James M. Reecy

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project

The Minimum Information for Biological and Biomedical Investigations (MIBBI) project aims to foster the coordinated development of minimum-information checklists and provide a resource for those exploring the range of extant checklists.

AnimalQTLdb: a livestock QTL database tool set for positional QTL information mining and beyond

The Animal Quantitative Trait Loci (QTL) database (AnimalQTLdb) is designed to house all publicly available QTL data on livestock animal species from which researchers can easily locate and compare QTL within species. The database tools are also added to link the QTL data to other types of genomic information, such as radiation hybrid (RH) maps, finger printed contig (FPC) physical maps, linkage maps and comparative maps to the human genome, etc. Currently, this database contains data on 1287 pig, 630 cattle and 657 chicken QTL, which are dynamically linked to respective RH, FPC and human comparative maps. We plan to apply the tool to other animal species, and add more structural genome information for alignment, in an attempt to aid comparative structural genome studies ().

Worldwide Patterns of Ancestry, Divergence, and Admixture in Domesticated Cattle

The domestication and development of cattle has considerably impacted human societies, but the histories of cattle breeds and populations have been poorly understood especially for African, Asian, and American breeds. Using genotypes from 43,043 autosomal single nucleotide polymorphism markers scored in 1,543 animals, we evaluate the population structure of 134 domesticated bovid breeds. Regardless of the analytical method or sample subset, the three major groups of Asian indicine, Eurasian taurine, and African taurine were consistently observed. Patterns of geographic dispersal resulting from co-migration with humans and exportation are recognizable in phylogenetic networks. All analytical methods reveal patterns of hybridization which occurred after divergence. Using 19 breeds, we map the cline of indicine introgression into Africa. We infer that African taurine possess a large portion of wild African auroch ancestry, causing their divergence from Eurasian taurine. We detect exportation patterns in Asia and identify a cline of Eurasian taurine/indicine hybridization in Asia. We also identify the influence of species other than Bos taurus taurus and B. t. indicus in the formation of Asian breeds. We detect the pronounced influence of Shorthorn cattle in the formation of European breeds. Iberian and Italian cattle possess introgression from African taurine. American Criollo cattle originate from Iberia, and not directly from Africa with African ancestry inherited via Iberian ancestors. Indicine introgression into American cattle occurred in the Americas, and not Europe. We argue that cattle migration, movement and trading followed by admixture have been important forces in shaping modern bovine genomic variation.

A QTL resource and comparison tool for pigs: PigQTLDB

During the past decade, efforts to map quantitative trait loci (QTL) in pigs have resulted in hundreds of QTL being reported for growth, meat quality, reproduction, disease resistance, and other traits. It is a challenge to locate, interpret, and compare QTL results from different studies. We have developed a pig QTL database (PigQTLdb) that integrates available pig QTL data in the public domain, thus, facilitating the use of this QTL data in future studies. We also developed a pig trait classification system to standardize names of traits and to simplify organization and searching of the trait data. These steps made it possible to compare primary data from diverse sources and methods. We used existing pig map databases and other publicly available data resources (such as PubMed) to avoid redundant developmental work. The PigQTLdb was also designed to include data representing major genes and markers associated with a large effect on economically important traits. To date, over 790 QTL from 73 publications have been curated into the database. Those QTL cover more than 300 different traits. The data have been submitted to the Entrez Gene and the Map Viewer resources at NCBI, where the information about markers was matched to marker records in NCBI’s UniSTS database. Having these data in a public resource like NCBI allows regularly updated automatic matching of markers to public sequence data by e-PCR. The submitted data, and the results of these calculations, are retrievable from NCBI via Entrez Gene, Map Viewer, and UniSTS. Efforts were undertaken to improve the integrated functional genomics resources for pigs.

