BACKGROUND:Cattle have undergone complex evolutionary trajectories shaped by domestication, migration, and selection. Although runs of homozygosity (ROH) are a ubiquitous genomic feature, their full potential to decipher the evolutionary history and functional consequences in global cattle populations remains underexplored. We analyzed whole-genome sequences from 102 breeds across 17 geographic regions to conduct a global investigation of ROH landscapes, population structure, genomic inbreeding, and functional variants. RESULTS:ROH patterns revealed elevated homozygosity burdens in intensively selected European breeds, whereas South Chinese indicine showed a high short ROH burden, suggestive of a unique ancient demography. ROH-based principal component analysis (PCA) and admixture delineated taurine-indicine lineages, region-specific ancestries, inbreeding, and breeding effects. ROH-based inbreeding coefficient (FROH) exhibited greater stability for cross-population inbreeding assessment, showing a high correlation with excess of homozygosity-based inbreeding coefficient (FHOM) and a negative association with heterozygosity. Region-specific ROH hotspots, identified via permutation test, reflected a combination of local adaptation and demographic legacies. Trait-focused analyses, cross-validated with multiple selection scans, identified genes underlying growth, milk, and climate adaptation. Notably, we found missense mutations in CHEK2, SPG7, FANCA, and MSRB3, whose frequencies were significantly correlated with temperature and humidity. CONCLUSION:This study establishes ROH as a pivotal genomic marker for illuminating the dynamics of domestication, migration, inbreeding, and selection. Our findings offer valuable resources and insights for advancing genetic conservation and precision breeding in cattle under the pressures of climate change.

Skeletal muscle is a crucial tissue involved in body movement and energy metabolism, and its growth and development directly influence the economic value of livestock. This study investigates the effects of the TEX10 gene on the proliferation, differentiation, and apoptosis of bovine myoblasts, as well as the underlying molecular mechanisms. Using techniques such as CCK-8, EdU incorporation, qPCR, Western blotting, and immunofluorescence, we observed that TEX10 significantly promotes the expression of cell cycle factors, including CDK2 and PCNA, thereby increasing cell proliferation and the proportion of cells in the S phase. Overexpression and knockdown experiments demonstrated that TEX10 enhances the differentiation and myotube formation of myoblasts, while upregulating key genes such as MYOG and MYOD. Additionally, flow cytometry analysis of the cell cycle revealed that TEX10 inhibits apoptosis in bovine myoblasts. Transcriptomic analysis showed that TEX10 regulates several signaling pathways associated with proliferation, differentiation, and apoptosis, including PI3K-Akt, cAMP, and IL-17. Overall, these findings suggest that TEX10 plays a significant regulatory role in bovine muscle growth, providing a theoretical foundation for molecular breeding strategies aimed at improving yellow cattle.

Pinan cattle, as the progeny of crossbreeding improvement between Nanyang cattle and Piedmontese, have attracted attention for their excellent growth performance. In this study, we constructed a copy number variation map by whole genome resequencing of 132 Pinan cattle. In the genome of Pinan cattle, deletion-type copy number variants occupied a higher proportion and only 3.31% of CNVRs overlapped with exonic regions. It showed that Pinan cattle was clearly distinguishable from other breeds and Pinan cattle was closer to Nanyang cattle by population genetic structure analysis based on CNVRs. The degree of inbreeding in the Pinan cattle population was explored by ROH analysis, which showed that the degree of inbreeding in Pinan cattle was lower than that in European beef cattle, suggesting that the risk of inbreeding was low. Candidate genes related to muscle development (CADM3, CNTFR, DOCK3), reproductive traits (SCAPER), embryonic development (RERE) and immune traits (CD84) were identified by VST selection analysis, ROH islands and iHS selection analysis, which provided a new scientific basis for the genetic basis of the excellent traits in Pinan cattle.

