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Objective: This study aimed to investigate the significant single nucleotide polymorphisms (SNPs) and genes associated with nine reproduction and morphological traits in three breed populations of Chinese goats.Methods: The genome-wide association of nine reproduction and morphological traits (litter size, nipple number, wattle, skin color, coat color, black dorsal line, beard, beard length, and hind leg hair) were analyzed in three Chinese native goat breeds (n = 336) using an Illumina Goat SNP50 Beadchip.Results: A total of 17 genome-wide or chromosome-wide significant SNPs associated with one reproduction trait (litter size) and six morphological traits (wattle, coat color, black dorsal line, beard, beard length, and hind leg hair) were identified in three Chinese native goat breeds, and the candidate genes were annotated. The significant SNPs and corresponding putative candidate genes for each trait are as follows: two SNPs located on chromosomes 6 (CSN3) and 24 (TCF4) for litter size trait; two SNPs located on chromosome 9 (KATNA1) and 1 (UBASH3A) for wattle trait; three SNPs located on chromosome 26 (SORCS3), 24 (DYM), and 20 (PDE4D) for coat color trait; two SNPs located on chromosome 18 (TCF25) and 15 (CLMP) for black dorsal line trait; four SNPs located on chromosome 8, 2 (PAX3), 5 (PIK3C2G), and 28 (PLA2G12B and OIT3) for beard trait; one SNP located on chromosome 18 (KCNG4) for beard length trait; three SNPs located on chromosome 17 (GLRB and GRIA2), 28 (PGBD5), and 4 for hind leg hair trait. In contrast, there were no SNPs identified for nipple number and skin color.Conclusion: The significant SNPs or genes identified in this study provided novel insights into the genetic mechanism underlying important reproduction and morphological traits of three local goat breeds in Southern China as well as further potential applications for breeding goats.

This study evaluated the effects of inoculation with adult goat ruminal fluid on growth, health, gut microbiota and serum metabolism in lambs during the first 15 days of life. Twenty four Youzhou dark newborn lambs were selected and randomly distributed across 3 treatments (n = 8/group): autoclaved goat milk inoculated with 20 mL sterilized normal saline (CON), autoclaved goat milk inoculated with 20 mL fresh ruminal fluid (RF) and autoclaved goat milk inoculated with 20 mL autoclaved ruminal fluid (ARF). Results showed that RF inoculation was more effective at promoting recovery of body weight. Compared with CON, greater serum concentrations of ALP, CHOL, HDL and LAC in the RF group suggested a better health status in lambs. The relative abundance of Akkermansia and Escherichia-Shigella in gut was lower in the RF group, whereas the relative abundance of Rikenellaceae_RC9_gut_group tended to increase. Metabolomics analysis shown that RF stimulated the metabolism of bile acids, small peptides, fatty acids and Trimethylamine-N-Oxide, which were found the correlation relationship with gut microorganisms. Overall, our study demonstrated that ruminal fluid inoculation with active microorganisms had a beneficial impact on growth, health and overall metabolism partly through modulating the gut microbial community.

Transportation stress is one of the most serious issues in the management of yak. Previous studies have demonstrated that transport stress is caused by a pro-oxidant state in the animal resulting from an imbalance between pro-oxidant and antioxidant status. In this context, vitamin C has the ability to regulate reactive oxygen species (ROS) synthesis and alleviate oxidative stress. Although this effect of vitamin C is useful in pigs, goats and cattle, the effect of vitamin C on the mitigation of transport stress in yaks is still unclear. The purpose of this study was to better assess the metabolic changes induced by the action of vitamin C in yaks under transportation stress, and whether these changes can influence antioxidant status. After the yaks arrived at the farm, control or baseline blood samples were collected immediately through the jugular vein (VC_CON). Then, 100 mg/kg VC was injected intramuscularly, and blood samples were collected on the 10th day before feeding in the morning (VC). Relative to the control group, the VC injection group had higher levels of VC. Compared with VC_CON, VC injection significantly (P P P > 0.05) in GGT, ALP, TBA, TP, ALBⅡ, GLO, A/G, TC, TG, HDL-C, LDL-C, GLU and L-lactate between VC_CON and VC. The injection of VC led to greater (P P > 0.05) the serum concentrations of LPO and ROS. The injection of VC led to greater (P P P > 0.05) in GSH, GSH-ST and GR was observed between VC_CON and VC. Compared with the control group, metabolomics using liquid chromatography tandem–mass spectrometry identified 156 differential metabolites with P 1.5 in the VC injection group. The injection of VC resulted in significant changes to the intracellular amino acid metabolism of glutathione, glutamate, cysteine, methionine, glycine, phenylalanine, tyrosine, tryptophan, alanine and aspartate. Overall, our study indicated that VC injections were able to modulate antioxidant levels by affecting metabolism to resist oxidative stress generated during transport.