Differential gene expression in the rat soleus muscle during early work overload-induced hypertrophy

Delineating the molecular mechanisms that are responsive to work overload is crucial to understanding the adaptive processes controlling skeletal muscle mass. We have examined the molecular events associated with increased workload by using microarray analysis to begin to define the mechanotransduction responsive transcription programs in skeletal muscle. Microarray analysis identified 112 mRNAs that were expressed differentially in the soleus muscle of sham‐operated vs. gastrocnemius‐ablated rats. These genes can be classified into cell proliferation, autocrine/paracrine, extracellular matrix, immune response, intracellular signaling, metabolism, neural, protein synthesis/degradation, structural, and transcription. These findings dramatically increase the number of known, differentially expressed mRNA during early skeletal muscle hypertrophy. In toto, our findings indicate that work overload induced skeletal muscle hypertrophy alters autocrine/paracrine signaling, intracellular signaling, and transcription factor expression, which likely results in a dramatic change in cellular metabolism, cell proliferation, and muscle structure. These data enhance our understanding of the complex molecular mechanisms controlling skeletal muscle mass in response to increased physical activity.

Transcriptional profiling of myostatin-knockout mice implicates Wnt signaling in postnatal skeletal muscle growth and hypertrophy

Myostatin is an inhibitor of skeletal muscle growth. Disruption of the Mstn gene in mice results in muscles that weigh two to three times those of controls, but precisely how myostatin signals to exert its effects on muscle is unclear. We used the Affymetrix GeneChip system to identify differences in gene expression between myostatin null and wild-type mice. The results indicated a switch in muscle fiber type, from slow to fast, in the absence of myostatin. They also indicated that myostatin may act upstream of Wnt pathway components. Notably, it repressed expression of Wnt4. Wnt4 was capable of stimulating satellite cell proliferation, while inhibition of Wnt signaling down-regulated satellite cell proliferation. This evidence points to a role for Wnt/calcium signaling in the growth and maintenance of postnatal skeletal muscle. This study offers new insight into potential downstream targets of myostatin, which will be beneficial for elucidation of the mechanism through which myostatin acts to inhibit muscle growth.

Development and application of bovine and porcine oligonucleotide arrays with protein-based annotation.

The design of oligonucleotide sequences for the detection of gene expression in species with disparate volumes of genome and EST sequence information has been broadly studied. However, a congruous strategy has yet to emerge to allow the design of sensitive and specific gene expression detection probes. This study explores the use of a phylogenomic approach to align transcribed sequences to vertebrate protein sequences for the detection of gene families to design genomewide 70-mer oligonucleotide probe sequences for bovine and porcine. The bovine array contains 23,580 probes that target the transcripts of 16,341 genes, about 72% of the total number of bovine genes. The porcine array contains 19,980 probes targeting 15,204 genes, about 76% of the genes in the Ensembl annotation of the pig genome. An initial experiment using the bovine array demonstrates the specificity and sensitivity of the array.

An evaluation of bovine respiratory disease complex in feedlot cattle: Impact on performance and carcass traits using treatment records and lung lesion scores.

The objective of this study was to investigate the effects of bovine respiratory disease (BRD) complex on economically important production traits with the use of health records in combination with lung lesion scores obtained at slaughter. Records from 5,976 animals were used in this study from cattle that were managed in Midwestern feedlots. Average daily gain for 3 different feeding periods (acclimation, on-test, and overall test) along with final BW were evaluated as performance measures. Hot carcass weight, LM area, subcutaneous fat cover, and marbling score were collected at slaughter. All calves were monitored by experienced feedlot personnel and treated according to the specific health protocol of each feedlot. Incidence of BRD was observed at a rate of 8.17%, and lung lesions at slaughter were present in 61.9% of cattle from a subpopulation (n = 1,665). From this group of cattle, the overall incidence of BRD, which was defined as cattle that had lung lesions, that were treated for BRD in the feedlot, or both, was 64.4%. Incidence of BRD in the feedlot decreased ADG during both the acclimation period (0.37 +/- 0.03 kg) and the overall test period (0.07 +/- 0.01 kg). Incidence of BRD also had significant effects on HCW and marbling score with reduction of 8.16 +/- 1.38 kg and 0.13 +/- 0.04, respectively, in treated cattle. The adverse effects on production traits tended to increase as the number of treatments increased. Potential decrease in performance and carcass merit observed in this study were associated with a decline of

DNA polymorphisms in bovine fatty acid synthase are associated with beef fatty acid composition.

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Evidence for a major QTL associated with host response to Porcine Reproductive and Respiratory Syndrome Virus challenge

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