Hoxc13 is a critical transcription factor that regulates the expression of hair keratin genes. Our previous study showed that during mammalian evolution, the Hoxc13 protein acquired a characteristic polyglycine repeat (polyG) insertion. This insertion distinguishes Hoxc13 from its non-mammalian homologs and may contribute to hair production. To investigate the effect of the polyG fragment on the DNA-binding profile of Hoxc13, the normal Hoxc13-W protein and a polyG-deleted Hoxc13-S protein from cashmere goats were synthesized using an in vitro expression system. Their genomic binding profiles were compared using DNA affinity purification sequencing (DAP-seq), genome alignment, pathway enrichment, motif analysis, and molecular docking. Hoxc13-W and Hoxc13-S exhibited markedly different genome-wide DNA-binding capacities. Hoxc13-W identified 12,679 binding peaks, whereas Hoxc13-S identified only 3,634, with only 243 peaks shared between the two proteins. Functional enrichment analysis showed that Hoxc13-W specifically bound genes involved in key pathways regulating hair follicle morphogenesis and cycling. In contrast, Hoxc13-S targets were enriched primarily in the axon guidance pathway. Within the Wnt signaling pathway, Hoxc13-W bound 30 genes, whereas Hoxc13-S bound only 5. Motif analysis further demonstrated that the polyG fragment substantially influenced cis-regulatory motifs beyond the core Hoxc13-binding motif (5′-ATAAA-3′). Molecular docking analysis indicated that the polyG fragment altered the N-terminal structure of Hoxc13, thereby affecting its protein-protein interaction capacity. Collectively, these findings suggest that the polyG fragment enhances the Hoxc13-mediated gene regulatory network during the evolutionary transition from non-mammalian to mammalian vertebrates and may have contributed to the evolution of mammalian hair-related phenotypic traits.

Background Hoxc13 is a critical transcription factor that regulates the expression of hair keratin genes. Our laboratory's previous research found that during mammalian evolution, its protein sequence gained a characteristic polyglycine repeat (polyG) insertion, which makes it significantly different from the homologous proteins of non-mammals, and may thus affect hair production. Methods To investigate the effect of the polyG fragment on the DNA-binding profiles of the Hoxc13 protein, this study synthesized in vitro the normal Hoxc13-W protein and the Hoxc13-S protein (with the polyG fragment deleted) from cashmere goats and used DAP-seq, genome alignment, pathway enrichment, motif detection, and molecular docking assays to compare the differences in genomic binding sites and alterations in binding capacity between the two proteins. Results The results showed that the DNA-binding capacity of Hoxc13-W and Hoxc13-S across the genome differed significantly. Specifically, Hoxc13-W identified 12,679 binding peaks, whereas Hoxc13-S identified only 3,634 binding peaks, with just 243 binding peaks shared between the two. Functional enrichment analysis revealed that Hoxc13-W specifically bound to genes involved in core pathways of hair follicle morphogenesis and cycling, whereas Hoxc13-S targets were enriched only in the Axon guidance pathway. In the Wnt signaling pathway, Hoxc13-W can bind up to 30 genes, whereas Hoxc13-S binds only 5. Motif analysis revealed that the polyG fragment significantly influences cis-regulatory motifs other than the core Hoxc13 binding motif (5'-ATAAA-3'). Further protein-protein interaction studies revealed that the polyG fragment significantly alters the N-terminal structure of the Hoxc13 protein and affects its capacity for such interactions. Conclusions This study demonstrates that the polyG fragment within the Hoxc13 protein modulates gene regulatory networks during the transition from non-mammalian to mammalian vertebrates, thereby potentially shaping the evolution of phenotypic traits.

Meat quality and carcass traits are the most economically important traits affecting the value and the quality characteristics of the animal at slaughter. In this study, we analyzed the genomes of 295 domestic cattle from 20 global breeds using next-generation sequencing to identify signatures of positive selection associated with meat production and quality traits. The results of population genetic analysis revealed genetic differentiation among worldwide cattle groups. We observed clustering of samples in agreement with their geographic origins and production characteristics. We further observed noticeable genetic variety between cattle groups from different geographical regions. Generally, the lowest genetic diversity was determined for commercial cattle breeds, while the highest genetic diversity was found in African local cattle breeds. Our search for putative selective genomic regions in beef cattle populations revealed several candidate genes such as BMP2, EGR1, MAGEL2, U6, TMEM201, ELK3 and 5S_rRNA that were previously explored to be associated with carcass traits and meat quality in beef cattle. The enriched pathways and candidate genes discovered in this study could supply a basis for future improvement through the use of whole-genome technologies and selective breeding.

