Cattle Breeds In China Research Articles

Classification accuracy of machine learning algorithms for Chinese local cattle breeds using genomic markers.

Accurate breed classification is required for the conservation and utilization of farm animal genetic resources. Traditional classification methods mainly rely on phenotypic characterization. However, it is difficult to distinguish between the highly similar breeds due to the challenges in qualifying the phenotypic character. Machine learning algorithms show unique advantages in breed classification using genomic information. To evaluate the classification methods for Chinese cattle breeds, this study utilized genomic SNP data from 213 individuals across seven Chinese local breeds and compared the classification accuracies of three feature selection methods (FST value sorting and screening, mRMR, and Relief-F) and three machine learning algorithms (Random Forest, Support Vector Machine, and Naive Bayes). Results showed that: 1) using the FST method to screen more than 1500 SNPs, or using the mRMR algorithm to screen more than 1000 SNPs, the SVM classification algorithm can achieve more than 99.47% classification accuracy; 2) the most effective algorithm was SVM, followed by NB, while the best SNP selection method was FST and mRMR, followed by Relief-F; 3) species misclassification often occurs between breeds with high similarity. This study demonstrates that machine learning classification models combined with genomic data are effective methods for the classification of local cattle breeds, providing a technical basis for the rapid and accurate classification of cattle breeds in China.

Geographic distribution of a missense mutation in the KRT38 gene in Chinese indigenous cattle breeds

Context China has a vast area across many temperature zones and a variety of cattle breeds. These cattle resources are ideal models to research their adaptability to the environment. The KRT38 gene is an acidic protein, and its coding product can be used as a component of hair production. Aims The objective of this study was to investigate the diversity of the KRT38 gene in Chinese local cattle and the association of different genotypes with mean temperature, relative humidity and temperature humidity index. Methods A missense mutation g.41650738 A > G in the KRT38 gene was screened from the database of bovine genomic variation (BGVD) and was genotyped in a total of 246 samples from 15 local cattle breeds in China by polymerase chain reaction amplification and sequencing. Finally, the correlation between the locus and the three climatic factors was analysed. Key results We successfully obtained the frequency of this single-nucelotide polymorphism in three groups of cattle in northern, central and southern China. The frequency of allele A gradually declined from north to south, whereas the frequency of allele G showed the opposite trend with a clear geographic distribution. Conclusions Our results indicate that KRT38 variation in Chinese indigenous cattle might be linked to heat tolerance. Implications Our analysis may assist in determining the importance of the variation as a genetic signal for heat tolerance in cattle reproduction and genetics.

The genetic secrets of adaptation: decoding the significance of the 30-bp insertion in the KRT77 gene for Chinese cattle

The KRT77 gene is a type II epithelial cell α-keratin gene family member that plays a crucial role in animal epidermal and coat formation. This study aimed to investigate the relationship between the KRT77 gene and the adaptability of Chinese cattle in varying environments by exploring the distribution of an exon insertion of the KRT77 gene in different cattle populations. Our analysis involved amplifying and sequencing DNA samples from 362 individuals from 24 cattle breeds in China. Our findings reveal a gradual increase in the frequency of insertion from the northwest to the southeast population. We conducted an association analysis between the genotypes and climate data, revealing a correlation between the insertion and local annual mean temperature, relative humidity, and temperature humidity index. The study highlights the significance of the newly identified KRT77 gene insertion as a variation associated with environmental adaptation in Chinese cattle. This insertion variation increased insights into the genetic mechanisms that drive adaptation in Chinese cattle, emphasizing the importance of the 30-bp insertion in the KRT77 gene. Our findings facilitate further research to improve cattle breeding strategies for adaptability to changing environments from the northwest to the southeast population. In conclusion, this study provides value.

Estimation of Linkage Disequilibrium, Effective Population Size, and Genetic Parameters of Phenotypic Traits in Dabieshan Cattle.