The conservation of agricultural animal resources holds significant importance for addressing future breeding demands and promoting sustainable utilization of regional livestock genetic resources. As one of China’s five major fine cattle breeds, Nanyang cattle exhibit notable characteristics, including strong adaptability and a docile temperament. Through whole-genome comparative analysis of the Nanyang cattle core conservation population and free-ranging populations in mountainous areas, this study systematically investigated the genetic diversity, population structure, and adaptive evolutionary mechanisms of this indigenous Chinese cattle breed. Population structure analysis revealed that both groups belong to a single genetic lineage of Nanyang cattle without significant genetic differentiation; however, the free-ranging population demonstrated a slower linkage disequilibrium decay rate. Combined FST and θπ ratio analyses identified 170 positively selected genes, with KEGG enrichment highlighting glutamatergic synapse and African trypanosomiasis immune pathways. PLCB4, as a shared gene across both pathways, may exert pleiotropic functions in environmental adaptation. The core conservation population likely exhibits reduced diversity in neuroplasticity-related genes under artificial selection, whereas the free-ranging population retained more genes associated with environmental adaptation and immune response. These findings provide genomic evidence for formulating differentiated conservation strategies for Nanyang cattle, necessitating balanced co-optimization of production trait breeding and natural adaptability preservation.

BACKGROUND:The crossbreeding of specialized beef cattle breeds with Chinese indigenous cattle is a common method of genetic improvement. Xia'nan cattle, a crossbreed of Charolais and Nanyang cattle, is China's first specialized beef cattle breed with independent intellectual property rights. After more than two decades of selective breeding, Xia'nan cattle exhibit a robust physique, good environmental adaptability, good tolerance to coarse feed, and high meat production rates. This study analyzed the population genetic structure, genetic diversity, and genomic variations of Xia'nan cattle using whole-genome sequencing data from 30 Xia'nan cattle and 178 published cattle genomic data.RESULT:The ancestry estimating composition analysis showed that the ancestry proportions for Xia'nan cattle were mainly Charolais with a small amount of Nanyang cattle. Through the genetic diversity studies (nucleotide diversity and linkage disequilibrium decay), we found that the genomic diversity of Xia'nan cattle is higher than that of specialized beef cattle breeds in Europe but lower than that of Chinese native cattle. Then, we used four methods to detect genome candidate regions influencing the excellent traits of Xia'nan cattle. Among the detected results, 42 genes (θπ and CLR) and 131 genes (FST and XP-EHH) were detected by two different detection strategies. In addition, we found a region in BTA8 with strong selection signals. Finally, we conducted functional annotation on the detected genes and found that these genes may influence body development (NR6A1), meat quality traits (MCCC1), growth traits (WSCD1, TMEM68, MFN1, NCKAP5), and immunity (IL11RA, CNTFR, CCL27, SLAMF1, SLAMF7, NAA35, and GOLM1).CONCLUSION:We elucidated the genomic features and population structure of Xia'nan cattle and detected some selection signals in genomic regions potentially associated with crucial economic traits in Xia'nan cattle. This research provided a basis for further breeding improvements in Xia'nan cattle and served as a reference for genetic enhancements in other crossbreed cattle.

Skeletal muscle growth and development in livestock and poultry play a pivotal role in determining the quality and yield of meat production. However, the mechanisms of myogenesis are remained unclear due to it finely regulated by a complex network of biological macromolecules. In this study, leveraging previous sequencing data, we investigated a differentially expressed circular RNA (circSGCB) present in fetal and adult muscle tissues among various ruminant species, including cattle, goat, and sheep. Our analysis revealed that circSGCB is a single exon circRNA, potentially regulated by an adjacent bovine enhancer. Functional analysis through loss-of-function tests demonstrated that circSGCB exerts inhibitory effects on bovine myoblast proliferation while promoting myocytes generation. Furthermore, we discovered that circSGCB primarily localizes to the cytoplasm, where it functions as a molecular sponge by binding to bta-miR-27a-3p. This interaction releases the mRNAs of KLF3 gene and further activates downstream functional pathways. In vivo, studies provided evidence that up-regulation of KLF3 contributes to muscle regeneration. These findings collectively suggest that circSGCB operates via a competing endogenous RNA (ceRNA) mechanism to regulate KLF3, thereby influencing myogenesis in ruminants and highlights it may as potential molecular targets for enhancing meat production in livestock and poultry industries.