Background/Objectives: Research on cashmere goat coat color is crucial for optimizing cashmere goat breeds and increasing their economic value. To identify key genes associated with the formation of cashmere goat coat color and to provide molecular markers for breeding purposes, three healthy, 3-year-old does with similar weights and distinct coat colors-white, black, and light brown-were selected. Methods: Skin samples were collected for transcriptome sequencing, and bioinformatics methods were applied to screen for differentially expressed genes (DEGs) in the skin of cashmere goats with varying coat colors. Real-time fluorescence quantitative PCR (qRT-PCR) and immunofluorescence were subsequently conducted to examine the expression patterns of these DEGs. Results: The results showed that a total of 1153 DEGs were identified across the three groups of cashmere goats. According to GO and KEGG analyses, these DEGs were involved in key biological processes and structures, such as the melanin biosynthetic process (GO:0042438), melanosome membrane (GO:0033162), and melanin biosynthesis from tyrosine (GO:0006583). Employing Cytoscape, a gene interaction network was plotted, highlighting a compact network of DEGs associated with coat color formation. Critical genes identified included TYRP1, TYR, DCT, ASIP, PMEL, LOC102180584, MLANA, TSPAN10, TRPM1, CLDN16, AHCY, LOC106503350, and LOC102175263. qRT-PCR and fluorescence immunohistochemistry further determined that TYRP1, TYR, DCT, and PMEL expression levels were high in black goats (BGs), while ASIP and AHCY expression levels were high in white goats (WGs). The expression levels of these six genes in light brown goats (RGs) were intermediate between those in BGs and WGs. Conclusions:TYRP1, TYR, DCT, and PMEL were believed to play pivotal roles in the formation of black coat color, while ASIP and AHCY regulated the formation of white coat color in cashmere goats.

During the wintering period characterized by feed scarcity, animals activate the sympathetic nervous system (SNS)-β-adrenergic receptor (βAR)-AMP-activated protein kinase (AMPK)/peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α) signaling pathway in their bodies. This activation increases the transcriptional activity of forkhead box O1 (FOXO1) transcription factor and pyruvate dehydrogenase kinase 4 (PDK4), leading to the upregulation of gluconeogenesis-limiting genes phosphoenolpyruvate carboxykinase (PEPCK) and glucose-6-phosphatase (G6Pase). Additionally, it enhances the functions of carnitine palmitoyltransferase 1 (CPT1), uncoupling protein 1 (UCP1), cluster of differentiation 36 (CD36), and fatty acid transport protein (FATP). This promotes promote intermuscular fat oxidation and the production of gluconeogenesis precursor glycerol, thereby enhancing animal skeletal muscle gluconeogenesis to maintain animal energy homeostasis and life activities under low temperature and starvation conditions. This article describes the effects of overwintering starvation stress on the AMPK/PGC-1α signaling pathway and its molecular mechanism in animal skeletal muscle gluconeogenesis. The aim to provide a theoretical basis for optimizing sustainable breeding strategies and improving animal production performance in alpine regions.

