Copy number variation (CNV) serves as a crucial source of genomic variation and significantly aids in the mining of genomic information in cattle. This study aims to analyze re–sequencing data from Chinese Hainan yellow cattle, to uncover breed CNV information, and to elucidate the resources of population genetic variation. We conducted whole–genome sequencing on 30 Chinese Hainan yellow cattle, thus generating 814.50 Gb of raw data. CNVs were called using CNVnator software, and subsequent filtering with Plink and HandyCNV yielded 197,434 high–quality CNVs and 5852 CNV regions (CNVRs). Notably, the proportion of deleted sequences (81.98%) exceeded that of duplicated sequences (18.02%), with the lengths of CNVs predominantly ranging between 20 and 500 Kb This distribution demonstrated a decrease in CNVR count with increasing fragment length. Furthermore, an analysis of the population genetic structure using CNVR databases from Chinese, Indian, and European commercial cattle breeds revealed differences between Chinese Bos indicus and Indian Bos indicus. Significant differences were also observed between Hainan yellow cattle and European commercial breeds. We conducted gene annotation for both Hainan yellow cattle and European commercial cattle, as well as for Chinese Bos indicus and Indian Bos indicus, identifying 206 genes that are expressed in both Chinese and Indian Bos indicus. These findings may provide valuable references for future research on Bos indicus. Additionally, selection signatures analysis based on Hainan yellow cattle and three European commercial cattle breeds identified putative pathways related to heat tolerance, disease resistance, fat metabolism, environmental adaptation, candidate genes associated with reproduction and the development of sperm and oocytes (CABS1, DLD, FSHR, HSD17B2, KDM2A), environmental adaptation (CNGB3, FAM161A, DIAPH3, EYA4, AAK1, ERBB4, ERC2), oxidative stress anti–inflammatory response (COMMD1, OXR1), disease resistance (CNTN5, HRH4, NAALADL2), and meat quality (EHHADH, RHOD, GFPT1, SULT1B1). This study provides a comprehensive exploration of CNVs at the molecular level in Chinese Hainan yellow cattle, offering theoretical support for future breeding and selection programs aimed at enhancing qualities of this breed.

This study was to investigate the effects of dietary supplementation with putrescine on the growth performance and meat quality of chickens. A total of 480 eighty-day-old female Wenchang chickens were randomly assigned into four groups, with 8 replications per group and 15 animals per replicate. The chickens in the control group (Con) were fed a basal diet; the 3 experimental groups were fed a basal diet with 0.01%, 0.03%, and 0.05% putrescine, respectively. The experiment lasted for 40 days. The results showed that dietary supplementation with 0.05% putrescine increased (p < 0.05) the final body weight and average daily weight gain, and decreased the ratio of feed intake to the body weight gain of Wenchang chickens. Dietary supplementation with putrescine decreased the concentrations of putrescine, spermidine, and spermine in serum (p < 0.05). The contents of methionine, phenylalanine, lysine, aspartic acid, tyrosine, total essential amino acids, and total amino acids in breast muscle were higher (p < 0.05) in 0.03% and 0.05% groups than those in Con group. However, the contents of undecanoic acid, lauric acid, tridecanoic acid, myristic acid, pentadecanoic acid, arachidic acid, docosanoic acid, tricosanic acid, lignoceric acid, erucic acid, cis-11,14,17-eicosatrienoate, linoleic acid, and total n-6 monounsaturated fatty acids in breast muscle were lower (p < 0.05) in 0.03% and 0.05% groups than those in Con group. In addition, putrescine supplementation decreased (p < 0.05) the ratio of n-6/n-3 polyunsaturated fatty acids in breast meat. Overall, dietary supplementation with 0.05% putrescine enhanced the growth performance and meat quality of Wenchang chickens.

Wuzhishan (WZS) pigs, which are minipigs native to Hainan Province in China, are characterized by strong resistance to extreme hot temperatures and humidity. The relationship between their immune response and growth still needs to be clarified. In this study, we used whole genome sequencing (WGS) to detect variations within 37 WZS pigs, 32 Large White (LW) pigs, and 22 Xiangxi black (XXB) pigs, and ~2.49 GB of SNPs were obtained. These data were combined with those of two other pig breeds, and it was found that most of the genes detected (354) were located within the distinct genetic regions between WZS pigs and LW pigs. The network that was constructed using these genes represented a center including 12 hub genes, five of which had structural variations (SVs) within their regulatory regions. Furthermore, RNA-seq and RT-qPCR data for 12 genes were primarily consistent in liver, spleen, and LDM tissues. Notably, the expression of HSPs (HSPD1 and HSPE1) was higher while that of most genes involved in the JAK3-STAT pathway were lower in liver tissue of WZS pigs, compared with LW pigs. This likely not only reduced inflammation-related immune response but also impaired their growth. Our findings demonstrated the role of HSPs in the connection between inflammation and growth rate, while also providing the fundamental genetic selection of the adaptability of WZS pigs.