Dabieshan cattle (DBSC) are a valuable genetic resource for indigenous cattle breeds in China. It is a small to medium-sized breed with slower growth, but with good meat quality and fat deposition. Genetic markers could be used for the estimation of population genetic structure and genetic parameters. In this work, we genotyped the DBSC breeding population (n = 235) with the GeneSeek Genomic Profiler (GGP) 100 k density genomic chip. Genotype data of 222 individuals and 81,579 SNPs were retained after quality control. The average minor allele frequency (MAF) was 0.20 and the average linkage disequilibrium (LD) level (r2) was 0.67 at a distance of 0-50 Kb. The estimated relationship coefficient and effective population size (Ne) were 0.023 and 86 for the current generation. In addition, we used genotype data to estimate the genetic parameters of the population's phenotypic traits. Among them, height at hip cross (HHC) and shin circumference (SC) were rather high heritability traits, with heritability of 0.41 and 0.54, respectively. The results reflected the current cattle population's extent of inbreeding and history. Through the principal breeding parameters, genomic breeding would significantly improve the genetic progress of breeding.

Effects of Vitamin A on Yanbian Yellow Cattle and Their Preadipocytes by Activating AKT/mTOR Signaling Pathway and Intestinal Microflora.

Simple SummaryVitamin A is a fat-soluble vitamin that not only plays a role in vision, growth, and development, but also in fat production and metabolism in animals. To improve the production of high-grade beef, it is necessary to explore the molecular mechanism of intramuscular fat deposition in beef cattle through molecular biology techniques. In this study, we selected Yanbian yellow cattle, one of the five major cattle breeds in China, to investigate the effects of vitamin A and its metabolite, all-trans retinoic acid (ATRA), on the proliferation and differentiation of preadipocytes and changes in intestinal microorganisms. It was found that ATRA inhibited adipogenic differentiation of preadipocytes in Yanbian yellow cattle via the AKT/mTOR signaling pathway. This study provides insight into nutritional management and reveals the role of vitamin A in lipid metabolism in Yanbian yellow cattle.In this study, the effects of vitamin A and its metabolite, all-trans retinoic acid (ATRA), on the proliferation and differentiation of preadipocytes and the intestinal microbiome in Yanbian yellow cattle were investigated. Preadipocytes collected from Yanbian yellow cattle treated with different concentrations of ATRA remained in the G1/G0 phase, as determined by flow cytometry. Quantitative reverse-transcription polymerase chain reaction and western blotting analyses showed that the mRNA and protein expression levels of key adipogenic factors, peroxisome proliferator- activated receptor gamma (PPARγ), CCAAT enhancer-binding protein α (C/EBPα), and extracellular signal-regulated kinase 2 (ERK2), decreased. ATRA was found to regulate the mTOR signaling pathway, which is involved in lipid metabolism, by inhibiting the expression of AKT2 and the adipogenic transcription factors SREBP1, ACC, and FAS; the protein and mRNA expression levels showed consistent trends. In addition, 16S rRNA sequencing results showed that a low concentration of vitamin A promoted the growth of intestinal microflora beneficial to lipid metabolism and maintained intestinal health. The results indicated that ATRA inhibited the adipogenic differentiation of preadipocytes from Yanbian yellow cattle through the AKT/mTOR signaling pathway, and that low concentrations of vitamin A may help maintain the intestinal microbes involved in lipid metabolism in cattle.

Transcriptome profiling of lncRNA related to fat tissues of Qinchuan cattle.

Qinchuan cattle is one of the five yellow cattle breeds in China with good performance of meat. The proliferation and differentiation level of muscle and fat are closely related to the growth and development of the organism and are the key factors affecting the quality of meat. In order to study the effect of lncRNA on the fat tissues of Qinchuan cattle, six calf and adult bovine adipose tissues were selected for high-throughput sequencing. We obtained 3,716 lncRNA candidates from calves and adult cattle fat samples, among them 789 lncRNA were annotated and 2,927 lncRNA were novel lncRNA. A number of lncRNAs were highly abundant, and 119 lncRNA were differentially expressed between two developmental stages. We further validated several differentially expressed lncRNAs using qPCR, and the results were consistent with the sequencing data. Therefore, we conclude that lncRNA may play an important role in adipose tissue in different age groups of cattle.