Background: Under fasting conditions, the pathway converting gluconeogenesis precursors into muscle glycogen becomes crucial due to reduced glycogen reserves. However, there is limited research on skeletal muscle gluconeogenesis and the impact of fasting on gluconeogenic gene expression. Methods: Sheep fetal skeletal muscle cells cultured in vitro were used to study the effects of varying lactic acid concentrations (0 to 30 mM) and 2.5 mM glucose on the expression of gluconeogenesis-related genes after 6 h of fasting. The effects on mRNA and protein expression of key genes involved in skeletal muscle gluconeogenesis were measured by quantitative real time polymerase chain reaction (qRT-PCR), immunofluorescence, and western blotting at 48 h. Results: Fasting increased the expression of key gluconeogenic genes, fructose-1,6-bisphosphatase 2 (FBP2), glucose-6-phosphatase 3 (G6PC3), pyruvate kinase M (PKM), monocarboxylate transporter1 (MCTS1), glucose transporter type 4 (GLUT4), pyruvate carboxylase (PC), and lactate dehydrogenase A (LDHA). The mRNA levels of FBP2, G6PC3, and MCTS1 significantly decreased with glucose addition. Additionally, 10 mM lactic acid significantly promoted the expression of FBP2, PC, MCTS1, LDHA, GLUT4, and PKM while inhibiting phosphoenolpyruvate carboxykinase (PEPCK) expression. At the protein level, 10 mM lactic acid significantly increased FBP2 and PKM protein expression. Conclusions: This study shows that fasting regulates key gluconeogenic gene expression in sheep skeletal muscle cells and highlights the role of lactic acid in inducing these gene expressions.

Abstract Background Understanding the evolutionary forces related to climate changes that have been shaped genetic variation within species has long been a fundamental pursuit in biology. In this study, we generated whole-genome sequence (WGS) data from 65 cross-bred and 45 Mongolian cattle. Together with 62 whole-genome sequences from world-wide cattle populations, we estimated the genetic diversity and population genetic structure of cattle populations. In addition, we performed comparative population genomics analyses to explore the genetic basis underlying variation in the adaptation to cold climate and immune response in cross-bred cattle located in the cold region of China. To elucidate genomic signatures that underlie adaptation to cold climate, we performed three statistical measurements, fixation index (FST), log2 nucleotide diversity (θπ ratio) and cross population composite likelihood ratio (XP-CLR), and further investigated the results to identify genomic regions under selection for cold adaptation and immune response-related traits. Results By generating WGS data, we investigated the population genetic structure and phylogenetic relationship of studied cattle populations. The results revealed clustering of cattle groups in agreement with their geographic distribution. We detected noticeable genetic diversity between indigenous cattle ecotypes and commercial populations. Analysis of population structure demonstrated evidence of shared genetic ancestry between studied cross-bred population and both Red-Angus and Mongolian breeds. Among all studied cattle populations, the highest and lowest levels of linkage disequilibrium (LD) per Kb were detected in Holstein and Rashoki populations (ranged from ~ 0.54 to 0.73, respectively). Our search for potential genomic regions under selection in cross-bred cattle revealed several candidate genes related with immune response and cold shock protein on multiple chromosomes. We identified some adaptive introgression genes with greater than expected contributions from Mongolian ancestry into Molgolian x Red Angus composites such as TRPM8, NMUR1, PRKAA2, SMTNL2 and OXR1 that are involved in energy metabolism and metabolic homeostasis. In addition, we detected some candidate genes probably associated with immune response-related traits. Conclusion The study identified candidate genes involved in responses to cold adaptation and immune response in cross-bred cattle, including new genes or gene pathways putatively involved in these adaptations. The identification of these genes may clarify the molecular basis underlying adaptation to extreme environmental climate and as such they might be used in cattle breeding programs to select more efficient breeds for cold climate regions.

Dkks have inhibitory effects on the Wnt signaling pathway, which is involved in the development of skin and its appendages and the regulation of hair growth. The nucleotide sequences were compared and analyzed to further investigate the relationship between the structure and function of the Dkk gene family and vertebrate epidermal hair. The analysis of the molecular evolution of the Dkk family revealed that the evolution rate of the genes changed significantly after speciation, with the Aves and Reptilia branches showing accelerated evolution. Additionally, positive selection was observed at specific sites. The tertiary structure of the protein was also predicted. The analysis of the functional divergence of the Dkk family revealed that the functional divergence coefficient of each gene was greater than 0, with most of the functional divergence sites were located in the Cys-2 domain and a few in the Cys-1 domain. This suggests that the amino acid and functional divergence sites may play a role in regulating the binding of the Dkk family to LRP5/6, and thus affect the inhibition of Wnt signaling, leading to different functions of Dkk1, Dkk2, and Dkk4 in the development of skin hair follicles. In addition, the Dkk families of Aves and Reptilia may have undergone adaptive evolution and functional divergence.

