Z L Hu

Publications of Z L Hu

• Assessment of the swine protein-annotated oligonucleotide microarray.

  Authors: J P Steibel, M Wysocki, J K Lunney, A M Ramos, Z L Hu, M F Rothschild, C W Ernst

  Animal genetics. 06/2009;

  The specificity and utility of the swine protein-annotated oligonucleotide microarray, or Pigoligoarray (http://www.pigoligoarray.org), has been evaluated by profiling the expression of transcriptsThe specificity and utility of the swine protein-annotated oligonucleotide microarray, or Pigoligoarray (http://www.pigoligoarray.org), has been evaluated by profiling the expression of transcripts from four porcine tissues. Tools for comparative analyses of expression on the Pigoligoarray were developed including HGNC identities and comparative mapping alignments with human orthologs. Hybridization results based on the Pigoligoarray's sets of control, perfect match (PM) and deliberate mismatch (MM) probes provide an important means of assessing non-specific hybridization. Simple descriptive diagnostic analyses of PM/MM probe sets are introduced in this paper as useful tools for detecting non-specific hybridization. Samples of RNA from liver, brain stem, longissimus dorsi muscle and uterine endothelium from four pigs were prepared and hybridized to the arrays. Of the total 20 400 oligonucleotides on the Pigoligoarray, 12 429 transcripts were putatively differentially expressed (DE). Analyses for tissue-specific expression [over-expressed in one tissue with respect to all the remaining three tissues (q < 0.01)] identified 958 DE transcripts in liver, 726 in muscle, 286 in uterine endothelium and 1027 in brain stem. These hybridization results were confirmed by quantitative PCR (QPCR) expression patterns for a subset of genes after affirming that cDNA and amplified antisense RNA (aRNA) exhibited similar QPCR results. Comparison to human ortholog expression confirmed the value of this array for experiments of both agricultural importance and for tests using pigs as a biomedical model for human disease.

• SNP discovery in Litopenaeus vannamei with a new computational pipeline.

  Authors: D M Gorbach, Z L Hu, Z-Q Du, M F Rothschild

  Animal genetics. 10/2008;

  Summary Litopenaeus vannamei (Pacific white shrimp) have been farmed in the Americas for many years and are growing in popularity in Asia with the development of specific pathogen-free stocks. TheSummary Litopenaeus vannamei (Pacific white shrimp) have been farmed in the Americas for many years and are growing in popularity in Asia with the development of specific pathogen-free stocks. The full genomic sequence of this species might not be available in the near future, so other tools are needed to discover the location of polymorphic sites for quantitative trait loci mapping, association studies and subsequent marker-assisted selection. Currently, 25 937 L. vannamei expressed sequence tags (ESTs) are publicly available. These sequences were manually screened, masked for tandem repeats and inputted into CAP3 for clustering. The resulting 3532 contigs were analysed for possible single nucleotide polymorphisms (SNPs) with snpidentifier, a newly developed computer program for predicting SNPs. snpidentifier is designed for ESTs without accompanying chromatogram sequence quality information, and therefore it performs quality control checks on all data. snpidentifier sets a threshold such that the sequences used have a poor quality nucleotide (N) frequency <0.1, and it trims off the first 10 bases of every sequence to ensure higher sequence quality. For a base to be predicted as an SNP, the minor nucleotide (allele) frequency must be >0.1, it must be observed at least four times and the 15 bases on either side must exactly match the consensus sequence. Using these conservative parameters, 504 SNPs were predicted from 141 contigs for L. vannamei. A small sample of 18 individuals from three lines have been sequenced to verify prediction results and 17 of 39 (44%) of the tested SNPs have been confirmed.

• Animal trait ontology: The importance and usefulness of a unified trait vocabulary for animal species.

  Authors: L M Hughes, J. Bao, Z L Hu, V. Honavar, J M Reecy

  Journal of animal science. 07/2008; 86(6):1485-91.

  Ontologies help to identify and formally define the entities and relationships in specific domains of interest. Bio-ontologies, in particular, play a central role in the annotation, integration,Ontologies help to identify and formally define the entities and relationships in specific domains of interest. Bio-ontologies, in particular, play a central role in the annotation, integration, analysis, and interpretation of biological data. Missing from the number of bio-ontologies is one that includes phenotypic trait information found in livestock species. As a result, the Animal Trait Ontology (ATO) project being carried out under the auspices of the USDA-National Animal Genome Research Program is aimed at the development of a standardized trait ontology for farm animals and software tools to assist the research community in collaborative creation, editing, maintenance, and use of such an ontology. The ATO is currently inclusive of cattle, pig, and chicken species, and will include other livestock species in the future. The ATO will eventually be linked to other species (e.g., human, rat, mouse) so that comparative analysis can be efficiently performed between species.