The Distribution Characteristics of a 19-bp Indel of the PLAG1 Gene in Chinese Cattle.

Simple SummaryGrowth traits are important quantitative traits for cattle performance, which influences herd productivity. Previous studies demonstrated that a 19-bp indel in pleomorphic adenoma gene 1 (PLAG1) is associated with bovine growth traits. In our studies, the distribution of the 19-bp indel of PLAG1 gene among 37 Chinese cattle breeds and the association between this indel and growth traits of Yunling cattle were explored. As a result, we found that the average body height of various Chinese cattle breeds showed an increasing trend from south to north of China, which was consistent with the distribution trend of the 19-bp indel in cattle at different geographic latitudes. Moreover, this indel was verified to be significantly associated with the growth traits of Yunling cattle. Our results showed that the 19-bp indel in PLAG1 strongly influences body size in Chinese cattle.Pleomorphic adenoma gene 1 (PLAG1) belongs to the PLAG family of zinc finger transcription factors. In cattle, a 19-bp insertion/deletion (indel) was identified in intron 1 of the PLAG1 gene (GenBank Accession No. AC_000171.1). Researches showed that the indel is polymorphic in Chinese cattle breeds such as Qinchuan cattle, Pinan cattle, Xianan cattle, and Jiaxian red cattle, and correlation analysis showed that the polymorphism is related to the height of these cattle breeds. Chinese cattle breeds show a difference in height related to geographical distribution. We investigated the distribution of the 19-bp indel polymorphism in 37 cattle breeds, including 1354 individuals. The results showed that there were three genotypes and two alleles (W, 366 bp; D, 347 bp). From northern cattle to southern cattle, the frequency of W allele gradually decreased, while the frequency of D allele showed an opposite trend, which was consistent with the distribution of cattle breeds of different height in China. Therefore, the polymorphism of this indel may be related to the regional distribution of cattle breeds in China. In addition, we chose Yunling cattle with a mixed genetic background to study the genetic effects of the 19-bp indel on body size traits. Statistical analysis showed that PLAG1 was significantly associated with the body height, cross height, and chest circumference of Yunling cattle (p < 0.05). This study provides new evidence that the 19-bp indel of the PLAG1 gene is a highly effective trait marker that can be used as a candidate molecular marker for cattle breeding.

A panel of SNP markers for meat traceability of Halal beef in the Chinese market

Genetic traceability in the whole food supply chain is a reliable method to protect the integrity of Halal beef, but there is no available SNPs panel for the meat traceability of cattle breeds in China. This study aimed at developing a useful SNP panel for Halal beef traceability in the Chinese market. Fifty-nine SNPs markers belonging to 29 autosomes of bovine genome were tested in seven cattle breeds which were the Chinese main breed source of Halal beef. SNPs with minor allele frequencies less than 30% were excluded and a thirty-six highly informative SNPs panel had been selected. With the SNPs panel, the probability that one individual is incorrectly assigned ranges from 1.12 out of 10 (×15) to 3.38 out of 10 (×12), depending on the breed. In addition, twelve most polymorphic SNPs markers in the pooled animals were successfully used for meat traceability of Halal beef by meat-blood pairs. The selected thirty-six SNPs of panel could be employed to further guarantee the safety of Halal beef in the Chinese market.

