SARS-CoV-2 exploits cellular RAD51 to promote viral propagation: implication of RAD51 inhibitor as a potential drug candidate against COVID-19.

IMPORTANCE: Viruses are constantly evolving to promote propagation in the host. Here, we show that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) utilizes host RAD51 for replication. Silencing of RAD51 impaired SARS-CoV-2 propagation. Viral RNA colocalized with RAD51 in the cytoplasm of SARS-CoV-2-infected cells, suggesting that both viral RNA and RAD51 may form a replication complex. We, therefore, evaluated RAD51 inhibitors as possible therapeutic agents against SARS-CoV-2. Indeed, RAD51 inhibitors exerted antiviral activities against not only Wuhan but also variants of SARS-CoV-2. Molecular docking model shows that RAD51 inhibitors impede SARS-CoV-2 propagation by interfering with dimerization of RAD51. These data suggest that RAD51 may represent a novel host-based drug target for coronavirus disease 2019 treatment.

Intrinsic expression of viperin regulates thermogenesis in adipose tissues.

Viperin is an interferon (IFN)-inducible multifunctional protein. Recent evidence from high-throughput analyses indicates that most IFN-inducible proteins, including viperin, are intrinsically expressed in specific tissues; however, the respective intrinsic functions are unknown. Here we show that the intrinsic expression of viperin regulates adipose tissue thermogenesis, which is known to counter metabolic disease and contribute to the febrile response to pathogen invasion. Viperin knockout mice exhibit increased heat production, resulting in a reduction of fat mass, improvement of high-fat diet (HFD)-induced glucose tolerance, and enhancement of cold tolerance. These thermogenic phenotypes are attributed to an adipocyte-autonomous mechanism that regulates fatty acid ß-oxidation. Under an HFD, viperin expression is increased, and its function is enhanced. Our findings reveal the intrinsic function of viperin as a novel mechanism regulating thermogenesis in adipose tissues, suggesting that viperin represents a molecular target for thermoregulation in clinical contexts.

A functional regulatory variant of MYH3 influences muscle fiber-type composition and intramuscular fat content in pigs.

Muscle development and lipid accumulation in muscle critically affect meat quality of livestock. However, the genetic factors underlying myofiber-type specification and intramuscular fat (IMF) accumulation remain to be elucidated. Using two independent intercrosses between Western commercial breeds and Korean native pigs (KNPs) and a joint linkage-linkage disequilibrium analysis, we identified a 488.1-kb region on porcine chromosome 12 that affects both reddish meat color (a*) and IMF. In this critical region, only the MYH3 gene, encoding myosin heavy chain 3, was found to be preferentially overexpressed in the skeletal muscle of KNPs. Subsequently, MYH3-transgenic mice demonstrated that this gene controls both myofiber-type specification and adipogenesis in skeletal muscle. We discovered a structural variant in the promotor/regulatory region of MYH3 for which Q allele carriers exhibited significantly higher values of a* and IMF than q allele carriers. Furthermore, chromatin immunoprecipitation and cotransfection assays showed that the structural variant in the 5'-flanking region of MYH3 abrogated the binding of the myogenic regulatory factors (MYF5, MYOD, MYOG, and MRF4). The allele distribution of MYH3 among pig populations worldwide indicated that the MYH3 Q allele is of Asian origin and likely predates domestication. In conclusion, we identified a functional regulatory sequence variant in porcine MYH3 that provides novel insights into the genetic basis of the regulation of myofiber type ratios and associated changes in IMF in pigs. The MYH3 variant can play an important role in improving pork quality in current breeding programs.

A genome-wide association study of social genetic effects in Landrace pigs.

