium cut yield. This suggests that while CL is optimized for total lean output, ST excels in the distribution of high-value retail segments.

4.2. Visceral Organ Development and Physiological Adaptation

The weights and development of visceral organs reflect the metabolic demands and physiological status of ruminants [37]. Research has found that the development of ruminant internal organs directly impacts livestock weight gain, feed intake, and digestive capacity [41]. A noteworthy observation in this study was the significantly higher liver and kidney mass in TY compared to CL. The liver is considered the largest detoxification organ in animals [42] and a key metabolic organ for energy and lipid conversion [43,44], and its development is closely related to the maintenance of bodily homeostasis [45]. Regulating fat metabolism in the animal body can help to reduce fatty liver deposits and metabolic burden, promote healthy liver development, and thereby improve liver function indicators [46]. The heavier hepatic mass in TY likely supports a more active metabolic system, which is required for its specific growth and protein turnover rates. Furthermore, the concurrently larger kidneys suggest an enhanced capacity for nitrogenous waste clearance [47], which is a physiological adaptation to its unique metabolic intensity. This visceral-heavy strategy extends to the digestive tract. TY exhibited a significantly heavier small intestine and omasum compared to CL and ST. As the small intestine is the primary site for the absorption of proteins and carbohydrates, its increased mass provides a larger absorptive surface area, potentially enhancing the nutrient utilization efficiency. It simultaneously protects the organism from harmful compounds within the intestinal lumen [48,49]. Similarly, the development of the rumen is influenced by age, feed composition, and feed nutritional components [50]. The heavier omasum suggests a more robust capacity for regulating the digesta flow and fluid absorption. Research indicates that improvements in volatile fatty acids within the rumen positively impact its growth and development [51,52]. Moreover, these results indicate that the enhanced digestive architecture in TY, characterized by higher small intestinal and omasal weights, likely facilitates nutrient extraction via an increased absorptive surface area—a potential adaptation to local feed resources [53]. However, this physiological advantage is offset by the substantial metabolic cost of maintaining a larger gastrointestinal mass [54]. Given that visceral tissues exhibit a high metabolic turnover, this “visceral-heavy” strategy in TY prioritizes nutrient partitioning toward organ maintenance over muscle accretion [55]. Consequently, this trade-off between nutrient extraction efficiency and maintenance energy requirements partially accounts for the lower carcass yields observed in the indigenous TY breed compared to the introduced counterparts.

4.3. Rumen Metabolomic Signatures: Mechanisms Driving Anabolic Divergence

The integration of rumen metabolomics provides a molecular lens to elucidate the mechanisms driving the observed phenotypic variations [56,57]. Our results showed that the abundance of metabolites related to purine and pyrimidine metabolism in the rumen fluid of CL and ST was significantly higher. It is important to note that these purine metabolites are primarily products of the microbial degradation and turnover of nucleic acids, rather than a direct reflection of the host’s systemic metabolism [58]. However, in ruminant physiology, the concentration of these derivatives serves as a reliable proxy for MCP synthesis and microbial anabolic intensity [59]. In the present experiment, the elevated levels of adenosine, inosine, and hypoxanthine in CL and ST cattle suggest a more dynamic microbial nitrogen flux and enhanced microbial biomass production [60,61]. This accelerated microbial turnover likely leads to a greater flow of high-quality microbial protein to the small intestine, providing the essential amino acid precursors required for muscle protein synthesis and rapid tissue accretion [62]. Consequently, these rumen metabolic signatures are intrinsically associated with the superior growth rates and hot carcass weights that characterize the anabolic divergence of these breeds. In contrast, the lower accumulation of these precursors in TY reflects a more conservative metabolic strategy, potentially prioritizing maintenance and energy efficiency over rapid tissue deposition [63,64].

5. Conclusions

In conclusion, this study demonstrates that there are significant breed-specific differences in the slaughter performance and visceral organ weight of beef cattle, and these differences are closely associated with the breed-specific characteristics of rumen metabolic profiles. The differentially abundant metabolites in pathways such as purine metabolism and nucleotide synthesis in the rumen provide important metabolic clues for analyzing breed-specific production performance. CL and ST exhibit superior carcass yield and premium cut proportions, respectively, supported by upregulated anabolic pathways in the rumen, such as purine and nucleotide metabolism. In contrast, TY tend to develop visceral organs and adaptive changes in rumen morphology, and their conservative metabolic profile is more conducive to internal environmental homeostasis and environmental adaptability. However, the high mass of visceral organs also brings higher maintenance energy consumption, leading to a trade-off in nutrient allocation between growth and visceral maintenance; thus, its growth rate and carcass meat yield are lower than those of introduced breeds. These findings provide valuable insights into the molecular mechanisms regulating production efficiency across diverse cattle breeds and offer a scientific basis for optimizing breed selection and regional breeding strategies in the beef industry.