A Genome-wide Scan for Selective Sweeps in Racing Horses.

Using next-generation sequencing, we conducted a genome-wide scan of selective sweeps associated with selection toward genetic improvement in Thoroughbreds. We investigated potential phenotypic consequence of putative candidate loci by candidate gene association mapping for the finishing time in 240 Thoroughbred horses. We found a significant association with the trait for Ral GApase alpha 2 (RALGAP2) that regulates a variety of cellular processes of signal trafficking. Neighboring genes around RALGAP2 included insulinoma-associated 1 (INSM1), pallid (PLDN), and Ras and Rab interactor 2 (RIN2) genes have similar roles in signal trafficking, suggesting that a co-evolving gene cluster located on the chromosome 22 is under strong artificial selection in racehorses.

Comparative transcriptomic analysis to identify differentially expressed genes in fat tissue of adult Berkshire and Jeju Native Pig using RNA-seq.

Pork is a major source of animal protein for humans. The subcutaneous, intermuscular and the intramuscular fat are the factors responsible for meat quality. RNA-seq is rapidly adopted for the profiling of the transcriptomes in the studies related to gene regulation. The discovery of differentially expressed genes (DEGs) between adult animals of Jeju Native Pig (JNP) and Berkshire breeds are of particular interest for the current study. RNA-seq was used to investigate the transcriptome profiling in the fat tissue. Sequence reads were obtained from Ilumina HiSeq2000 and mapped to the pig genome using Tophat2. Total 153 DEGs were identified and 71 among the annotated genes, have BLAST matches in the non- redundant database. Metabolic, immune response and protein binding are enriched pathways in the fat tissue. In our study, biological adhesion, cellular, developmental and multicellular organismal processes in fat were up-regulated in JNP as compare to Berkshire. Multicellular organismal process, developmental process, embryonic morphogenesis and skeletal system development were the most significantly enriched terms in fat of JNP and Berkshire breeds (p = 1.17E-04, 0.044, 3.47E-04 and 4.48E-04 respectively). COL10A1, COL11A2, PDK4 and PNPLA3 genes responsible for skeletal system morphogenesis and body growth were down regulated in JNP. This study is the first statistical analysis for the detection of DEGs from RNA-seq data generated from fat tissue sample. This analysis can be used as stepping stone to understand the difference in the genetic mechanisms that might influence the identification of novel transcripts, sequence polymorphisms, isoforms and noncoding RNAs.

Intra-arterial contrast enhanced computed tomography of the deep digital flexor tendon and palmar veins in the distal forelimb in Jeju horses: Evaluating contrast-enhancing factors.

BACKGROUND: Few studies have investigated the adequate contrast enhancement (CE) evaluation depending on concentration, volume, and rate of administration of contrast media (CM) and the scan parameters in equine contrast enhanced computed tomography (CECT). OBJECTIVES: To investigate CE of the deep digital flexor tendon (DDFT) and veins depending on the computed tomography (CT) voltage and concentration, volume, and rate of CM administration during intra-arterial CECT of equine distal forelimbs. STUDY DESIGN: In vivo experiments. METHODS: Six horses underwent 54 CT scans. First, the CE of DDFT and veins was evaluated depending on the voltage (80 kV and 250 mA or 120 kV and 150 mA) and CM concentration (150, 120, or 90 mg I/mL in 50 mL of CM). Second, CE of DDFT and veins was evaluated depending on the CM volume (50, 100, or 150 mL) and administration rate (2, 4, or 6 mL/s) with a fixed iodine delivery rate (IDR; 300 or 180 mg I/s). RESULTS: Contrast enhancement of DDFT was significantly higher at 80 kV of voltage and 150 mg I/mL of CM concentration (Median: 29.65; IQR: 1.74; p < 0.05). CE of the DDFT positively correlated with CM concentration (p < 0.001; r = 0.75). At 180 mg I/s IDR, contrast attenuation in the medial and lateral palmar veins significantly decreased at a CM of 30 mg I/mL, rate of 6 mL/s, and volume of 150 mL (median and IQR: 985.93 and 71.8 Hounsfield units [HU] and 988.73 and 41.16 HU, respectively); the CE was sufficient to distinguish between the vessels and the adjacent structures. MAIN LIMITATIONS: The number of animals was small. CONCLUSIONS: Our results suggest that a low CM concentration could yield sufficient CE of the DDFT and arteries with adjusted CT scanning parameters or volume and injection rate of CM.

Computed tomographic dimensions and densities of the normal eye in Jeju horses.

