National Animal Husbandry Services

Beijing, China

National Animal Husbandry Services

Beijing, China

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Yang Q.-F.,National Animal Husbandry Services | Wu Y.-L.,Ningbo Academy of Agricultural science
Chromatographia | Year: 2012

A fast analytical method for the simultaneous determination of fumonisin B1 (FB 1) and fumonisin B 2 (FB 2) in corn using a novel QuEChERS method and LC-MS-MS was developed and validated. Samples were extracted with methanol-water (3:1 v/v) by means of ultrasonic extraction. The extract was purified with a novel modified QuEChERS method. Firstly, FB 1 and FB2 in the extract were retained with primary secondary amine (PSA). Then, FB1 and FB 2 were released from PSA with 1.0 % formic acid in methanol. The final eluate was diluted with water, and analyzed by LC-MS-MS on a Waters Acquity BEH C 18 column with 0.1 % formic acid in water/methanol as mobile phase with gradient elution. Mean recoveries of 83.5-102.4 % with CVs of 3.6-10.5 % were obtained at fortification levels of 2, 50 and 1,000 μg kg -1. The limit of quantification was 2.0 μg kg -1. © 2012 Springer-Verlag.


Chen Q.,Shanghai JiaoTong University | Ma Y.,Shanghai JiaoTong University | Yang Y.,Shanghai JiaoTong University | Yang Y.,Jiangsu University | And 15 more authors.
PLoS ONE | Year: 2013

Next-generation sequencing (NGS) approaches are widely used in genome-wide genetic marker discovery and genotyping. However, current NGS approaches are not easy to apply to general outbred populations (human and some major farm animals) for SNP identification because of the high level of heterogeneity and phase ambiguity in the haplotype. Here, we reported a new method for SNP genotyping, called genotyping by genome reducing and sequencing (GGRS) to genotype outbred species. Through an improved procedure for library preparation and a marker discovery and genotyping pipeline, the GGRS approach can genotype outbred species cost-effectively and high-reproducibly. We also evaluated the efficiency and accuracy of our approach for high-density SNP discovery and genotyping in a large genome pig species (2.8 Gb), for which more than 70,000 single nucleotide polymorphisms (SNPs) can be identified for an expenditure of only $80 (USD)/sample. © 2013 Chen et al.


Yang Y.,Shanghai JiaoTong University | Wang Q.,Shanghai JiaoTong University | Chen Q.,Shanghai JiaoTong University | Liao R.,Shanghai JiaoTong University | And 7 more authors.
PLoS ONE | Year: 2014

We report a novel algorithm, iBLUP, to impute missing genotypes by simultaneously and comprehensively using identity by descent and linkage disequilibrium information. The simulation studies showed that the algorithm exhibited drastically tolerance to high missing rate, especially for rare variants than other common imputation methods, e.g. BEAGLE and fastPHASE. At a missing rate of 70%, the accuracy of BEAGLE and fastPHASE dropped to 0.82 and 0.74 respectively while iBLUP retained an accuracy of 0.95. For minor allele, the accuracy of BEAGLE and fastPHASE decreased to -0.1 and 0.03, while iBLUP still had an accuracy of 0.61.We implemented the algorithm in a publicly available software package also named iBLUP. The application of iBLUP for processing real sequencing data in an outbred pig population was demonstrated. © 2014 Yang et al.


PubMed | Washington State University, Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai JiaoTong University and National Animal Husbandry Services
Type: Journal Article | Journal: PloS one | Year: 2014

We report a novel algorithm, iBLUP, to impute missing genotypes by simultaneously and comprehensively using identity by descent and linkage disequilibrium information. The simulation studies showed that the algorithm exhibited drastically tolerance to high missing rate, especially for rare variants than other common imputation methods, e.g. BEAGLE and fastPHASE. At a missing rate of 70%, the accuracy of BEAGLE and fastPHASE dropped to 0.82 and 0.74 respectively while iBLUP retained an accuracy of 0.95. For minor allele, the accuracy of BEAGLE and fastPHASE decreased to -0.1 and 0.03, while iBLUP still had an accuracy of 0.61.We implemented the algorithm in a publicly available software package also named iBLUP. The application of iBLUP for processing real sequencing data in an outbred pig population was demonstrated.

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