Jiancheng Han

The Leizhou black goat is a prized indigenous breed in southern China, renowned for its superior meat quality. However, its productivity is constrained by a relatively small body size. Understanding the genetic basis of growth differences between purebred and crossbred populations is essential for designing effective conservation and breeding strategies. To this end, we conducted comparative whole-genome resequencing on 22 purebred (WL) and 50 crossbred (JN: Nubian × Leizhou) goats. Population structure was assessed via principal component analysis, and genomic regions exhibiting elevated genetic differentiation were identified using the population differentiation index (F_ST). Functional enrichment analyses were subsequently applied to genes within these regions. Our results revealed clear genetic differentiation between the two populations. Among the highly differentiated genomic regions, we identified several genes, such as MYOM2, TMTC4, DPP6, and MIDN, whose known functions in neural signaling and muscle development make them plausible candidates for contributing to the growth differences between populations. A particularly notable discovery was a non-coding intronic mutation in the RNGTT gene (rs646826802), which is fixed in the paternal Nubian line and prevalent across 25 other global goat breeds but is completely absent in the purebred Leizhou black goat. This study identifies key genetic components associated with trait variation in crossbred goats and reports a breed-specific genomic marker that can serve as a practical tool for verifying breed purity, thereby supporting the conservation of this valuable indigenous genetic resource.

Macadamia integrifolia husk (MIH) is a major byproduct of Macadamia integrifolia processing; however, there is limited information available on its rumen fermentation characteristics and associated bacterial communities when used as a feed for ruminants. This study evaluated the effects of different Bacillus subtilis (BS; ≥10¹³ CFU/g) inclusion levels on MIH using an in vitro technique. A total of six healthy goats (female, 7-month-old) with an average body weight of 15.20 ± 0.20 kg were selected as rumen fluid donors, and the rumen fluid was collected before morning feeding. Four BS inclusion levels were studied: a control group with 0 g/kg (CON), and three treatment groups supplemented with 1.5 g/kg (low dose, BSL), 3.0 g/kg (medium dose, BSM), and 4.5 g/kg (high dose, BSH) of BS. MIH supplemented with BS improved the gas production at all the observed incubation times (p < 0.05). The in vitro dry matter degradability was increased by 3.5%, 2.0%, and 3.1% in the BSL, BSM, and BSH groups, respectively, compared to the CON group at a 48 h incubation time (p = 0.049). The in vitro neutral detergent fiber degradability was increased by 6.0% and 7.8% in the BSL and BSM groups, respectively, compared to the CON group at a 48 h incubation time (p = 0.027). The in vitro acid detergent fiber degradability was increased by 11.7%, 16.8%, and 3.2% in the BSL, BSM, and BSH groups, respectively, compared with the CON group at the 48 h incubation time (p = 0.014). The concentrations of ammonia-N, microbial protein, total VFAs, acetate, propionate, butyrate, iso-butyrate, valerate, and iso-valerate were quadratically changed with increasing BS supplementation levels (p < 0.05). The relative abundances of Bacteroidota and Pseudomonadota were highest in the BSL group and lowest in the BSM group (p < 0.05), whereas Bacillota and Kiritimatiellota were highest in the BSH group and lowest in the BSL group (p < 0.05). Synergistota was highest in the BSM group and lowest in the BSH group (p < 0.05). The relative abundances of norank_p_Bacteroidota and norank_o_Bacteroidoles were highest in the BSL group, whereas they were lowest in the BSM group (p < 0.05). The relative abundances Hoyesella and Succinivibrio were highest in the BSL group, whereas they were lowest in the BSH group (p < 0.05). The relative abundances of Prevotella, Succiniclasticum, and Selenomonas were highest in the BSM group, whereas they were lowest in the BSL group (p < 0.05). These in vitro results indicate that supplementation with Bacillus subtilis could improve the utilization of MIH in goats, which is possibly associated with the altered rumen bacteria communities. The supplementation of 1.5 to 3.0 g/kg Bacillus subtilis (≥10¹³ CFU/g) on Macadamia integrifolia husk could improve its utilization as a feasible alternative feed for ruminants using an in vitro technique.

