Genetic variation in eight Chinese cattle breeds based on the analysis of microsatellite markers

Genetic variability and genetic relationships were investigated among eight Chinese cattle breeds using 12 microsatellite markers. Three hundred and fifty-two alleles were detected and the average number of alleles per locus ranged from 8.33 ± 1.67 in the Jiaxian breed to 21.33 ± 5.60 in the Qinchuan breed with a mean value of 13.91. The total number of alleles per microsatellite ranged from 21 (INRA005, HEL1) to 40 (HEL13), with a mean of 29.33 per locus. The fixation indices at the 12 loci in the eight breeds were very low with a mean of 0.006. A principal components analysis and the construction of a neighborjoining tree showed that these eight Chinese cattle breeds cluster into three groups i.e. the Yanbian andChineseHolstein, theNanyang and Jiaxian, and the four remaining breeds.This clustering agrees with the origin and geographical distributions of these Chinese breeds

OmniEvent: A Comprehensive, Fair, and Easy-to-Use Toolkit for Event Understanding

Event understanding aims at understanding the content and relationship of events within texts, which covers multiple complicated information extraction tasks: event detection, event argument extraction, and event relation extraction. To facilitate related research and application, we present an event understanding toolkit OmniEvent, which features three desiderata: (1) Comprehensive. OmniEvent supports mainstream modeling paradigms of all the event understanding tasks and the processing of 15 widely-used English and Chinese datasets. (2) Fair. OmniEvent carefully handles the inconspicuous evaluation pitfalls reported in Peng et al. (2023), which ensures fair comparisons between different models. (3) Easy-to-use. OmniEvent is designed to be easily used by users with varying needs. We provide off-the-shelf models that can be directly deployed as web services. The modular framework also enables users to easily implement and evaluate new event understanding models with OmniEvent. The toolkit (https://github.com/THU-KEG/OmniEvent) is publicly released along with the demonstration website and video (https://omnievent.xlore.cn/)

Characterization of lncRNA–miRNA–mRNA Network to Reveal Potential Functional ceRNAs in Bovine Skeletal Muscle

There is growing evidence that non-coding RNAs are emerging as critical regulators of skeletal muscle development. In order to reveal their functional roles and regulatory mechanisms, we constructed a lncRNA–miRNA–mRNA network according to the ceRNA (competitive endogenous RNA) theory, using our high-throughput sequencing data. Subsequently, the network analysis, GO (Gene Ontology) analysis, and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis were performed for functional annotation and exploration of lncRNA ceRNAs. The results uncovered a scale-free characteristics network which exhibited high functional specificity for bovine skeletal muscle development: co-expression lncRNAs were significantly enriched in muscle development related biological processes and the Wnt signaling pathway. Furthermore, GSEA (Gene Set Enrichment Analysis) indicated that the risk score has a tendency to associate with myogenesis, and differentially expressed RNAs were validated by qPCR, further confirming the credibility of our network. In summary, this study provides insights into lncRNA-mediated ceRNA function and mechanisms in bovine skeletal muscle development and will expand our understanding of lncRNA biology in mammals

Detection of copy number variations and their effects in Chinese bulls

BACKGROUND: Copy number variations (CNVs) are a main source of genomic structural variations underlying animal evolution and production traits. Here, with one pure-blooded Angus bull as reference, we describe a genome-wide analysis of CNVs based on comparative genomic hybridization arrays in 29 Chinese domesticated bulls and examined their effects on gene expression and cattle growth traits. RESULTS: We identified 486 copy number variable regions (CNVRs), covering 2.45% of the bovine genome, in 24 taurine (Bos taurus), together with 161 ones in 2 yaks (Bos grunniens) and 163 ones in 3 buffaloes (Bubalus bubalis). Totally, we discovered 605 integrated CNVRs, with more “loss” events than both “gain” and “both” ones, and clearly clustered them into three cattle groups. Interestingly, we confirmed their uneven distributions across chromosomes, and the differences of mitochondrion DNA copy number (gain: taurine, loss: yak & buffalo). Furthermore, we confirmed approximately 41.8% (253/605) and 70.6% (427/605) CNVRs span cattle genes and quantitative trait loci (QTLs), respectively. Finally, we confirmed 6 CNVRs in 9 chosen ones by using quantitative PCR, and further demonstrated that CNVR22 had significantly negative effects on expression of PLA2G2D gene, and both CNVR22 and CNVR310 were associated with body measurements in Chinese cattle, suggesting their key effects on gene expression and cattle traits. CONCLUSIONS: The results advanced our understanding of CNV as an important genomic structural variation in taurine, yak and buffalo. This study provides a highly valuable resource for Chinese cattle’s evolution and breeding researches. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-480) contains supplementary material, which is available to authorized users

Y-Single Nucleotide Polymorphisms Diversity in Chinese Indigenous Horse

In contrast to high genetic diversity of mitochondrial DNA (mtDNA), equine Y chromosome shows extremely low variability, implying limited patrilines in the domesticated horse. In this study, we applied direct sequencing and restriction fragment length polymorphism (RFLP) methods to investigate the polymorphisms of 33 Y chromosome specific loci in 304 Chinese indigenous horses from 13 breeds. Consequently, two Y-single nucleotide polymorphisms (SNPs) (Y-45701/997 and Y-50869) and one Y-indel (Y-45288) were identified. Of those, the Y-50869 (T>A) revealed the highest variation frequency (24.67%), whereas it was only 3.29% and 1.97% in Y-45288 (T/-) and Y-45701/997 (G>T) locus, respectively. These three mutations accounted for 27.96% of the total samples and identified five Y-SNP haplotypes, demonstrating genetic diversity of Y chromosome in Chinese horses. In addition, all the five Y-SNP haplotypes were shared by different breeds. Among 13 horse breeds analyzed, Balikun horse displayed the highest nucleotide diversity (π = 5.6×10−4) and haplotype diversity (h = 0.527), while Ningqiang horse showed the lowest nucleotide diversity (π = 0.00000) and haplotype diversity (h = 0.000). The results also revealed that Chinese horses had a different polymorphic pattern of Y chromosome from European and American horses. In conclusion, Chinese horses revealed genetic diversity of Y chromosome, however more efforts should be made to better understand the domestication and paternal origin of Chinese indigenous horses