为全面分析近 30 年(1995-2021 年)国内外肉牛肠道菌群功能基因相关研究的发展现状、研究热点和前沿动态,本研究以Web of Science、中国知网为来源数据库,检索肉牛肠道菌群功能基因的相关文献信息为研究对象;应用CiteSpace(6.0.R1)分别对文献年度发文量、国家、作者、机构、关键词进行共现分析、聚类分析、突显分析以及可视化呈现.结果显示:共发表英文文献 170 篇,中文文献 45 篇.近 30 年国内外肉牛肠道菌群功能基因相关研究领域论文数量整体呈上升趋势,且自 2011 年以来迅速增长;欧美学者逐步建立了理论框架、模型方法,奠定了该领域的研究基础,其中美国占主导地位,Guan Leluo、Auffret M D和Bryan A White等关键作者具有突出贡献.我国起步较晚但发展迅速,发文被引量居第 2,中国农业科学院等机构研究水平世界领先,毛胜勇、蒋林树、王加启和杨舒黎等研究团队代表了我国该领域研究的先进水平.近 30 年,该领域研究热点从 1995 年关注抗菌肽,到 2005 年首次关注 16S rRNA多样性和宏基因组;随着二代测序技术的成熟,自 2015 年以后 16S rRNA和宏基因组研究再度火热,以宏基因组、宏转录组等多组学对瘤胃微生物分解纤维素以及生成甲烷的功能基因研究成为目前的研究热点.此外,肠道微生物功能基因在肉牛营养代谢、饲料开发、免疫调控以及肉牛品种选育中的作用机制及应用是未来该领域的研究方向.

In the present study, we generated complete genome sequence data from 45 Mongolian cattle.Together with published sequence data from worldwide cattle populations, we explored the genetic diversity and population structure of worldwide cattle breeds.Our findings revealed clustering of cattle populations into three major groups, including commercial (Red-Angus, Hereford, Holstein and Jersey), Chinese (Mongolian and Tibetan) and other native cattle (including African cattle and Rashoki breed from Iran) breeds.The results from admixture analysis revealed evidence of shared genetic ancestry between different cattle populations.Furthermore, our findings showed a markedly higher level of linkage disequilibrium (LD) across all genomic distances in commercial breeds (specially Holstein cattle) compare to other native cattle groups.Our results provide valuable insights into the architecture of Mongolian Indigenous cattle breeds and their genomic relationship with other cattle populations.Pomelo.

DNA methylation is an important epigenetic regulatory form that regulates gene expression and tissue development. This study compared the effects of high fiber, low protein (HFLP) and low fiber, high protein (LFHP) diets on the DNA methylation profile of twin lambs' muscles, their effect on glycolysis/gluconeogenesis and related pathways by transcriptome and deep whole-genome bisulfite sequencing (WGBS). Results identified 1,945 differentially methylated regions (DMRs) and 1,471 differentially methylated genes (DMGs). Also, 487 differentially expressed transcripts belonging to 368 differentially expressed genes (DEGs) were discovered between the twin lambs under different diets. Eleven overlapped genes were detected between the DEGs and the DMGs. FKBP5 and FOXO1 were detected to be significantly different. The FOXO1 regulated cAMP and the glycolysis/gluconeogenesis pathways. The glycolysis/gluconeogenesis, and the FOXO pathways were significantly enriched. The expressions of HOMER1 and FOXO1 in the HFLP group were significantly higher than those in the LFHP group. There is a significant correlation between the upregulated gene expression and hypomethylation of HOMER1 and FOXO1 gene in HFLP group. The results showed that FOXO1 induces PDK4 expression in muscle while regulating FKBP5 activity, which stimulates glucose production by activating specific gluconeogenesis target genes. The FOXO1 was able to regulate the glucose metabolism, the cAMP and the occurrence of glycolysis/gluconeogenesis pathways. This study showed that feed type can affect the methylation levels of the glycolysis related gluconeogenesis genes and interaction pathways, providing new ideas for a better understanding of the regulation of muscle energy metabolism and feed development.

