Accuracy of Genomic Predictions Cross Populations with Different Linkage Disequilibrium Patterns.

Background/objectives: There is a considerable global population of beef cattle, with numerous small-scale groups. Establishing separate reference groups for each breed in breeding practices is challenging, severely limiting the genome selection (GS) application. Combining data from multiple populations becomes particularly attractive and practical for small-scale populations, offering increased reference population size, operational ease, and data sharing.

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.

Genetic Diversity and Selective Signature in Dabieshan Cattle Revealed by Whole-Genome Resequencing.

Dabieshan cattle are a typical breed of southern Chinese cattle that have the characteristics of muscularity, excellent meat quality and tolerance to temperature and humidity. Based on 148 whole-genome data, our analysis disclosed the ancestry components of Dabieshan cattle with Chinese indicine (0.857) and East Asian taurine (0.

Polymorphisms of the Growth Hormone Releasing Hormone Receptor Gene Affect Body Conformation Traits in Chinese Dabieshan Cattle.

This study was performed to expose the polymorphisms of the growth hormone-releasing hormone receptor gene in Chinese Dabieshan cattle, evaluate its effect on body conformation traits, and find potential molecular markers in Chinese cattle. The GHRHR structure and the phylogenetic tree were analyzed using bioinformatics software. The polymorphism of the GHRHR gene in 486 female cattle was genotyped by PCR-RFLP and DNA sequencing, and the association between SNPs and body conformation traits of Chinese Dabieshan cattle was analyzed by one-way ANOVA in SPSS software.

Genetic variants of the growth differentiation factor 8 affect body conformation traits in Chinese Dabieshan cattle.

Objective: The growth differentiation factor 8 (GDF8) gene plays a key role in bone formation, resorption, and skeletal muscle development in mammals. Here, we studied the genetic variants of GDF8 and their contribution to body conformation traits in Chinese Dabieshan cattle.

Methods: Single nucleotide polymorphisms (SNPs) were identified in the bovine GDF8 gene by DNA sequencing.

Genomic analyses reveal distinct genetic architectures and selective pressures in buffaloes.

Background: The domestic buffalo (Bubalus bubalis) is an essential farm animal in tropical and subtropical regions, whose genomic diversity is yet to be fully discovered.

Results: In this study, we describe the demographic events and selective pressures of buffalo by analyzing 121 whole genomes (98 newly reported) from 25 swamp and river buffalo breeds. Both uniparental and biparental markers were investigated to provide the final scenario.

polymorphism is associated with milk production traits in Chinese cattle.

The production traits of cattle, especially milk trait, are of great significance to human life. A quantitative trait loci (QTL) associated with milk fat content was detected in the centromeric region of cattle chromosome 14. This QTL harbors a strong candidate gene called responsible for the milk quality.

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

Pleomorphic adenoma gene 1 () belongs to the family of zinc finger transcription factors. In cattle, a 19-bp insertion/deletion (indel) was identified in intron 1 of the gene (GenBank Accession No. AC_000171.

Four Novel SNPs of Gene Associated with Heat-Tolerance in Chinese Cattle.

Based on the previous GWAS research related to bovine heat tolerance trait, this study aimed to explore the effect of myosin-1a () gene on bovine heat tolerance trait, and find the molecular markers related to the heat tolerance of Chinese cattle. In our study, four novel candidate SNPs highly conserved in breeds but barely existed in were identified in gene according to Bovine Genome Variation Database and Selective Signatures (BGVD). PCR and DNA sequencing were used to genotype 1072 individuals including 34 Chinese indigenous cattle breeds as well as Angus and Indian zebu.

Variation Related to Heat Resistance of Chinese Cattle.

With the inexorable rise of global temperature, heat stress deserves more and more attention in livestock agriculture. Previous studies have shown that the mechanistic target of rapamycin () (NC_037343.1:c.

Two Novel SNPs in Gene Are Associated with Cattle Body Measurement Traits.