• Development of an in silico coding gene SNP map in pigs.

  Authors: X P Li, Z L Hu, S J Moon, K T Do, Y K Ha, H Kim, M J Byun, B H Choi, M F Rothschild, J M Reecy, K S Kim

  Animal genetics. 06/2008;

  A total of 5450 sequences obtained from the NCBI pig SNP database were consolidated into 465 unique sequences (189 singleton sequences and 276 contigs). These 465 sequences contained 1787 putativeA total of 5450 sequences obtained from the NCBI pig SNP database were consolidated into 465 unique sequences (189 singleton sequences and 276 contigs). These 465 sequences contained 1787 putative SNPs and had strong sequence homology to 433 human protein-coding genes based on blast analyses. These genes were assigned to the pig QTL maps (http://www.animalgenome.org/QTLdb/pig.html) via the human and pig comparative maps established by a pig radiation hybrid (RH) map. The SNP information characterized from this study provides a useful functional gene variation resource to facilitate QTL data mining in the pig genome.

• A data resource of 838 porcine microsatellite sequences with repeat motifs of three to six bases.

  Authors: P Karlskov-Mortensen, Z L Hu, J M Reecy, M Fredholm

  Animal genetics. 03/2008; 39(1):85-6.

• Identification of 10 882 porcine microsatellite sequences and virtual mapping of 4528 of these sequences.

  Authors: P Karlskov-Mortensen, Z L Hu, J Gorodkin, J M Reecy, M Fredholm

  Animal genetics. 09/2007; 38(4):401-5.

  A total of 10 882 porcine microsatellite repeats were identified in genomic shotgun sequences from the Sino-Danish Pig Genome Sequencing Consortium (http://www.piggenome.dk). Of these, 4528A total of 10 882 porcine microsatellite repeats were identified in genomic shotgun sequences from the Sino-Danish Pig Genome Sequencing Consortium (http://www.piggenome.dk). Of these, 4528 microsatellites were placed on a pig-human comparative map by blast analysis of porcine sequences against the human genome (blast cut-off threshold =1 x 10(-5)). All microsatellite sequences placed on the comparative map are accessible at http://www.animalgenome.org/QTLdb/pig.html. These sequences increase the number of identified microsatellites in the porcine genome by several orders of magnitude. They are a new resource of microsatellite sequences for generating markers to be used in linkage studies and in fine mapping and positional cloning of quantitative trait loci.

• Rapid communication: mapping of the titin (TTN) gene to pig chromosome 15.

  Authors: G R Bertani, N J Larsen, S Marklund, Z L Hu, M F Rothschild

  Journal of animal science. 11/1999; 77(10):2857-8.

• Rapid communication: mapping of the glutathione-peroxidase-5 (GPX5) gene to pig chromosome 7.

  Authors: G R Bertani, S Marklund, Z L Hu, M F Rothschild

  Journal of animal science. 11/1999; 77(10):2855-6.

• Genetic linkage and physical mapping of the porcine androgen receptor (AR) gene.

  Authors: J N Seifert, N J Larsen, S Marklund, Z L Hu, G A Rohrer, M F Rothschild

  Journal of animal science. 04/1999; 77(3):785-6.

• The progesterone receptor (PGR) gene maps to porcine chromosome 9p13-p11 by a rodent-porcine somatic cell hybrid panel.

  Authors: Z L Hu, M A Abbott, M Yerle, M F Rothschild

  Journal of animal science. 11/1998; 76(10):2749-50.

• Expeditor: a pipeline for designing primers using human gene structure and livestock animal EST information.

  Authors: Z L Hu, K Glenn, A M Ramos, C J Otieno, J M Reecy, M F Rothschild

  The Journal of heredity. 96(1):80-2.

  We have developed software, called Expeditor, that can be used to combine known gene structure information from human and coding sequence information from farm animal species for a streamlined primerWe have developed software, called Expeditor, that can be used to combine known gene structure information from human and coding sequence information from farm animal species for a streamlined primer design in target farm animal species. This software has many utilities, which include PCR-based SNP discovery for identification of genes/markers associated with economically important traits in farm animals, comparative mapping analysis, and evolution studies. The use of this software helps minimize tedious manual operations and reduces the chance of errors by more conventional approaches.

• Global Perspectives on animal trait ontology

  Authors: J M Reecy, C.A. Park, Z L Hu, B. Hulsegge, Steen, H.A.M, J.F. Hocquette