Background Youzhou dark goat is a rare indigenous goat breed that features its two outstanding characters including the dark skin with the white coat hair and the excellent adaptability to hygrothermal environment. Elucidation of the mechanisms of domestication and selection for these two traits on genome-wide level would greatly benefit medical and agricultural production. In the present study, we first de novo assembled and characterized the reference genome of the Youzhou dark goat on the Illumina HiSeqX platform. Then we identified its variation, selection signatures and the geographical events to reveal the phenotypic evolution and speciation in goat by comparative genomics and whole-genome resequencing methods. In addition, we also investigated the population structure and domestication of goat with different purpose of production in 11 populations of domestic goat. Results We achieved the reference genome in Youzhou dark goat (Contig N50 = 94 kb, size = 2.62Gb) and identified the gene families that contribute to their phenotypic characteristics. Comparative genome analysis illustrated that a single base mutation in MC1R gene (c.676A > G) and structural variation in ASIP gene are most likely the candidate causative genes for the phenotype of epidermal hyperpigmentation in Youzhou dark goat. Strong selection of PIK3R3, GNAS, and GNA11 genes suggests a coevolution of the melanogenesis and the resistance to parasite, which further contributes to the excellent adaptability to the hygrothermal environment for Youzhou dark goat. Population genetic analysis indicated that Youzhou dark goat was a relative ancient goat population and that the domestication of dairy trait occurred ahead of cashmere and meat trait in goat. Conclusions The Youzhou dark goat was a relative ancient goat population and the MC1R-ASIP signaling is most likely the candidate signaling pathway of epidermal pigmentation. Strong selection of PIK3R3, GNAS, and GNA11 genes play key roles in its excellent adaptability to the hygrothermal environment for Youzhou dark goat.

Boer goats, as kemp in meat-type goats, are selected and bred from African indigenous goats under a long period of artificial selection. Their advantages in multiple economic traits, particularly their plump growth, have attracted worldwide attention. The current study displayed the genome-wide selection signature analyses of South African indigenous goat (AF), African Boer (BH), and Australian Boer (AS) to investigate the hereditary basis of artificial selection in different stages. Four methods (principal component analysis, nucleotide diversity, linkage disequilibrium decay, and neighbor-joining tree) implied the genomic diversity changes with different artificial selection intensities in Boer goats. In addition, the θπ, FST, and XP-CLR methods were used to search for the candidate signatures of positive selection in Boer goats. Consequently, 339 (BH vs. AF) and 295 (AS vs. BH) candidate genes were obtained from SNP data. Especially, 10 genes (e.g., BMPR1B, DNER, ITGAL, and KIT) under selection in both groups were identified. Functional annotation analysis revealed that these genes are potentially responsible for reproduction, metabolism, growth, and development. This study used genome-wide sequencing data to identify inheritance by artificial selection. The results of the current study are valuable for future molecular-assisted breeding and genetic improvement of goats.

Sichuan, China, has abundant genetic resources of sheep (Ovis aries). However, their genetic diversity and population structure have been less studied, especially at the genome-wide level. In the present study, we employed the specific-locus amplified fragment sequencing for identifying genome-wide single nucleotide polymorphisms (SNPs) among five breeds of sheep distributed in Sichuan, including three local pure breeds, one composite breed, and one exotic breed of White Suffolk. From 494 million clean paired-end reads, we obtained a total of 327,845 high-quality SNPs that were evenly distributed among all 27 chromosomes, with a transition/transversion ratio of 2.56. Based on this SNP panel, we found that the overall nucleotide diversity was 0.2284 for all five breeds, with the highest and lowest diversity observed in Mage sheep (0.2125) and Butuo Black (0.1963) sheep, respectively. Both Wright’s fixation index and Identity-by-State distance revealed that all individuals of Liangshan Semifine-wool, White Suffolk, and Butuo Black sheep were respectively clustered together, and the breeds could be separated from each other, whereas Jialuo and Mage sheep had the closest genetic relationship and could not be distinguished from each other. In conclusion, we provide a reference panel of genome-wide and high-quality SNPs in five sheep breeds in Sichuan, by which their genetic diversity and population structures were investigated.

MicroRNAs (miRNAs) are highly conserved, endogenous small RNAs that regulate gene expression at the post-transcriptional level. miR-127 plays an essential role in myogenic differentiation in vivo and in vitro. However, it is not clear whether miR-127-3p affects myogenic cell proliferation. The detailed function of miR-127-3p in proliferative C2C12 cell lines and further identified its regulatory mechanism by qRT-PCR, western blot, flow cytometry analysis and luciferase reporter assay. Overexpression of miR-127-3p significantly inhibited proliferation of C2C12 cells and vice versa. Sept7 was a target gene of miR-127-3p using dual-luciferase reporter assay, qRT-PCR, and western blotting. The RNA interference analysis, in which Sept7 was downregulated, showed that Sept7 significantly promoted the proliferation of C2C12 cells. Besides, the expression level of Sept7 was detected analysis in muscle cells and tissues. These findings reveal that miR-127-3p regulates myoblast proliferation by targeting Sept7.