This study was conducted to measure Macadamia integrifolia husk (MIH) as a feed ingredient for goats using an in vitro rumen fermentation system. Four isonitrogenous and isoenergetic substrates were prepared by using MIH to replace 0, 5%, 10%, or 15% of corn as a dry matter basis, namely MIH0, MIH5, MIH10, and MIH15 groups, respectively. Gas production decreased linearly as corn was replaced by increasing levels of MIH. The DMD decreased linearly at the 24 h and 48 h incubation times as corn was replaced by increasing levels of MIH (p < 0.01). The NDFD decreased linearly at the 6 h, 12 h, 24 h, and 48 h incubation times as corn was replaced by increasing levels of MIH. At 48 h, pH differed extremely significantly (p < 0.001) and followed a quadratic trend (p < 0.05). The MIH0 group had the highest NH₃–N, butyric, and isovaleric acids concentration (p < 0.05); the MIH5 group had the highest MCP, acetic acid, and propionic acid concentration (p < 0.05). Bacteroidota and Pseudomonadota were the dominant phyla in the fermentation fluid at the 48 h incubation timepoint among the four groups. The relative abundance of Kiritimatiellota and Synergistota was highest in the MIH15 group. The relative abundance of Pseudomonadota was highest in the MIH5 group. At the genus level, norank_p_Bacteroidota and Ruminobacter were the dominant genera, and the bacterial community structure differed significantly among the four treatments (p < 0.05). In conclusion, we suggest that the MIH replacing 5% of corn did not affect fermentation, VFA profile, or microbial protein synthesis and it could alter the bacterial communities. Moreover, it is necessary to conduct an in vivo study to investigate the growth performance of goats in a further study.

The Leizhou goat is a vital indigenous breed, yet its disease resilience can complicate early health monitoring. The white blood cell (WBC) count is a key indicator of immune status, but its relationship with the gut microbiota remains uncharacterized in this breed. This study aimed to characterize the fecal microbiota of Hainan black goats stratified based on their WBC counts. The goats were stratified into Lower, Middle, and High WBC groups based on peripheral WBC counts to compare their fecal microbiota and identify potential associations with systemic immunity. Significant differences in microbial alpha- and be-ta-diversity were observed among the groups, with the High WBC group showing the greatest richness. The microbiota was dominated by Bacillota and Bacteroidota at the phylum level. Linear discriminant analysis Effect Size (LEfSe) identified specific taxa en-riched in each group, such as Ruminococcusin the High WBC group. Critically, Spearman correlation analysis demonstrated significant positive correlations between WBC counts and the relative abundance of genera like unclassified_f_Oscillospiraceae and unclassi-fied_c_Clostridia. These findings demonstrate that WBC counts are significantly associated with distinct shifts in the gut microbial community structure of Hainan black goats. The identified WBC-associated microbial biomarkers suggest a link between the gut microbi-ome and host immune regulation, providing a foundation for future research on microbi-ota-mediated health assessment in goats.

In intensive breeding systems, goats reared for meat production are often housed in group pens at high stocking densities. This study aimed to investigate the correlation between expressed behaviours and stocking density, and to compare the time budget of these confined goats with that of pasture-based goats. A detailed ethogram of 19 mutually exclusive behavioural activities was developed. Behavioural observations were conducted continuously over 72 h on group pens selected for their variation in stocking density and homogeneity in breed, age, body condition and acclimation period since arrival. Using the scan-sampling method (96 scans per goat daily), data were collected from 42 goats. The time budget, expressed as the mean frequency (%) ± standard deviation for each behavioural activity, was calculated. The associations between time budget and stocking density were assessed via bivariate analysis, with the strength and direction of relationships quantified using Pearson’s correlation coefficient (r). Results indicated that self-grooming and Bipedal stance/Climbing were positively correlated with increased space allowance (i.e., lower stocking density), suggesting their potential utility as positive welfare indicators for housed fattening goats in group pens. Furthermore, the time budget differed notably from pasture-based patterns, primarily characterized by resting (53.09% ± 2.72%), eating (16.05% ± 2.88%), and moving (2.30% ± 0.75%).

