Estimation of Genetic Parameters and Correlation between Yearling Ultrasound Measurements and Carcass Traits in Hanwoo Cattle.

Genetic parameters have a significant role in designing a breeding program and are required to evaluate economically important traits. The objective of this study was to estimate heritability and genetic correlation between yearling ultrasound measurements, such as backfat thickness (UBFT), eye muscle area (UEMA), intramuscular fat content (UIMF), and carcass traits, such as backfat thickness (BFT), carcass weight (CW), eye muscle area (EMA), marbling score (MS) at approximately 24 months of age, as well as yearling weight (YW) in Hanwoo bulls (15,796) and steers (5682). The (co) variance components were estimated using a multi-trait animal model. Moderate to high heritability estimates were obtained and were 0.42, 0.50, 0.56, and 0.59 for CW, EMA, BFT, and MS, respectively. Heritability estimates for yearling measurements of YW, UEMA, UBFT, and UIMF were 0.31, 0.32, 0.30, and 0.19, respectively. Favorable and strong genetic correlations were observed between UIMF and MS (0.78), UBFT and BFT (0.63), and UEMA and EMA (0.65). Moreover, the estimated genetic correlation between YW and CW was high (0.84) and relatively moderate between YW and EMA (0.43). These results suggest that genetic improvement can be achieved for carcass traits when using yearling ultrasound measurements as selection criteria in ongoing Hanwoo breeding programs.

Transcriptome analysis of the threatened snail Ellobium chinense reveals candidate genes for adaptation and identifies SSRs for conservation genetics.

Ellobium chinense (Pfeiffer, 1854) is a brackish pulmonate species that inhabits the bases of mangrove trees and is most commonly found in salt grass meadows. Threats to mangrove ecosystems due to habitat degradation and overexploitation have threatened the species with extinction. In South Korea, E. chinense has been assessed as vulnerable, but there are limited data on its population structure and distribution. The nucleotide and protein sequences for this species are not available in databases, which limits the understanding of adaptation-related traits. We sequenced an E. chinense cDNA library using the Illumina platform, and the subsequent bioinformatics analysis yielded 227,032 unigenes. Of these unigenes, 69,088 were annotated to matched protein and nucleotide sequences in databases, for an annotation rate of 30.42%. Among the predominant gene ontology terms, cellular and metabolic processes (under the biological process category), membrane and cell (under the cellular component category), and binding and catalytic activity (under the molecular function category) were noteworthy. In addition, 4850 unigenes were distributed to 15 Kyoto Encyclopaedia of Genes and Genomes based enrichment categories. Among the candidate genes related to adaptation, angiotensin I converting enzyme, adenylate cyclase activating polypeptide, and AMP-activated protein kinase were the most prominent. A total of 15,952 simple sequence repeats (SSRs) were identified in sequences of > 1 kb in length. The di- and trinucleotide repeat motifs were the most common. Among the repeat motif types, AG/CT, AC/GT, and AAC/GTT dominated. Our study provides the first comprehensive genomics dataset for E. chinense, which favors conservation programs for the restoration of the species and provides sufficient evidence for genetic variability among the wild populations.

Transcriptome Analysis of the Tadpole Shrimp (Triops longicaudatus) by Illumina Paired-End Sequencing: Assembly, Annotation, and Marker Discovery.

The tadpole shrimp (Triops longicaudatus) is an aquatic crustacean that helps control pest populations. It inhabits freshwater ponds and pools and has been described as a living fossil. T. longicaudatus was officially declared an endangered species South Korea in 2005; however, through subsequent protection and conservation management, it was removed from the endangered species list in 2012. The limited number of available genetic resources on T. longicaudatus makes it difficult to obtain valuable genetic information for marker-aided selection programs. In this study, whole-transcriptome sequencing of T. longicaudatus generated 39.74 GB of clean data and a total of 269,822 contigs using the Illumina HiSeq 2500 platform. After clustering, a total of 208,813 unigenes with an N50 length of 1089 bp were generated. A total of 95,105 unigenes were successfully annotated against Protostome (PANM), Unigene, Eukaryotic Orthologous Groups (KOG), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases using BLASTX with a cut-off of 1E-5. A total of 57,731 unigenes were assigned to GO terms, and 7247 unigenes were mapped to 129 KEGG pathways. Furthermore, 1595 simple sequence repeats (SSRs) were detected from the unigenes with 1387 potential SSR markers. This is the first report of high-throughput transcriptome analysis of T. longicaudatus, and it provides valuable insights for genetic research and molecular-assisted breeding of this important species.