MicroRNAs (miRNAs) have been reported that can regulate skeletal muscle growth and development. Previously, we demonstrated that miR-127-3p were differently expressed in skeletal muscle and muscle cells. However, the molecular mechanism of miR-127-3p regulation of skeletal myogenesis are not well elucidated. In this study, we transfected miR-127-3p into C2C12 cells, and found miR-127-3p induces myogenesis by targeting Vamp2. Moreover, the regulatory mechanism of Vamp2 in myoblasts proliferation and differentiation was further confirmed. In conclusion, our data providedevidences that miR-127-3p reciprocally regulated myoblasts proliferation and differentiation through directly targeting Vamp2.

The Youzhou dark goat is a natural mutant with dark skin over the whole body including the visible mucous membranes. In the present study, we characterized 100-day-old fetal skin at the histomorphological and transcriptomic levels in dark-skinned (Youzhou dark goat) and white-skinned (Yudong white goat) goats with deep RNA sequencing, quantitative PCR, and histological methods. Histological analysis indicated that there were marked differences in both melanin distribution and epidermal ultrastructure between the hyperpigmented and normal skin in two breeds of goat. Subsequent analyses suggested that a presumed structure variation (duplication or insertion) in ASIP might be responsible for its lower expression in the hyperpigmented skin (Youzhou dark goat) by determining the distribution of melanocytes across the body at early development stage. Analyses for genes with differential expression between the dark-skinned and white-skinned goats indicated the network composed of ASIP-MC1R, ECM-receptor interaction, and MAPK signaling might play crucial roles in the determination of skin pigmentation in fetal goats. Moreover, we also identified 1,616 novel transcripts in goat skin by RNA sequencing, which may represent two distinct groups of transcript based on their characteristics. Our findings contribute to the understanding of the characteristics of global gene expression in early-stage skin pigmentation and development and describe an animal model for human diseases associated with pigmentation.

MicroRNAs (miRNAs) are highly conserved, short non-coding RNAs that regulate gene expression at the posttranscriptional level. Although many miRNAs are identified in muscles and muscle cells, their individual roles are still not fully understood. In the present study, we investigated a muscle highly-expressed miRNA, miR-127-3p, in C2C12 myoblasts and tissues of goats with different muscle phenotypes (Boer vs Wushan black goats). Our results demonstrated that i) miR-127-3p was extensively expressed in tissues of goats; ii) miR-127-3p was higher expressed in muscle, spleen, heart, and skin in the muscular goats (Boer goats) than the control (Wushan black goats). Then we further characterized the dynamical expression of miR-127-3p, MyoD, MyoG, Myf5, Mef2c, and Myosin in the proliferating and differentiating C2C12 myoblasts at day of 0, 1, 3, 5, and 7 in culture mediums. Especially, we found that miR-127-3p was significantly higher expressed in the proliferating than differentiating cells. Our findings suggest that miR-127-3p probably plays roles in the proliferation and differentiation of myoblasts, which further underlies regulation of muscle phenotype in goats.

The objective of this study was to assess the genetic diversity and population structure of goats in the Yangtze River region using microsatellite and mtDNA to better understand the current status of those goat genetic diversity and the effects of natural landscape in fashion of domestic animal genetic diversity. The genetic variability of 16 goat populations in the littoral zone of the Yangtze River was estimated using 21 autosomal microsatellites, which revealed high diversity and genetic population clustering with a dispersed geographical distribution. A phylogenetic analysis of the mitochondrial D‐loop region (482 bp) was conducted in 494 goats from the Yangtze River region. In total, 117 SNPs were reconstructed, and 173 haplotypes were identified, 94.5% of which belonged to lineages A and B. Lineages C, D, and G had lower frequencies (5.2%), and lineage F haplotypes were undetected. Several high‐frequency haplotypes were shared by different ecogeographically distributed populations, and the close phylogenetic relationships among certain low‐frequency haplotypes indicated the historical exchange of genetic material among these populations. In particular, the lineage G haplotype suggests that some west Asian goat genetic material may have been transferred to China via Muslim migration.

The Youzhou dark goat is a natural mutant with dark skin over the whole body including the visible mucous membranes. In the present study, we characterized 100-day-old fetal skin at the histomorphological and transcriptomic levels in dark-skinned (Youzhou dark goat) and white-skinned (Yudong white goat) goats with deep RNA sequencing, quantitative PCR, and histological methods. Histological analysis indicated that there were marked differences in both melanin distribution and epidermal ultrastructure between the hyperpigmented and normal skin in two breeds of goat. Subsequent analyses suggested that a presumed structure variation (duplication or insertion) in

Pipeline for lncRNA analysis of the present study. (DOCX 13Â kb)