Postnatal muscle development involves complex transcriptional regulation that remains poorly characterized in goats. This study employed RNA-Seq to profile the Longissimus dorsitranscriptome of Leizhou Black goats across three developmental stages: birth, six months, and two years. We identified dynamic gene expression patterns, widespread alternative splicing events, and stage-specific co-expression networks that collectively orchestrate muscle maturation. A significant transcriptional shift occurred between six months and two years, marked by the downregulation of proliferation-related genes (e.g., RRM2, TOP2A) and the activation of pathways governing muscle contraction and energy metabolism. Functional enrichment analyses highlighted the importance of PI3K-Akt, PPAR, and calcium signaling pathways throughout development. Additionally, 905 novel transcripts were discovered, many enriched in mitochondrial functions, indicating incompleteness in the current goat genome annotation. Weighted gene co-expression network analysis revealed modules correlated with developmental stages, and protein–protein interaction analysis identified hub genes regulating cell cycle progression and muscle function. Key results were validated via qRT-PCR, confirming the temporal expression patterns of genes such as CYP4B1, HACD1, and ACTC1. These findings provide mechanistic insights into the transcriptional reprogramming driving postnatal muscle development and offer valuable genetic resources for improving meat production in goats through molecular breeding.

This study investigated the effects of Bacillus subtilis (B. subtilis) supplementation on microbiota and metabolites in the feces of Leizhou goats. Eight Leizhou goats were used in a replicated 4 × 4 Latin square design according to their gender (nanny goats and billy goats) with a 4 × 2 factorial arrangement of treatments that included four B. subtilis additive doses (control [0 g/d; NC, BC], low [2.5 g/d, NL, BL], medium [5 g/d, NM, BM], and high [7.5 g/d, NH, BH]) and 28 d periods (n = 4 per group), each consisting of 27 d adaption and 1 d sample collection. After collecting 32 fecal samples, 16S rRNA gene sequencing and LC-MS were performed to analyze microbial composition and metabolites, respectively. At the genus level, the relative abundance of Rikenellaceae_RC9_gut_group was significantly higher (p < 0.05) in the NM group than in the NC group. The relative abundance of Treponema sp. was significantly lower (p < 0.05) in the NM group than in the NC group. In billy goats, the relative abundances of UCG-005 and Rikenellaceae_RC9_gut_group were significantly higher (p < 0.05) in the BH group than in the BC group. The relative abundance of Treponema sp. was significantly lower (p < 0.05) in the BL, BM, and BH groups than in the BC group. Furthermore, metabolomic analysis revealed that B. subtilis significantly altered the concentrations of glucose metabolism modulators (1-deoxynojirimycin, 1-DNJ) and certain bioactive peptides. Many amino acid metabolic pathways were also enriched. Correlation analysis demonstrated close connections between differential metabolites and the top 10 bacterial genera in fecal samples. These results provide new insights into the impact of B. subtilis on the microbial community and metabolic profile of the feces of Leizhou goats. In this experiment, the appropriate doses of B. subtilis for nanny goats and billy goats were 5 g/d and 7.5 g/d, respectively, but the optimal doses still need to be verified based on performance-based feeding tests in the next study.