Antimicrobial peptides in the centipede Scolopendra subspinipes mutilans.

The centipede Scolopendra subspinipes mutilans is an environmentally beneficial and medically important arthropod species. Although this species is increasingly applied as a reliable source of new antimicrobial peptides, the transcriptome of this species is a prerequisite for more rational selection of antimicrobial peptides. In this report, we isolated total RNA from the whole body of adult centipedes, S. subspinipes mutilans, that were nonimmunized and immunized against Escherichia coli, and we generated a total of 77,063 pooled contigs and singletons using high-throughput sequencing. To screen putative antimicrobial peptides, in silico analyses of the S. subspinipes mutilans transcriptome were performed based on the physicochemical evidence of length, charge, isoelectric point, and in vitro and in vivo aggregation scores together with the existence of continuous antimicrobial peptide stretches. Moreover, we excluded some transcripts that showed similarity with both previously known antimicrobial peptides and the human proteome, had a proteolytic cleavage site, and had downregulated expression compared with the nonimmunized sample. As a result, we selected 17 transcripts and tested their antimicrobial activity with a radial diffusion assay. Among them, ten synthetic peptides experimentally showed antimicrobial activity against microbes and no toxicity to mouse erythrocytes. Our results provide not only a useful set of antimicrobial peptide candidates and an efficient strategy for novel antimicrobial peptide development but also the transcriptome data of a big centipede as a valuable resource.

Identification and analysis of MC4R polymorphisms and their association with economic traits of Korean cattle (Hanwoo).

Signaling by the melanocortin-4 receptor (MC4R) is important for mediation the effect of leptin on food intake and energy homeostasis, and is associated with obesity, energy homeostasis and control of feeding behavior. Presently, the bovine MC4R gene was characterized to detect genetic variation at this locus and to relate it to economic traits in Korean cattle (Hanwoo). Five single nucleotide polymorphisms (SNPs) were identified in the coding region (G709A, C927T, C1069G, C1343A, and C1786T). G709A changed amino acid 166 of the MC4R protein from valine to methionine and C1069G changed amino acid 286 of the MC4R protein from leucine to valine. A SNP at C927T significantly influenced the Marbling score, SNP markers C1069G and C1343A significantly affected the Backfat thickness, and the SNP marker C1786T significantly influenced backfat and Marbling score. The MC4R gene may thus be a candidate gene for carcass traits with MC4R SNPs being potentially valuable as genetic markers for economic traits in Hanwoo.

Synthesis and characterization of biocompatible poly(organophosphazenes) aiming for local delivery of protein drugs.

Biocompatible and thermosensitive poly(organophosphazenes) with a lower critical solution temperature (LCST) below body temperature have been designed with the aim for the local delivery of peptide and protein drugs. These polymers could be synthesized by introducing short chain tri- or tetraethylene glycol as a hydrophilic group and a dipeptide, GlyGluEt2 as a hydrophobic group into the polyphosphazene backbone. The local tolerance tests using rabbits have shown that our polymers are biocompatible. Using the amphiphilic properties of these polymers, in vitro studies were performed for loading and releasing of a human growth hormone (hGH) as a model drug. The entrapment efficiency (%) of hGH by the polymer decreased as its polymer concentration increased, but exhibited high efficiency of more than 95% even at 20% hGH concentration in the polymer. The entrapped hGH has shown to be controlled releasing for 3-4 days.