Developmental expression patterns and association study with growth traits of bovine Bhlhe40 gene

As a member of the basic helix-loop-helix (bHLH) family of transcription factors, Bhlhe40 plays an important role in the regulation of adipogenesis, myogenesis and the development of the metabolic syndrome. In this study, we investigated the tissue expression patterns and differences of bovine Bhlhe40 gene during three developmental stages. The result showed that Bhlhe40 was ubiquitously expressed in most tissues of cattle. In addition, the expression of bovine Bhlhe40 gene showed a decreasing trend in skeletal muscle and fat during the developmental stages. Then, two novel mutations (EX5 + 114 T>C, L166P and EX5 + 733 A > G, S372S) of bovine Bhlhe40 gene were identified by BamHI and ApaI ACRS PCR-RFLP in 1226 individuals from five indigenous cattle breeds in China. Frequencies of allele C at the BamHI locus varied from 0.210 to 0.340 among breeds, while frequencies of allele C at the ApaI locus varied from 0.030 to 0.114. Association analysis revealed no significant association of the ApaI locus with growth traits in Nanyang breed. However, the BamHI locus was significantly associated with the average daily gain at 18 months in Nanyang cattle (P < 0.05). This study aimed to lay the groundwork to further study of Bhlhe40 function at myogenesis and adipogenesis in bovine and should significantly contribute to cattle breeding and genetics through the MAS program.

The Polymorphisms of β2-Adrenergic Receptor Gene on two Cattle Breeds in China

The Polymorphisms of β2-Adrenergic Receptor Gene on two Cattle Breeds in China

Sequence variants in the bovine nucleophosmin 1 gene, their linkage and their associations with body weight in native cattle breeds in China

The nucleophosmin (nucleolar phosphoprotein B23, numatrin) gene (NPM1, previously known as nucleophosmin/nucleoplasmin family, member 1) encodes a multifunctional nucleolar phosphoprotein that plays a crucial role in cell growth and homeostasis. Seven sequence variants (SVs) were identified in the coding region of bovine NPM1, five of which were in complete linkage disequilibrium. Eight different haplotypes were identified, of which two major haplotypes have a frequency of 23.2% and 20.4%. Three SVs were significantly associated with body weight in the Nanyang population as analysed at different ages. No significant association was detected between 18 combined genotypes and body weight at five different ages. Our results suggest that some polymorphisms in NPM1 are associated with body weight at some ages and may be used as candidates for marker-assisted selection and management in beef cattle breeding programmes.

Association of polymorphisms of the &amp;lt;i&amp;gt;DCN&amp;lt;/i&amp;gt; gene with growth traits in cattle (Brief Report)

Abstract. Mammalian decorin (DCN) consists of a protein core and a single dermatan or chondroitin sulfate glycosaminoglycan chain (CHOPRA et al. 1985), contributing multifunctionally to processes like matrix assembly, modulation of the activity of growth factors and cell migration and proliferation. Recently, LINDA et al. (2008) have reported that eight SNPs were identified in human. However, the related information in bovine is scarce. Hence, in the present experiment the exons and intron/exon boundaries of DCN were scanned for SNPs in the predominant cattle breeds of China.

Matrilineal genetic inter-introgression of Bos taurus and Bos indicus in China

The genetic resources of cattle breeds in China are very abundant, with the existence of 28 indigenous and other cattle breeds. To further understand the population structure of these indigenous breeds from different geographical locations, we carried out a phylogenetic analysis in maternal lineages by employing mtDNA polymorphisms. The entire mtDNA D-loop sequences of 73 individuals from 14 representative native cattle breeds were determined and analyzed in conjunction with the published 144 D-loop sequences for 19 Chinese cattle breeds retrieved from GenBank. These sequences belonged to 100 haplotypes defined by polymorphisms at 122 polymorphic sites. These haplotypes were clustered into two distinct lineages: taurine Bos taurus and zebu Bos indicus. The two main peaks of the poly-peaked mismatch curve revealed the inter-mismatch distribution between the Bos taurus and Bos indicus sequence types within the cattle samples. The zebu mtDNA dominated in the southern breeds (62.5%), while taurine mtDNA dominated in the northern breeds (96.7%). The geographical distribution of these frequencies revealed an inter-introgression pattern of Bos taurus and Bos indicus in maternal lineages in China. The significant genetic divergence between the northern and the southern breeds resulted from the dominant geographical segregation of the Qinling Moutains and temperature weather conditions. The heterogeneous distribution of taurine and zebu types in other regions could be attributed to the historical events and introgression of taurine cattle imported from home and abroad.