OBJECTIVE: The genetic effects of an individual on the phenotypes of its social partners, such as its pen mates, are known as social genetic effects. This study aims to identify the candidate genes for social (pen-mates') average daily gain (ADG) in pigs by using the genome-wide association approach. METHODS: Social ADG (sADG) was the average ADG of unrelated pen-mates (strangers). We used the phenotype data (16,802 records) after correcting for batch (week), sex, pen, number of strangers (1 to 7 pigs) in the pen, full-sib rate (0% to 80%) within pen, and age at the end of the test. A total of 1,041 pigs from Landrace breeds were genotyped using the Illumina PorcineSNP60 v2 BeadChip panel, which comprised 61,565 single nucleotide polymorphism (SNP) markers. After quality control, 909 individuals and 39,837 markers remained for sADG in genome-wide association study. RESULTS: We detected five new SNPs, all on chromosome 6, which have not been associated with social ADG or other growth traits to date. One SNP was inside the prostaglandin F2α receptor (PTGFR) gene, another SNP was located 22 kb upstream of gene interferon-induced protein 44 (IFI44), and the last three SNPs were between 161 kb and 191 kb upstream of the EGF latrophilin and seven transmembrane domain-containing protein 1 (ELTD1) gene. PTGFR, IFI44, and ELTD1 were never associated with social interaction and social genetic effects in any of the previous studies. CONCLUSION: The identification of several genomic regions, and candidate genes associated with social genetic effects reported here, could contribute to a better understanding of the genetic basis of interaction traits for ADG. In conclusion, we suggest that the PTGFR, IFI44, and ELTD1 may be used as a molecular marker for sADG, although their functional effect was not defined yet. Thus, it will be of interest to execute association studies in those genes.

Lacinutrix chionocetis sp. nov., isolated from gut of a red snow crab.

A Gram-negative, aerobic, non-motile, rod-shaped bacterial strain, designated MAB-07T, was isolated from the gut of a red snow crab. The novel strain grew optimally at 20 °C, pH 7.0-8.0, and in the presence of 3% (w/v) NaCl. A phylogenetic analysis based on the 16S rRNA gene sequence indicated that the strain MAB-07T belongs to the type strains of species of the genus Lacinutrix. Strain MAB-07T exhibited 16S rRNA gene sequence similarity values of 95.5-97.8% with the type strains of species of the genus Lacinutrix. The predominant cellular fatty acids of strain MAB-07T were iso-C15:1 G (27.5%) and iso-C15:0 (21.7%). The major respiratory quinine was identified as MK-6. The polar lipids consisted of phosphatidylethanolamine, four unidentified aminolipids, and two unidentified lipids. The genomic DNA G + C content was determined to be 33.3%, and its DNA-DNA relatedness values with the type strains of L. venerupis, L. mariniflava, L. jangbogonensis, L. algicola, and Olleya aquimaris were 28-32%. Based on the data from this polyphasic taxonomic study, strain MAB-07T is considered to represent a novel species of the genus Lacinutrix, for which the name L. chionocetis sp. nov. is proposed. The type strain is MAB-07T (=KCTC 42767T = JCM 30988T).

Functional status and amount of hip displacement independently affect acetabular dysplasia in cerebral palsy.

AIM: Acetabular dysplasia is the one of main causes of hip displacement in patients with cerebral palsy (CP). Although several studies have shown a relationship between hip displacement and acetabular dysplasia, relatively few have evaluated the association between quantitative acetabular dysplasia and related factors, such as Gross Motor Function Classification System (GMFCS) level. METHOD: We performed a morphometric analysis of the acetabulum in patients with CP using multiplanar reformation of computed tomography data. The three directional acetabular indices (anterosuperior, superolateral, and posterosuperior) were used to evaluate acetabular dysplasia. Consequently, linear mixed-effects models were used to adjust for related factors such as age, sex, GMFCS level, and migration percentage. RESULTS: A total of 176 patients (mean age 9y 5mo, range 2y 4mo-19y 6mo; 104 males, 72 females) with CP and 55 typically developing individuals (mean age 13y 6mo, range 2y 5mo-19y 10mo; 37 males, 18 females) in a comparison group were enrolled in this study. Statistical modelling showed that all three directional acetabular indices independently increased with GMFCS level (p<0.001) and migration percentage (p<0.001). INTERPRETATION: Acetabular dysplasia was independently affected by both the amount of hip displacement and the GMFCS level. Thus, physicians should consider not only the migration percentage but also three-dimensional evaluation in patients at high GMFCS levels.

Association of a missense mutation in the positional candidate gene glutamate receptor-interacting protein 1 with backfat thickness traits in pigs.