Genome-wide analysis emancipates genomic diversity and signature of selection in Altay white-headed cattle of Xinjiang, China

Altay white-headed cattle have not received enough attention for several reasons. Due to irrational breeding and selection practices, the number of pure Altay white-headed cattle has decreased significantly and the breed is now on the eve of extinction. The genomic characterization will be a crucial step towards understanding the genetic basis of productivity and adaptability to survival under native Chinese agropastoral systems; nevertheless, no attempt has been made in Altay white-headed cattle. In the current study, we compared the genomes of 20 Altay white-headed cattle to the genomes of 144 individuals in representative breeds. Population genetic diversity revealed that the nucleotide diversity of Altay white-headed cattle was less than that of indicine breeds and comparable to that of Chinese taurus cattle. Using population structure analysis, we also found that Altay white-headed cattle carried the ancestry of the European and East Asian cattle lineage. In addition, we used three different methods (FST, θπ ratio and XP-EHH) to investigate the adaptability and white-headed phenotype of Altay white-headed cattle and compared it with Bohai black cattle. We found EPB41L5, SCG5 and KIT genes on the list of the top one percent genes, these genes might have an association with environmental adaptability and the white-headed phenotype for this breed. Our research reveals the distinctive genomic features of Altay white-headed cattle at the genome-wide level

Analysis of genomic copy number variations through whole-genome scan in Chinese Qaidam cattle

Qaidam cattle (CDM) are indigenous breed inhabiting Northwest China. In the present study, we newly sequenced 20 Qaidam cattle to investigate the copy number variants (CNVs) based on the ARS-UMD1.2 reference genome. We generated the CNV region (CNVR) datasets to explore the genomic CNV diversity and population stratification. The other four cattle breeds (Xizang cattle, XZ; Kazakh cattle, HSK; Mongolian cattle, MG; and Yanbian cattle, YB) from the regions of North China embracing 43 genomic sequences were collected and are distinguished from each of the other diverse populations by deletions and duplications. We also observed that the number of duplications was significantly more than deletions in the genome, which may be less harmful to gene formation and function. At the same time, only 1.15% of CNVRs overlapped with the exon region. Population differential CNVRs and functional annotations between the Qaidam cattle population and other cattle breeds revealed the functional genes related to immunity (MUC6), growth (ADAMTSL3), and adaptability (EBF2). Our analysis has provided numerous genomic characteristics of some Chinese cattle breeds, which are valuable as customized biological molecular markers in cattle breeding and production

Selection response and estimation of the genetic parameters for multidimensional measured breast meat yield related traits in a long-term breeding Pekin duck line

Objective This study was conducted to estimate the genetic parameters and breeding values of breast meat related traits of Pekin ducks. Selection response was also determined by using ultrasound breast muscle thickness (BMT) measurements in combination with bosom breadth (BB) and keel length (KL) values. Methods The traits analyzed were breast meat weight (BMW), body weight (BW), breast meat percentage (BMP) and the three parameters of breast meat (BB, KL, and BMT). These measurements were derived from studying 15,781 Pekin ducks selected from 10 generations based on breast meat weight. Genetic parameters and breeding value were estimated for the analysis of the breeding process. Results Estimated heritability of BMW and BMP were moderate (0.23 and 0.16, respectively), and heritability of BW was high (0.48). Other traits such as BB, KL, and BMT indicated moderate heritability ranging between 0.11 and 0.28. Significant phenotypic correlations of BMW with BW and BMP were discovered (p<0.05), and genetic correlations of BMW with BW and BMP were positive and high (0.83 and 0.66, respectively). It was noted that BMW had positive correlations with all the other traits. Generational average estimated breeding values of all traits increased substantially over the course of selection, which demonstrated that the ducks responded efficiently to increased breast meat yield after 10 generations of breeding. Conclusion The results indicated that duck BMW had the potential to be increased through genetic selection with positive effects on BW and BMP. The ultrasound BMT, in combination with the measurement of BB and KL, is shown to be essential and effective in the process of high breast meat yield duck breeding

Global dispersal and adaptive evolution of domestic cattle: a genomic perspective

Domestic cattle have spread across the globe and inhabit variable and unpredictable environments. They have been exposed to a plethora of selective pressures and have adapted to a variety of local ecological and management conditions, including UV exposure, diseases, and stall-feeding systems. These selective pressures have resulted in unique and important phenotypic and genetic differences among modern cattle breeds/populations. Ongoing efforts to sequence the genomes of local and commercial cattle breeds/populations, along with the growing availability of ancient bovid DNA data, have significantly advanced our understanding of the genomic architecture, recent evolution of complex traits, common diseases, and local adaptation in cattle. Here, we review the origin and spread of domestic cattle and illustrate the environmental adaptations of local cattle breeds/populations