Genetic diversity and population structure of indigenous yellow cattle breeds of China using 30 microsatellite markers

Twenty-seven domesticated yellow cattle breeds of China and three introduced cattle breeds were analysed by means of 30 microsatellite markers to determine the level of genetic variation within and among populations as well as the population structure. In all, 480 microsatellite alleles were observed across the 30 breeds with the mean number of alleles per locus of 9.093 for native breeds and 6.885 for the three introduced breeds. Mean F-statistics (0.08) for Chinese native cattle breeds implied that 92% of the total genetic variation was from genetic differentiation within each breed and 8% of the genetic variation existed among breeds. A phylogenetic tree was constructed based on Nei's genetic distances, and three clusters were obtained. According to the tree, the three introduced breeds were distinct from the 27 native breeds. The indigenous cattle breeds were divided into two clusters, one cluster including five humpless breeds and the other cluster containing 22 humped breeds. This study identifies multiple origins of yellow cattle of China from Bos taurus and Bos indicus. Furthermore, population structure analysis implies that there are possibly five independent original domestications for yellow cattle in China. Four of five origins were four different Bos indicus types, mainly in areas of the Chang Jiang, the Zhu Jiang River basin, the Yellow River and the Huai River basin. The other origin was for Bos taurus type of Mongolian descent, mainly located in Northwestern China, the Mongolian plateau and Northeastern China or north of the Great Wall.

Five novel single nucleotide polymorphisms (SNPs) of the prophet of PIT1 (&amp;lt;i&amp;gt;PROP1&amp;lt;/i&amp;gt;) gene in bovine (Brief report)

Abstract. The prophet of Pit1 (PROP1) gene encodes a paired class homeodomain transcription factor of 226 amino acids and is organized of 3 exons. PROP1 is necessary for the specification, differentiation and proliferation of cells. Its function is essential for anterior pituitary organogenesis, and heritable mutations in this gene are associated with combined pituitary hormone deficiency (CPHD) in human patients and animals (SAVAGE et al., 2003; CARVALHO et al., 2006). To date, no polymorphisms of the bovine PROP1 gene were described. In the present experiment, the 5' flanking region, the coding region and partial introns of bovine PROP1 were scanned for single nucleotide polymorphism (SNPs) in five cattle breeds of China.

MtDNA Diversity and genetic lineages of eighteen cattle breeds from Bos taurus and Bos indicus in China

In order to clarify the origin and genetic diversity of indigenous cattle breeds in China, we carried out phylogenetic analysis of representatives of those breeds by employing mitochondrial gene polymorphism. Complete cyt b gene sequences, 1140 bp in length, were determined for a total of 136 individuals from 18 different breeds and these sequences were clustered into two distinct genetic lineages: taurine (Bos taurus) and zebu (Bos indicus). In analysis of the cyt b gene diversity, Chinese cattle showed higher nucleotide (0.00923) and haplotype diversity (0.848) than the reports from other studies, and the animals from the taurine lineage indicated higher nucleotide diversity (0.00330) and haplotype diversity (0.746) than the ones from the zebu lineage (0.00136; 0.661). The zebu mtDNA dominated in the southern breeds (63.3-100%), while the taurine dominated in the northern breeds (81.8-100%). Six cattle breeds from the central area of China exhibited intermediate frequencies of zebu mtDNA (25-71.4%). This polymorphism revealed a declining south-to-north gradient of female zebu introgression and a geographical hybrid zone of Bos taurus and Bos indicus in China.