目的 了解犊牛在不同生长发育的过程中肠道菌群的建立及肠道菌群结构的动态变化.方法 采集不同时间点(1d、3d、6d、9d、12d、24d、36d、48d、60 d和72 d)新生6头健康犊牛的新鲜直肠粪便样本,利用16SrDNA测序技术及生物信息学测序方法,分析犊牛不同时间点的肠道微生物结构组成及多样性.结果 OTUs聚类分析中共有的OTUs有413个.Alpha多样性指数显示,随着日龄的增加,物种的相对丰度逐渐增多.通过不同组间相对丰度展示了在科水平不同种类物种的相对丰度,包括厌氧环境、致病菌等方面生成了物种丰富度柱形累加图.在厌氧环境中,梭菌科随着日龄的增加逐渐增加.真菌科在48d后逐渐出现在肠道菌群中.毛螺菌科从犊牛出生就一直存在肠道中,并逐渐增加成为优势菌群.在致病菌中,肠杆菌科随着日龄的增加逐渐减少,梭菌与瘤胃球菌不断增加.结论 通过分析新生犊牛肠道微生物菌群多样性的动态结构变化,对新生犊牛胃肠道微生态环境的改善和免疫调控及其生产性能具有重要的意义.

紫外线(ultraviolet,UV)是位于光谱中紫色光之外的射线,为不可见光,照射动物体后会诱导动物机体产生一系列的生理变化,影响动物的生物节律.畜牧业生产中,家畜的生产性能大多数具有年节律或季节性节律,且UV的节律性变化对动物皮肤的生理状态有影响.皮肤是动物内外环境交互的屏障,皮肤细胞的周期、增殖和凋亡与生物钟紧密地交织在一起.文章综述了UV对皮肤相关基因的表达调控,以及对DNA结构、基因转录、蛋白质翻译、Wnt信号通路的影响等方面的研究进展,分析UV影响动物组织-细胞-基因的分子调控网络来维持动物皮肤生理状态的机制,探讨利用紫外线调控家畜生产性能的可行性,同时为研究UV如何调控动物皮肤生理状态奠定坚实的理论基础.

生物统计附试验设计是高等农业院校动物科学与医学专业的重要通选课程.本文通过利用两种假设检验方法x2检验与u检验对生物统计附试验设计教材中同一样本数据进行假设检验,结果显示两种方法得出的结论完全相反.进而引入效力分析(Power Analysis)比较了两种检测方法的可靠性.结果表明,两种方法对教材中例题的检测效力都不高,分别为power(x2)=0.5173613,power(x2)=0.1396603,均没能达到0.8.该结果说明,有必要将效力分析引入生物统计附试验设计这门课中,让各种统计检验可以被评价,使试验设计更加合理.

In order to more accurately obtain the full-length mRNA sequences and complete structural information of cashmere goat skin,and conduct more comprehensive research on new genes and ISO form,and supplement the cashmere goat transcriptome data,cashmere goat was used as an experimental animal in the study.The full-length transcriptome of mixed samples of cashmere goat skin tissue using SMRT sequencing technology as test animals were sequenced.The sequences of coding regions and their corresponding amino acid sequences,variable splice types,and functional enrichment were predicted by using TransDecoder,Astalavista,Cytoscape and other analysis tools.The results showed that:1)A total of 42.41Gb of clean data were obtained by sequencing,with 591 585CCS（Circular consensus sequencing）sequences,including 466 058full-length non-chimeric sequences.2)A total of 6 166new genes,55 875new transcripts,66 951 SSR（Simple Sequence Repeat）,39 346 ORF（Open Reading Frame）sequences,5 641TF（Transcription Factors）and 10 927lncRNAs were identified,and the functional annotation of49 573new transcripts were annotated.3)Based on the results of functional enrichment analysis and variable splice site information,we found that melanocortin 1receptor（MC1R）and microtubulin class 3（Tubulin-β-Ⅲ,TUBB3）could undergo variable splicing and share TUBB3first exon.There were 8 251new lncRNAs identified,and the main type was intronic lncRNA.In conclusion,the full-length sequence and complete structural information of the mRNA of the skin of cashmere goat is obtained,which lays the foundation for further study of the gene structure and interaction mechanism of the skin of cashmere goat.At the same time,the data are supplemented for cashmere goat genome resources.