Macadamia integrifolia husk has great potential for use as a feedstuff in ruminants. However, little information regarding its effects on ruminal fermentation traits is available at present. Hence, this in vitro study aims to investigate the effects of Macadamia integrifolia husk as a substrate, supplemented with enzymes at different levels (0 g/kg cellulases + pectinases, CON; 0.5 cellulases + 0.5 g/kg pectinases, TRE1; 1.0 g/kg cellulases + 0.5 g/kg pectinases, TRE2; 1.5 cellulases + 0.5 g/kg pectinases, TRE3), on gas production, fermentation traits, and bacterial communities in goats. The results demonstrate that gas production was increased in TRE1 and TRE3 groups compared to the CON group at 6, 9, 12, 24, and 48 h (p < 0.05); DMD was the highest in the TRE3 group and the lowest in the CON group at 6, 12, 24, and 48 h (p < 0.05); and NDFD was the highest in the TRE1 group and the lowest in the CON group at 6 h, then the highest in the TRE3 group and the lowest in the CON group at 12, 24, and 48 h (p < 0.05). The concentrations of MCP, TVFAs, acetate, and propionate were the highest in the TRE3 group and the lowest in the CON group (p< 0.05). The abundance of Bacillota was the highest in the TRE1 group and the lowest in the TRE2 group (p < 0.05), whereas that of Synergistota and Actinomycetota was the lowest in the CON group and the highest in the TRE2 group (p < 0.05). Acidobacteriota was the most abundant in the TRE3 group and the least abundant in the TRE1 group (p < 0.05). The most abundant genus was norank_p_Bacteroidota, comprising approximately 29.3%, 30.6%, 30.4%, and 31.7% of the total bacteria in the CON, TRE1, TRE2, and TRE3 groups, respectively; this was followed by Succiniclasticum, comprising approximately 6.3%, 5.8%, 6.1%, and 7.0% of the total bacteria in the CON, TRE1, TRE2, and TRE3 groups, respectively. This study provides new insights regarding the use of Macadamia integrifolia husk as a feedstuff in goats; in particular, supplementation with cellulases and pectinases could effectively improve its utilization. The results suggest that the optimal supplementary levels of cellulases and pectinases are 1.5 g/kg and 0.5 g/kg, respectively.

This study investigates the effects of rumen-protected methionine and lysine (RPML) on the fecal microbiota of Leizhou goats, focusing on growth performance and fecal microbial community composition. A total of 10 three-month female Leizhou goats (9.90 ± 0.08 kg) were randomly assigned to one of two dietary treatments: a CON group fed a basal diet and an RPML group receiving the basal diet supplemented with 1.5 g/d/head of rumen-protected methionine and 4.5 g/d/head of rumen-protected lysine. Results indicated that RPML significantly enhanced average daily gain (ADG) and final body weight (FBW), as well as significantly decreased the ratio of dry matter intake (DMI) to ADG (p < 0.001). Fecal microbiota composition showed a decrease in abundance of UCG-005, Phascolarctobacterium, and norank_f__Bacteroidales_RF16_group and an increase in others like Christensenellaceae R-7 and unclassified_c__Clostridia (p < 0.05). Moreover, the correlations between the abundance of certain bacterial genera and the concentrations of short-chain fatty acids (SCFAs) suggest that the modulation of the gut microbiota is associated with improved growth performance and feed efficiency in Leizhou goats, indicating that RPML supplementation can modulate the gut microbiota to improve growth performance and feed efficiency in Leizhou goats.

The VRTN (vertebrin) gene plays a crucial role in regulating thoracic vertebral number in mammals; however, its function in goats remains largely unexplored. This study aimed to investigate genetic variations in the VRTN gene in Hainan black goats (HNBGs) and evaluate their associations with growth and meat traits. Using whole-genome and Sanger sequencing, we identified four SNPs in the VRTN gene, including three missense mutations (p.Pro615Ser, p.Arg490Lys, p.Thr476Met) and one synonymous mutation (p.Asp688Asp). Tissue expression profiling revealed high VRTN mRNA expression in skeletal muscle and low expression in internal organs, suggesting a potential role in muscle development. Temporal expression analysis indicated dynamic regulation during growth, with higher expression levels observed in early developmental stages. Association analyses revealed significant correlations between specific SNPs and key traits, including body length, chest circumference, carcass weight, and meat quality parameters. Notably, the p.Pro615Ser mutation was associated with a 0.441-fold reduction in VRTN expression and showed strong associations with multiple traits, underscoring its functional importance. These findings demonstrate that VRTN polymorphisms influence growth and muscle development in HNBGs, providing valuable insights for marker-assisted selection in goat breeding.