OBJECTIVE: Previously, we reported quantitative trait loci (QTLs) affecting backfat thickness (BFT) traits on pig chromosome 5 (SW1482-SW963) in an F2 intercross population between Landrace and Korean native pigs. The aim of this study was to evaluate glutamate receptor-interacting protein 1 (GRIP1) as a positional candidate gene underlying the QTL affecting BFT traits. METHODS: Genotype and phenotype analyses were performed using the 1,105 F2 progeny. A mixed-effect linear model was used to access association between these single nucleotide polymorphism (SNP) markers and the BFT traits in the F2 intercross population. RESULTS: Highly significant associations of two informative SNPs (c.2442 T>C, c.3316 C>G [R1106G]) in GRIP1 with BFT traits were detected. In addition, the two SNPs were used to construct haplotypes that were also highly associated with the BFT traits. CONCLUSION: The SNPs and haplotypes of the GRIP1 gene determined in this study can contribute to understand the genetic structure of BFT traits in pigs.

Genome scan linkage analysis identifies a major quantitative trait loci for fatty acid composition in longissimus dorsi muscle in an F2 intercross between Landrace and Korean native pigs.

OBJECTIVE: This study was conducted to locate quantitative trait loci (QTL) influencing fatty acid (FA) composition in a large F2 intercross between Landrace and Korean native pigs. METHODS: Eighteen FA composition traits were measured in more than 960 F2 progeny. All experimental animals were genotyped with 165 microsatellite markers located throughout the pig autosomes. RESULTS: We detected 112 QTLs for the FA composition; Forty seven QTLs reached the genome-wide significant threshold. In particular, we identified a cluster of highly significant QTLs for FA composition on SSC12. QTL for polyunsaturated fatty acid on pig chromosome 12 (F-value = 97.2 under additive and dominance model, nominal p-value 3.6×10-39) accounted for 16.9% of phenotypic variance. In addition, four more QTLs for C18:1, C18:2, C20:4, and monounsaturated fatty acids on the similar position explained more than 10% of phenotypic variance. CONCLUSION: Our findings of a major QTL for FA composition presented here could provide helpful information to locate causative variants to improve meat quality traits in pigs.

Transcriptome sequencing and de novo characterization of Korean endemic land snail, Koreanohadra kurodana for functional transcripts and SSR markers.

The Korean endemic land snail Koreanohadra kurodana (Gastropoda: Bradybaenidae) found in humid areas of broadleaf forests and shrubs have been considered vulnerable as the number of individuals are declining in recent years. The species is poorly characterized at the genomic level that limits the understanding of functions at the molecular and genetics level. In the present study, we performed de novo transcriptome sequencing to produce a comprehensive transcript dataset of visceral mass tissue of K. kurodana by the Illumina paired-end sequencing technology. Over 234 million quality reads were assembled to a total of 315,924 contigs and 191,071 unigenes, with an average and N50 length of 585.6 and 715 bp and 678 and 927 bp, respectively. Overall, 36.32 % of the unigenes found matches to known protein/nucleotide sequences in the public databases. The direction of the unigenes to functional categories was determined using COG, GO, KEGG, and InterProScan protein domain search. The GO analysis search resulted in 22,967 unigenes (12.02 %) being categorized into 40 functional groups. The KEGG annotation revealed that metabolism pathway genes were enriched. The most prominent protein motifs include the zinc finger, ribonuclease H, reverse transcriptase, and ankyrin repeat domains. The simple sequence repeats (SSRs) identified from >1 kb length of unigenes show a dominancy of dinucleotide repeat motifs followed with tri- and tetranucleotide motifs. A number of unigenes were putatively assessed to belong to adaptation and defense mechanisms including heat shock proteins 70, Toll-like receptor 4, AMP-activated protein kinase, aquaporin-2, etc. Our data provide a rich source for the identification and functional characterization of new genes and candidate polymorphic SSR markers in K. kurodana. The availability of transcriptome information ( http://bioinfo.sch.ac.kr/submission/ ) would promote the utilization of the resources for phylogenetics study and genetic diversity assessment.