Circular RNA (circRNA), a stable ring-shaped RNA molecule found in eukaryotic cells, plays significant roles in biological regulation, particularly by interfering with transcription factor binding or enhancing gene expression. Using transcriptomic sequencing, we identified differentially expressed circRNAs in bovine muscle at various time points. Specifically, circDYRK1A was discovered and shown to enhance differentiation while suppressing proliferation of adult myoblasts. Rescue experiments further demonstrated that circDYRK1A regulates the KLF5 gene expression by interacting with miR21-5p, thus exerting its influence at the transcriptional level. This study marks the first identification of circDYRK1A in cattle and elucidates its role in bovine myoblast development through the circDYRK1A-miR21-5p-KLF5 regulatory axis. These findings contribute novel insights into molecular breeding of cattle and advance fundamental research on beef cattle breeding and muscle development.

With a rich breeding history, Nanyang cattle (NY cattle) have undergone extensive natural and artificial selection, resulting in distinctive traits such as high fertility, excellent meat quality, and disease resistance. This makes them an ideal model for studying the mechanisms of environmental adaptability. To assess the population structure and genetic diversity of NY cattle, we performed whole-genome resequencing on 30 individuals. These data were then compared with published whole-genome resequencing data from 432 cattle globally. The results indicate that the genetic structure of NY cattle is significantly different from European commercial breeds and is more similar to North–Central Chinese breeds. Furthermore, among all breeds, NY cattle exhibit the highest genetic diversity and the lowest population inbreeding levels. A genome-wide selection signal analysis of NY cattle and European commercial breeds using Fst, θπ-ratio, and θπ methods revealed significant selection signals in genes associated with reproductive performance and immunity. Our functional annotation analysis suggests that these genes may be responsible for reproduction (MAP2K2, PGR, and GSE1), immune response (NCOA2, HSF1, and PAX5), and olfaction (TAS1R3). We provide a comprehensive overview of sequence variations in the NY cattle genome, revealing insights into the population structure and genetic diversity of NY cattle. Additionally, we identify candidate genes associated with important economic traits, offering valuable references for future conservation and breeding efforts of NY cattle.

Copy number variation (CNV), as one of the important variations in the biological genome, refers to the deletion and duplication of genomic segments between 1 kb and 50 kb caused by genomic rearrangements. Currently, many copy number variations have been found to be significantly associated with important economic traits such as growth, development and reproduction of cattle. However, the study of MUC19 gene has not been reported. In this study, we detected an appropriate correlation between MUC19 gene and growth traits of Chinese cattle. We detected the distribution of MUC19-CNV across Qinchuan cattle (QC), Pinan cattle (PN), Xianan cattle (XN), Yunling cattle (YL), Guyuan cattle (GY), Jiaxian cattle (JX), and analyzed the association between types of MUC19-CNV and growth traits through SPSS20.0 software and method of ANOVA. The results showed that various types of CNV were present in each breed of cattle, but there were discrepancies in the distribution of copy number variant types. The Association analysis result showed that CNV of MUC19 gene showed a postive effect in cattle growth traits: the copy number of MUC19 was significantly correlated with hip width of PN cattle (P < 0.01), height at hip cross and withers height of PN cattle (P < 0.05), hip width and body length of JX cattle (P < 0.05), Huckle bone width of YL cattle (P < 0.05).

黑素亲和素(melanophilin,MLPH)是黑色素小体转运过程中重要的结构蛋白.在黑色素细胞中.该试验为了探究淅川乌骨鸡的肤色差异与候选基因启动子区DNA甲基化的关系,首先将1日龄的黄肤乌骨鸡和乌肤乌骨鸡各7只用NR色差仪测定乌肤组与黄肤组的色差情况和偏色大小;之后对不同肤色淅川乌骨鸡的背肤进行黑色素染色切片和H.E染色切片,然后观察其黑色素染色分布情况,最后对MLPH启动子区域进行甲基化引物设计和测序,从而得到MLPH启动子区CPG岛甲基化程度.试验结果表明:乌肤组与黄肤组NR色差仪结果相比,偏色差值较大.乌肤组的L、a、b值远小于黄肤组,且两种切片染色方法观察乌肤组均比黄肤组的黑色素沉积要丰富.甲基化测序结果表明,乌肤组的MLPH启动子区域甲基率为38.69%,黄肤组的甲基率为51.19%,即淅川乌骨鸡背肤颜色的深浅与黑素亲和体甲基化的程度是呈负相关的关系.即肤色越黑,MLPH启动子区甲基化的程度越低.该试验为从表观遗传学角度解释淅川乌骨鸡黑色素沉积的分子机制提供理论参考.

Serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3 (SERPINA3) belongs to the serine protease inhibitor family A subtype, and contains 8 genes from SERPINA3-1 to SERPINA3-8. Although the regulatory effects of these 8 genes have been revealed one by one in recent years, the related effects of SERPINA3-1 gene on cattle growth is still unclear. This study used quantitative Real time PCR (qPCR) to detect the type of copy number variation (CNV) of SERPINA3-1 gene in a total of 542 Chinese cattle, and expression of SERPINA3-1 gene in different tissues of Qinchuan cattles (adult) on mRNA level. Then association analysis was conducted between the detection results and cattle growth traits. The results showed that the Duplication type in SERPINA3-1 gene performed better on the growth traits and the CNV was significantly correlated with multiple growth traits (p < 0.05). In addition, SERPINA3-1 gene has different expression conditions in different tissues, results showed that SERPINA3-1 gene has a low expression in muscle. In conclusion, we speculate that the SERPINA3-1 gene can be used as a molecular marker and the result of this study could be a basic material for candidate functional genes for beef cattle growth and development. Simple summary In order to detect the gene expression diversification of the SERPINA3-1 gene, blood samples were collected from five Chinese cattle breeds, we detected related signal and made an associated analyze with cattle growth traits. We determined the copy number variation distribution of the SERPINA3-1 gene in cattle populations and found that the SERPINA3-1 gene has a certain promoting effect on the growth and development of Chinese cattle. For example, Pinan cattle with Duplication type copy number have a better performance on growth traits. This study has enriched the candidate genes of Chinese cattle molecular breeding and provided basic data for Chinese cattle breeding.

3月25日上午,2023年河南省第三次畜禽遗传资源普查工作推进会在郑州市成功召开.河南省农业农村厅种业管理处副处长胡赓,河南省第三次畜禽遗传资源普查工作办公室主任、河南省畜牧技术推广总站站长睢富根,河南省第三次畜禽遗传资源普查技术专家组组长、河南农业大学康相涛教授,河南省畜牧技术推广总站书记李鹏飞出席了会议.

近年来,面对市场消费结构升级和丰富的秸秆资源优势,河南省明确将优质草畜作为农业"四优"之一突出来抓.针对肉牛产业,河南省政府先后出台了《支持肉牛奶牛产业发展的若干意见》《河南省肉牛奶牛产业发展行动计划》等一系列政策文件,将肉牛产业摆在全省农业结构调整的优先位置.笔者结合河南省肉牛产业发展调研,在此基础上分析问题、提出建议.

Copy number variation (CNV) is an important member of genetic structural variation that exists widely in animal genomes and is between 50 bp and several Mb in length and widely used in research's of animal genetics and breeding. ZNF679 is an important transcription factor, which has been found association with diseases in the human genome many times. This gene has also been found to be associated with cattle growth traits in previous re-sequencing studies. We tested the CNVs of the ZNF679 gene in 809 individuals from 7 Chinese cattle breeds and tested the association between the CNVs and growth traits in 552 individuals from 5 breeds. The results demonstrated the correlation the correlation between the CNVs of the ZNF679 gene and some Chinese cattle (QC cattle and XN cattle) growth traits. To sum up, this study indicated that ZNF679-CNVs can be used as a candidate gene for molecular genetic marker-assisted selection breeding for cattle growth traits to contribute to the development of genetic improvement of Chinese cattle.

豫西黑猪是国家畜禽遗传资源委员会新审定的河南省优良地方猪种质资源,具有肉质好、抗逆性强等优点.为进一步了解豫西黑猪遗传资源多样性及其与本地品种和外来品种间的遗传距离,本研究通过对 108 头豫西黑猪mtDNA D-loop 区序列进行PCR扩增及序列测定,并结合外来品种杜洛克猪、长白猪、大白猪以及河南地区的确山黑猪、南阳黑猪、淮南猪进行生物信息学分析.结果显示,豫西黑猪单倍型多样度 0.854、核苷酸多样度 0.00373、平均核苷酸差异数 2.515,表现出了较丰富的遗传多样性.在 108 头豫西黑猪个体中,共存在 25 种单倍型,其中 14 头公猪共有 6 种单倍型.遗传距离分析显示,豫西黑猪单独聚为一支,与南阳黑猪、确山黑猪等河南省地方品种猪以及杜长大等外来猪种亲缘关系均较远.本研究结果表明:豫西黑猪整体与河南省地方猪、西方商业猪种关系均较远.研究结果为豫西黑猪的保种、开发和利用提供重要理论依据.