Despite identifying genes regulating the coat colour in Western pig breeds, the genetic basis of the coat colour in Chinese indigenous pigs is still not understood due to the diversity of indigenous breeds and their genetic differences from exotic pigs. In this study, 215 Wuzhishan pigs with three coat colour patterns (white, black, and black-back/white-belly) were used to conduct a genome-wide association analysis. We found that genes responsible for the coat colour in the Wuzhishan breed are located on chromosome 8. Ninety-seven genome-wide significant SNPs are related to the animal’s coat colour. Using a haplotype-sharing analysis, we narrowed the potential candidate region to a 10.1 Mb interval encompassing only one gene, RAPGEF2, which participates in the regulation of melanogenesis. Two additional candidate genes, PDGFRA and KIT, are located within 1 Mb of the genome-wide significant SNPs. Gene ontology analysis and literature mining suggest that these candidate genes are associated with the animal’s coat colour. mRNA expression results revealed that RAPGEF2 and PDGFRA had significantly higher expressions in black pigs than in white pigs and higher expressions in black skin than in white skin from the same black-back/white-belly pigs. These results suggest that RAPGEF2 and PDGFRA are potential candidate genes regulating the coat colour in Wuzhishan pigs. Interestingly, mutations of KIT (a gene duplication and a G to A substitution at the splicing site in intron 17) were detected in white Wuzhishan pigs but not in black-back/white-belly or black pigs, suggesting a close genetic relationship between white Wuzhishan pigs and Western white pig breeds. In summary, these results indicate that the expression of RAPGEF2 and PDGFRA may cause the coat colour variation by influencing the deposition of melanin, while the mutation of KIT causes the white coat colour. Our results may provide a theoretical basis for the breeding of white coat colour Wuzhishan pigs, and shed light on the complex genetic background of coat colour variations in indigenous Chinese pig breeds.

Compared to commercial breeds, Chinese local pig breeds have a greater ability to digest dietary fiber, which may be due to differences in intestinal microbiota. In this study, we fed Ding’an and DLY pigs high and low levels of dietary fiber, respectively, to investigate factors contributing to high dietary fiber adaption in Ding’an pigs. Twelve Ding’an pigs and DLY pigs were randomly divided into a 2 (diet) × 2 (breed) factorial experiment (n = 3). Compared with commercial pigs, Ding’an pigs have a stronger ability to digest dietary fiber. Prevotella was more prevalent in Ding’an pigs than in DLY pigs, which may be an important reason for the stronger ability of fiber degradation in Ding’an pigs. When the effects of feed and breed factors are considered, differences in abundance of 31 species and 14 species, respectively, may result in a greater ability of fiber degradation in Ding’an pigs. Among them, Prevotella. sp. CAG:520 may be a newly discovered bacterium related to fiber degradation, which positively correlated with many fiber-degrading bacteria (r > 0.7). We also found that the concentration of plant metabolites with anti-inflammatory and antioxidant effects was higher in the colonic chyme of Ding’an pigs after increasing the fiber content, which resulted in the downregulated expression of inflammatory factors in colonic mucosa. Spearman’s correlation coefficient revealed a strong correlation between microbiota and the apparent digestibility of dietary fiber (r > 0.7). The mRNA expressions of SLC16A1, PYY, and GCG were significantly increased in the colonic mucosa of Ding’an pigs fed on high-fiber diets, which indicates that Ding’an pigs have an enhanced absorption of SCFAs. Our results suggested that an appropriate increase in dietary fiber content can reduce the inflammatory response and improve feed efficiency in Ding’an pigs, and differences in the intestinal microbial composition may be an important reason for the difference in the fiber degradation capacity between the two breeds of pigs.

The polysaccharide of Millettia speciosa Champ. ex Benth (MSCP) has antioxidant properties, but its impact on chicken growth and development is not yet known. This study used chlortetracycline as a control to assess MCSP as a feed antibiotic substitute and its effects on Wenchang chicken production, slaughter performance, and meat quality. A total of 576 healthy 80-day-old Wenchang chickens were randomly allocated to six experimental groups. The control group (Control) received a basal diet, while the antibiotic group (CTC) was supplemented with 2 g/kg chlortetracycline (CTC). Four additional experimental groups were administered varying doses of MSCP: 400 mg/kg (MSCP₄₀₀), 800 mg/kg (MSCP₈₀₀), 1600 mg/kg (MSCP₁₆₀₀), and 3200 mg/kg (MSCP₃₂₀₀), respectively. The study discovered that incorporating MSCP and CTC into chicken diets significantly boosted the final body weight and average daily feed intake compared to the control group (p < 0.01), with MSCP notably enhancing average daily weight gain. With the addition of 800 mg/kg MSCP, chicken growth performance is comparable to that achieved with antibiotics in feed. However, it did not impact slaughtering performance (p > 0.05). In addition, MSCP significantly raised the pH after 24 h (p < 0.05) and decreased the yellowness (p < 0.01) of breast muscle. MSCP increased the essential amino acids (EAA) proportion in breast muscle (p < 0.05), EAA to nonessential amino acids (NEAA) ratio (p < 0.05), and diversity of fatty acids while decreasing C20:0 and increasing C18:2N6 and C22:1N9 content. Moreover, MSCP significantly reduced muscle fiber size (p < 0.01), increased fiber density (p < 0.01), boosted MYOD1 expression (p < 0.05), and decreased MSTN expression in breast muscle (p < 0.01). Overall, our study showed that supplementing the diet with MSCP, particularly at a dose of 800 mg/kg, enhanced growth, meat quality, muscle morphology, amino acid content, fatty acid composition, and gene expression related to muscle development in breast muscle. The results indicate that MSCP is a feed additive with the potential to replace antibiotics and improve meat quality, showing promising application potential.