Energy Budget of Liquid Drop Impact at Maximum Spreading: Numerical Simulations and Experiments.

The maximum spreading of an impinging droplet on a rigid surface is studied for low to high impact velocity, until the droplet starts splashing. We investigate experimentally and numerically the role of liquid properties, such as surface tension and viscosity, on drop impact using three liquids. It is found that the use of the experimental dynamic contact angle at maximum spreading in the Kistler model, which is used as a boundary condition for the CFD-VOF calculation, gives good agreement between experimental and numerical results. Analytical models commonly used to predict the boundary layer thickness and time at maximum spreading are found to be less correct, meaning that energy balance models relying on these relations have to be considered with care. The time of maximum spreading is found to depend on both the impact velocity and surface tension, and neither dependency is predicted correctly in common analytical models. The relative proportion of the viscous dissipation in the total energy budget increases with impact velocity with respect to surface energy. At high impact velocity, the contribution of surface energy, even before splashing, is still substantial, meaning that both surface energy and viscous dissipation have to be taken into account, and scaling laws depending only on viscous dissipation do not apply. At low impact velocity, viscous dissipation seems to play an important role in low-surface-tension liquids such as ethanol.

Modeling the Maximum Spreading of Liquid Droplets Impacting Wetting and Nonwetting Surfaces.

Droplet impact has been imaged on different rigid, smooth, and rough substrates for three liquids with different viscosity and surface tension, with special attention to the lower impact velocity range. Of all studied parameters, only surface tension and viscosity, thus the liquid properties, clearly play a role in terms of the attained maximum spreading ratio of the impacting droplet. Surface roughness and type of surface (steel, aluminum, and parafilm) slightly affect the dynamic wettability and maximum spreading at low impact velocity. The dynamic contact angle at maximum spreading has been identified to properly characterize this dynamic spreading process, especially at low impact velocity where dynamic wetting plays an important role. The dynamic contact angle is found to be generally higher than the equilibrium contact angle, showing that statically wetting surfaces can become less wetting or even nonwetting under dynamic droplet impact. An improved energy balance model for maximum spreading ratio is proposed based on a correct analytical modeling of the time at maximum spreading, which determines the viscous dissipation. Experiments show that the time at maximum spreading decreases with impact velocity depending on the surface tension of the liquid, and a scaling with maximum spreading diameter and surface tension is proposed. A second improvement is based on the use of the dynamic contact angle at maximum spreading, instead of quasi-static contact angles, to describe the dynamic wetting process at low impact velocity. This improved model showed good agreement compared to experiments for the maximum spreading ratio versus impact velocity for different liquids, and a better prediction compared to other models in literature. In particular, scaling according to We(1/2) is found invalid for low velocities, since the curves bend over to higher maximum spreading ratios due to the dynamic wetting process.

Water Touch-and-Bounce from a Soft Viscoelastic Substrate: Wetting, Dewetting, and Rebound on Bitumen.

Understanding the interaction between liquids and deformable solid surfaces is a fascinating fundamental problem, in which interaction and coupling of capillary and viscoelastic effects, due to solid substrate deformation, give rise to complex wetting mechanisms. Here we investigated as a model case the behavior of water drops on two smooth bitumen substrates with different rheological properties, defined as hard and soft (with complex shear moduli in the order of 10(7) and 10(5) Pa, respectively, at 1 Hz), focusing both on wetting and on dewetting behavior. By means of classical quasi-static contact angle measurements and drop impact tests, we show that the water drop behavior can significantly change from the quasi-static to the dynamic regime on soft viscoelastic surfaces, with the transition being defined by the substrate rheological properties. As a result, we also show that on the hard substrate, where the elastic response is dominant under all investigated conditions, classical quasi-static contact angle measurements provide consistent results that can be used to predict the drop dynamic wetting behavior, such as drop deposition or rebound after impact, as typically observed for nondeformable substrates. Differently, on soft surfaces, the formation of wetting ridges did not allow to define uniquely the substrate intrinsic advancing and receding contact angles. In addition, despite showing a high adhesion to the soft surface in quasi-static measurements, the drop was surprisingly able to rebound and escape from the surface after impact, as it is typically observed for hydrophobic surfaces. These results highlight that measurements of wetting properties for viscoelastic substrates need to be critically used and that wetting behavior of a liquid on viscoelastic surfaces is a function of the characteristic time scales.