长链非编码RNA(long non-coding RNA,lncRNA)是基因转录过程中产生的一类长度大于200 个核苷酸(nt)的非编码RNA(non-coding RNA,ncRNA).lncRNA的表达水平通常低于mRNA,且无高度保守序列,缺少开放阅读框,但它们具有更强的组织特异性表达模式.lncRNA可以通过与DNA、RNA(mRNA,miRNA,环状RNA)和蛋白质进行相互作用来发挥其功能,因此可作为信号分子、诱导物等来调节复杂的基因表达网络.作为一种新的调节分子,lncRNA正在成为基因表达调控中新的重要参与者,且近年研究表明,其与家畜动物性状调控密切相连.本文对lncRNA在动物肌肉生长分化、脂肪沉积、毛囊发育和繁殖方面进行了综述,旨在为lncRNA在家畜遗传育种上的应用提供依据.

加快推进畜禽粪污资源化利用是解决畜禽养殖污染,实现畜牧业绿色发展的根本途径.笔者通过实地调研、查阅资料、座谈交流等形式,分析了豫西山区畜牧业绿色发展的典型模式、畜禽粪污资源化利用存在的问题,并针对存在的问题提出对策建议,以期为推动豫西山区畜牧业绿色发展提供参考.

Recently, Coiled-coil serine-rich protein 1 (CCSER1) gene is reported to be related to economic traits in livestock, and become a hotspot. In our study, we detected CCSER1 gene CNV in 693 goats from six breeds (GZB, GZW, AN, BH, HG, TH) by quantitative real-time PCR (qPCR) and the association analysis between the types of CNV and growth traits. Then, CCSER1 gene expression pattern was discovered in seven tissues from NB goats. Our results showed that the CCSER1 gene copy numbers were distributed differently in the aforementioned six breeds. The type of CCSER1 gene CNV was significantly associated with body weight and heart girth traits in GZW goat, in which individuals with deletion type were dominant in body weight trait (P < 0.05), while the normal type individuals were more advantageous in heart girth trait (P < 0.01); and there was a significant association with heart girth in TH goat (P < 0.05), which normal type was the dominant one. The expression profile revealed that CCSER1 gene has the highest level in the lung, followed by the small intestine and heart. In conclusion, our result is dedicated to an in-depth study of the novel CCSER1 gene CNV site and to provide essential information for Chinese goats molecular selective breeding in the future.

在全国第三次畜禽遗传资源普查过程中,方城县提请"方城灰鹅"(暂定名)作为新的遗传资源.河南省畜牧总站组织有关专家进行现场调查,对"方城灰鹅"成年种鹅群的外貌特征进行观察,对鹅群的生产性能、产地条件和形成历史等进行深入访谈.与国内主要灰鹅品种外貌特征和生产性能进行对比.

Copy number variant (CNV), a common genetic polymorphism, is closely related to the phenotypic variation traits of organisms. Vesicle-associated membrane protein 7 gene (VAMP7) codes a protein, which is a member of the SNARE proteins family and plays an important role in the process of intracellular vesicle transport. In this study, a total of four cattle breeds (Yunling cattle, Xianan cattle, Pinan cattle, Jiaxian red cattle) were used to investigate the copy numbers, and we found an association relationship between CNV of VAMP7 gene and growth traits of cattle by SPSS 20.0 software. The results showed that the CNV type of VAMP7 gene in four cattle breeds had the same distribution, Duplication type occupies a dominant position among the four varieties. In Yunling cattle, the Duplication type of VAMP7 is significantly related to the height at the hip cross (p < 0.05), Individuals with Duplication type commonly have less performance on growth and development, which indicates that the Duplication type of the VAMP7 gene may have a negative effect on cattle growth. Individuals with the other two CNV types may become the breeding direction of the VAMP7 gene. This study provided a new perspective and basic material for the molecular genetics of the CNV of the VAMP7 gene, and also promoted the breeding progress of Chinese local cattle.