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BACKGROUND The recent completion of the swine genome sequencing project and development of a high density porcine SNP array has made genome-wide association (GWA) studies feasible in pigs. METHODOLOGY/PRINCIPAL FINDINGS Using Illumina's PorcineSNP60 BeadChip, we performed a pilot GWA study in 820 commercial female pigs phenotyped for backfat, loin muscle(More)
The chicken (Gallus gallus) is an important model organism that bridges the evolutionary gap between mammals and other vertebrates. Copy number variations (CNVs) are a form of genomic structural variation widely distributed in the genome. CNV analysis has recently gained greater attention and momentum, as the identification of CNVs can contribute to a(More)
Scrotal hernia in pigs is a complex trait likely affected by genetic and environmental factors. A large-scale association analysis of positional and functional candidate genes was conducted in four previously identified genomic regions linked to hernia susceptibility on Sus scrofa chromosomes 2 and 12, as well as the fifth region around 67 cM on chromosome(More)
Peroxinectin (PX) with cell adhesion and peroxidase activities is important in invertebrate immune responses. We identified a novel PX homolog from Scylla paramamosain (designated as Sp-PX) through transcriptome sequencing. The full-length of cDNA sequence was 3,165 bp. And there was a peroxidase domain in the deduced protein sequence. A cell-adhesive(More)
Through posttranscriptional gene regulation, microRNA (miRNA) is linked to a wide variety of biological processes, including adipogenesis and lipid metabolism. Although miRNAs in mammalian adipogenesis have been worked on extensively, their study in chicken adipogenesis is still very limited. To find miRNAs potentially important for chicken preadipocyte(More)
Meiotic maturation of mammalian oocytes is a precisely orchestrated and complex process. Dimethyl sulfoxide (DMSO), a widely used solvent, drug, and cryoprotectant, is capable of disturbing asymmetric cytokinesis of oocyte meiosis in mice. However, in pigs, DMSO's effect on oocyte meiosis still remains unknown. We aimed to evaluate if DMSO treatment will(More)
In this study, the tail muscle microbiota of pacific white shrimp (Litopenaeus vannamei) sourced from five countries across Central and South America and Southeast Asia were determined and compared. The genomic DNA was sequenced at around 10 × coverage for each geographical location and was assembled de novo for comparative analysis. The assembled sequences(More)
Ordinal regression is to predict categories of ordinal scale and it has wide applications in many domains where the human evaluation plays a major role. So far several algorithms have been proposed to tackle ordinal regression problems from a machine learning perspective. However, most of these algorithms only seek one direction where the projected samples(More)
Most studies on the origin and evolution of microRNA in the human genome have been focused on its relationship with repetitive elements and segmental duplications. However, duplication events at a smaller scale (<1 kb) could also contribute to microRNA expansion, as demonstrated in this study. Using comparative genome analysis and bioinformatics methods, we(More)
Anti-lipopolysaccharide factors (ALFs) are a group of effector molecules that are classified as antimicrobial peptides (AMPs). They are found in limulids and crustaceans and show a broad range of antimicrobial activity. In the current study, an ALF gene from Macrobrachium rosenbergii (MrALF) was identified. Its full length was 690 bp and it encoded a 124(More)