Peipei Ma

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Genome-wide association studies (GWAS) based on high throughput SNP genotyping technologies open a broad avenue for exploring genes associated with milk production traits in dairy cattle. Motivated by pinpointing novel quantitative trait nucleotide (QTN) across Bos Taurus genome, the present study is to perform GWAS to identify genes affecting milk(More)
CD4+ T cells play a key role in the immune response of pathogen-induced mastitis in dairy cattle. Mammary gland factor STAT5b is involved in the regulation of CD4+T cell differentiation during inflammatory response and milk production. Little is known about the genetic variation effects of bovine CD4 and STAT5b genes on somatic cell score (SCS) and milk(More)
BACKGROUND Genomic breeding value estimation is the key step in genomic selection. Among many approaches, BLUP methods and Bayesian methods are most commonly used for estimating genomic breeding values. Here, we applied two BLUP methods, TABLUP and GBLUP, and three Bayesian methods, BayesA, BayesB and BayesCπ, to the common dataset provided by the 15th(More)
Bovine mastitis is a typical inflammatory disease causing seriously economic loss. Genome-wide association study (GWAS) can be a powerful method to promote marker assistant selection of this kind of complex disease. The present study aimed to analyze and identify single nucleotide polymorphisms (SNPs) and candidate genes that associated with mastitis(More)
DNA methylation is a major part of epigenetics. DNA methylation on the CpG sites in gene promoter and the first exon often represses gene expression, but demethylation activates gene expression. Previous research has shown that a negative correlation was found between mastitis index (somatic cell count, SCC) and milk production traits in Holsteins. The(More)
Genotype imputation is commonly used as an initial step in genomic selection since the accuracy of genomic selection does not decline if accurately imputed genotypes are used instead of actual genotypes but for a lower cost. Performance of imputation has rarely been investigated in crossbred animals and, in particular, in pigs. The extent and pattern of(More)
BACKGROUND The mixed model based single locus regression analysis (MMRA) method was used to analyse the common simulated dataset of the 15th QTL-MAS workshop to detect potential significant association between single nucleotide polymorphisms (SNPs) and the simulated trait. A Wald chi-squared statistic with df =1 was employed as test statistic and the(More)
Effective populations size (Ne) is an important population parameter that helps to explain genetic variation, population evolution and understanding of the genetic architecture underlying complex traits. With the availability of high-dense SNP panels, more and more researches focus on estimating of Ne using linkage disequilibrium (LD) between SNPs. In this(More)
Reproductive performance of stock sows is one of the important factors of economic impact in pig farms. In this study, 8491 litter records from 2699 sows of Yorkshire, Landrace, and Duroc were analyzed using fixed model to determine the effect of parity, mating season, and breed on total number born (TNB), number healthy birth (NHB), litter birth weight(More)
Missing genotypes are a common feature of high density SNP datasets obtained using SNP chip technology and this is likely to decrease the accuracy of genomic selection. This problem can be circumvented by imputing the missing genotypes with estimated genotypes. When implementing imputation, the criteria used for SNP data quality control and whether to(More)