反刍家畜瘤胃及肠道微生物处于一个复杂的微生态系统,其多样性及营养代谢与该系统中的各项因素存在紧密联系.了解反刍家畜瘤胃及肠道微生物多样性变化和营养代谢机制,是通过人为干预手段改善动物福利、提高动物生产效率、提升动物产品质量、减少温室气体排放的基础.关于反刍动物瘤胃及肠道微生物多样性及营养代谢与单个环境因子的关系得到了广泛的研究并取得了一些进展,对指导生产实践和保护环境起到了一定作用.综述了近年来国内外反刍家畜瘤胃及肠道微生物多样性,以及微生物与宿主动物、日粮结构、环境因子相互作用及机制方面的研究进展,以期为探索瘤胃及肠道微生物在反刍动物营养代谢中的作用及其机制提供参考.

为挖掘脊椎动物胚胎发育过程中皮肤调控模式的改变,以鸡胚作为模型,利用来源于NCBI数据库的SRA数据子库中胚胎发育第6～21天的皮肤组织RNA-Seq数据进行聚类分析,在基因共表达网络、信号通路、蛋白互作网路3个层面基于网络拓扑属性逐步挖掘核心基因集,并分析核心基因集在不同发育阶段的互作网络变化.结果表明:1)鸡胚皮肤发育过程在基因谱水平上可分成5个阶段,分别为6～9 d、10～12 d、13～14 d、15～17 d和18～21 d;2)功能富集分析表明发育早期的皮肤分化程度低、可塑性强,中期是皮肤毛囊发育关键期,最后4 d为皮肤细胞外基质建立期,分子发育过程存在严格的顺序模式;3)在基因调控网络层面深度挖掘并筛选鸡胚皮肤发育的分子调控过程.综上,本研究根据网路拓扑属性结合蛋白互作数据库提出参与不同发育模块的关键枢纽基因,为转录组测序数据的分析及脊椎动物皮肤发育过程的分子机制研究提供一些新的视角和分析方法.

饲料的营养成分可直接影响家畜的屠宰性能与肉品质,试验旨在研究高纤维牧草和高蛋白牧草对羔羊肉品质的影响.试验分别选取高纤维牧草驼绒藜和高蛋白牧草苜蓿作为饲料主要成分.选取4对(共8只)3月龄、体重(24±2.3) kg、健康的双胞胎羔羊为试验对象,分析了两种饲料对羔羊屠宰性能与羊肉品质指标的影响.结果 表明,饲喂苜蓿颗粒饲料对羔羊增重效果极显著,达到0.187 kg/d,显著高于驼绒藜为主的颗粒饲料(0.097 kg/d,P＜0.01).同时,苜蓿饲料也显著增加了肌肉中脂肪的含量,而驼绒藜饲料显著增加了羊肉的水分含量(P＜0.05),提高羊肉的嫩度.虽然两种饲料对屠宰率、骨重、净肉率、肉骨比、净肉重、系水力、眼肌面积等指标的影响均差异不显著(P＞0.05),但是对宰前活重、胴体重、GR值的影响显著(P＜0.05).与苜蓿组相比,驼绒藜可增加羔羊肌肉中对人体有益的必需脂肪酸亚油酸和花生四烯酸的含量.该研究结果为畜牧业生产功能性肉品提供了新的思路.

The Cashmere goat (Capra hircus) is renowned for its high-quality fiber production trait. The hair cycle in Cashmere goat has an annual rhythm. To deepen the understanding of the molecular foundation of annual rhythm in the skin of Cashmere goat, we did a comparative analysis of the Cashmere goat skin transcriptome all year round. 4002 Differentially expressed genes (DEGs) were identified with seasonal variations. 12 months transcriptome were divided into four developmental stages: Jan–Mar, Apr–Jul, Aug–Oct, and Nov–Dec based on gene expression patterns. 13 modules of highly correlated genes in skin were identified using WGCNA. Ten of these modules were consistent with the development stages. The gene function of those genes in each module was analyzed by functional enrichment. The results indicated that Wnt and Hedgehog signaling pathways were inhibited from January to March and activated from April to July. The cutaneous immune system of Cashmere goats has high activity from August to October. Fatty acid metabolism dominates goat skin from November to December. This study provides new information related to the annual skin development cycle, which could provide molecular biological significance for understanding the seasonal development and response to the annual rhythm of skin.

EDITORIAL article Front. Syst. Biol., 15 October 2021 | https://doi.org/10.3389/fsysb.2021.771644