The rearrangement of the transfection () gene, which mediates the functions of the ganglion in the gastrointestinal tract, plays an important role in the development of the gastrointestinal nervous system. Therefore, the gene is a potential factor influencing animal body measurement. The aim of this study was to reveal the significant genetic variations in the bovine gene and investigate the relationship between genotypes and body measurement in two Chinese cattle breeds (Qinchuan and Nanyang cattle).

Genome-Wide SNPs and InDels Characteristics of Three Chinese Cattle Breeds.

We report genome characterization of three native Chinese cattle breeds discovering ~34.3 M SNPs and ~3.8 M InDels using whole genome resequencing.

Genome-wide assessment of genetic diversity and population structure insights into admixture and introgression in Chinese indigenous cattle.

Background: China exhibits a great diversity of ecosystems and abundant cattle resources, with nearly 30 million cattle from 53 indigenous breeds reared in specific geographic regions. To explore the genetic diversity and population structure of Chinese indigenous cattle, a population genetic analysis at both the individual and population levels was conducted and the admixture analysis was performed. We genotyped 572 samples from 20 Chinese indigenous cattle breeds using GeneSeek Genomic Profiler Bovine LD (GGP-LD, 30 K) and downloaded the published data of 77 samples from 4 worldwide commercial breeds genotyped with Illumina BovineSNP50 Beadchip (SNP50, 50 K).

Whole-genome resequencing reveals world-wide ancestry and adaptive introgression events of domesticated cattle in East Asia.

Cattle domestication and the complex histories of East Asian cattle breeds warrant further investigation. Through analysing the genomes of 49 modern breeds and eight East Asian ancient samples, worldwide cattle are consistently classified into five continental groups based on Y-chromosome haplotypes and autosomal variants. We find that East Asian cattle populations are mainly composed of three distinct ancestries, including an earlier East Asian taurine ancestry that reached China at least ~3.

Associations between polymorphisms in the NICD domain of bovine NOTCH1 gene and growth traits in Chinese Qinchuan cattle.

NOTCH1 is one of the four mammalian Notch receptors, which is involved in the Notch signaling pathway. Specifically, NOTCH1 promotes the proliferation of myogenic precursor cells, and the NICD domain of NOTCH1 can impair regeneration of skeletal muscles. However, similar research on the bovine NOTCH1 gene is lacking.

SNP and haplotype analysis of paired box 3 (PAX3) gene provide evidence for association with growth traits in Chinese cattle.

Paired box 3 (PAX3) belongs to the PAX superfamily of transcription factors and plays essential roles in the embryogenesis and postnatal formation of limb musculature through affecting the survival of muscle progenitor cells. By genetic mapping, PAX3 gene is assigned in the interval of quantitative trait loci for body weight on bovine BTA2. The objectives of this study were to detect polymorphisms of PAX3 gene in 1,241 cattle from five breeds and to investigate their effects on growth traits.

SNP and haplotype analysis reveal IGF2 variants associated with growth traits in Chinese Qinchuan cattle.

Insulin-like growth factor 2 (IGF2) is a potent cell growth and differentiation factor and is implicated in mammals' growth and development. The objective of this study was to evaluate the effects of the mutations in the bovine IGF2 with growth traits in Chinese Qinchuan cattle. Four single nucleotide polymorphisms (SNPs) were detected of the bovine IGF2 by DNA pool sequencing and forced polymerase chain reaction-restriction fragment length polymorphism (forced PCR-RFLP) methods.

Association analysis of bovine Foxa2 gene single sequence variant and haplotype combinations with growth traits in Chinese cattle.

Forkhead box A2 (Foxa2) has been recognized as one of the most potent transcriptional activators that is implicated in the control of feeding behavior and energy homeostasis. However, similar researches about the effects of genetic variations of Foxa2 gene on growth traits are lacking. Therefore, this study detected Foxa2 gene polymorphisms by DNA pool sequencing, PCR-RFLP and PCR-ACRS methods in 822 individuals from three Chinese cattle breeds.