This study aimed to describe the computed tomographic (CT) dimensions and the contrast attenuation of the eye in Jeju horses and Thoroughbreds. We evaluated the CT images of 10 Jeju horses and 6 Thoroughbreds without ocular abnormalities to assess the ocular dimensions and contrast attenuation. The following measurements showed significant differences between Jeju horses and Thoroughbreds (P<0.05): the diameters of the lens, globe, posterior segment, orbital fossa, and lateromedial distance of the anterior chamber; and the Hounsfield units of the vitreous body. This study describes the CT anatomical characteristics of Jeju horses and Thoroughbreds and the differences between the two breeds and provides useful information for understanding and evaluating of the eyes of Jeju horses through a CT scan.

Porcine SPP1 gene polymorphism association with phenotypic traits in the Landrace × Jeju (Korea) Black pig F2 population.

This study examined polymorphisms of the secreted phosphoprotein 1 (SPP1) gene and its association with growth and carcass traits in the F(2) population of the crossbred Landrace × Jeju (Korea) Black pig. The authors detected the presence/absence polymorphisms of short interspersed nuclear element in the SPP1 intron 6 of the population; they then designated the longer fragment as allele A and the shorter one as allele B. The SPP1 A/B heterozygous pigs evidenced significantly heavier body weight at birth and on days 21 and 70, and a higher level of average daily gain during the early developmental period than was seen in the A/A and B/B homozygous pigs (P < 0.05). Further, the SPP1 A/B heterozygous pigs evidenced significantly greater body length, less backfat thickness measured at three different sites, and larger loin muscle area than the homozygotes (P < 0.05). On the other hand, the levels of late average daily gain, 140th-day body weight, and marbling score were not significantly associated (P > 0.05). The results of this study reveal faster growth rate and differences in pig productivity according to genotypes of the SPP1 gene. These findings demonstrate that SPP1 genotypes may effectively function as molecular genetic markers for the improvement of Jeju Black pig-related crossbreeding systems.

Computed tomographic features of the temporomandibular joint in 10 Jeju horses.

BACKGROUND: The equine temporomandibular joint (TMJ) has a complex anatomical structure that makes diagnosis of TMJ disorders difficult. Computed tomography (CT) is now available in equine medicine; hence, TMJ evaluation has become more convenient. OBJECTIVES: The objectives of this study were to describe the CT features of the TMJ in Jeju horses and to compare these features with those of Thoroughbreds. METHODS: In this report, the TMJs of 10 Jeju horses (mean age: 4.5 ± 1.9 yr; mean body weight: 282.6 ± 40.3 kg) and 6 Thoroughbreds (mean age: 7.3 ± 1.6 yr; mean body weight: 479.7 ± 44.0 kg) were examined using CT. After CT scanning, the Hounsfield units (HU) and height to width ratio (H:W) of the mandibular condyle were measured. RESULTS: The mean H:W in Jeju horses was significantly lower than that in Thoroughbreds. The mean HU in Jeju horses was lower than that in Thoroughbreds; however, the difference was not significant. The most frequent CT finding was an irregular medial margin of the mandibular condyle in both breeds. CONCLUSIONS: In this study, the shape of the mandibular condyle in Jeju horses was flatter than that in Thoroughbreds. This report could be useful in evaluating the TMJ in Jeju horses. Moreover, CT could be a pragmatic choice for the examination of the TMJ in horses.

SINE indel polymorphism of AGL gene and association with growth and carcass traits in Landrace x Jeju Black pig F(2) population.

Genetic polymorphisms in the glycogen debrancher enzyme (AGL) gene were assessed with regard to their association with growth and carcass traits in the F(2) population crossbred Landrace and Jeju (Korea) Black pig. Three genotypes representing the insertion and/or deletion (indel) polymorphisms of short interspersed nuclear element were detected at frequencies of 0.278 (L/L), 0.479 (L/S), and 0.243 (S/S), respectively. The AGL S allele-containing pigs evidenced significantly heavier body weights at birth, the 3rd week, 10th week, and 20th week during developmental stages and higher average daily gains during the late period than were noted in the L/L homozygous pigs (P < 0.05), respectively. However, average daily gains during the early period were not significantly associated with genotype distribution (P > 0.05). With regard to the carcass traits, the S allele pigs (S/-) evidenced significantly heavier carcass weights and thicker backfat than was measured in L/L homozygous pigs (P < 0.05). However, body lengths, meat color, and marbling scores were all found not to be statistically significant (P > 0.05). Consequently, the faster growth rate during the late period and backfat deposition rather than intramuscular fat deposition cause differences in pig productivity according to genotypes of the AGL gene. These findings indicate that the AGL genotypes may prove to be useful genetic markers for the improvement of Jeju Black pig-related crossbreeding systems.