De novo Transcriptome Generation and Annotation for Two Korean Endemic Land Snails, Aegista chejuensis and Aegista quelpartensis, Using Illumina Paired-End Sequencing Technology.

Aegista chejuensis and Aegista quelpartensis (Family-Bradybaenidae) are endemic to Korea, and are considered vulnerable due to declines in their population. The limited genetic resources for these species restricts the ability to prioritize conservation efforts. We sequenced the transcriptomes of these species using Illumina paired-end technology. Approximately 257 and 240 million reads were obtained and assembled into 198,531 and 230,497 unigenes for A. chejuensis and A. quelpartensis, respectively. The average and N50 unigene lengths were 735.4 and 1073 bp, respectively, for A. chejuensis, and 705.6 and 1001 bp, respectively, for A. quelpartensis. In total, 68,484 (34.5%) and 77,745 (33.73%) unigenes for A. chejuensis and A. quelpartensis, respectively, were annotated to databases. Gene Ontology terms were assigned to 23,778 (11.98%) and 26,396 (11.45) unigenes, for A. chejuensis and A. quelpartensis, respectively, while 5050 and 5838 unigenes were mapped to 117 and 124 pathways in the Kyoto Encyclopedia of Genes and Genomes database. In addition, we identified and annotated 9542 and 10,395 putative simple sequence repeats (SSRs) in unigenes from A. chejuensis and A. quelpartensis, respectively. We designed a list of PCR primers flanking the putative SSR regions. These microsatellites may be utilized for future phylogenetics and conservation initiatives.

Association of the Single Nucleotide Polymorphisms in RUNX1, DYRK1A, and KCNJ15 with Blood Related Traits in Pigs.

The aim of this study was to detect positional candidate genes located within the support interval (SI) regions based on the results of red blood cell, mean corpuscular volume (MCV), and mean corpuscular hemoglobin quantitative trait locus (QTL) in Sus scrofa chromosome 13, and to verify the correlation between specific single-nucleotide polymorphisms (SNPs) located in the exonic region of the positional candidate gene and the three genetic traits. The flanking markers of the three QTL SI regions are SW38 and S0215. Within the QTL SI regions, 44 genes were located, and runt-related transcription factor 1, dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A (DYRK1A), and potassium inwardly-rectifying channel, subfamily J, member 15 KCNJ15-which are reported to be related to the hematological traits and clinical features of Down syndrome-were selected as positional candidate genes. The ten SNPs located in the exonic region of the three genes were detected by next generation sequencing. A total of 1,232 pigs of an F2 resource population between Landrace and Korean native pigs were genotyped. To investigate the effects of the three genes on each genotype, a mixed-effect model which is the considering family structure model was used to evaluate the associations between the SNPs and three genetic traits in the F2 intercross population. Among them, the MCV level was highly significant (nominal p = 9.8×10-9) in association with the DYRK1A-SNP1 (c.2989 G

Jejuia marina nov., isolated from gravel adjacent to Geommeolle beach on Udo Island, South Korea.

A bacterial strain, JH03(T), was isolated from gravel adjacent to Geommeolle beach on Udo Island, South Korea. The cells were Gram-stain-negative, aerobic, non-motile and rod shaped. The ranges of temperature, pH and NaCl concentration for growth of the bacterium were 10-45 °C, pH 6.0-9.5 and 0.5-5.0 % (w/v), respectively. The major fatty acids of the bacterium were iso-C(15:0) (15.4 %), iso-C(15:1) G (14.1 %), iso-C(16:0) 3-OH (14.1 %), iso-C(17:0) 3-OH (11.5 %) and anteiso-C(15:0) (11.3 %). The major isoprenoid quinone was MK-6. The polar lipids included phosphatidylethanolamine, two unidentified amino lipids and three unidentified lipids. The DNA G+C content was 34.2 mol%. The phylogenetic analysis of the 16S rRNA gene sequences showed that strain JH03(T) was most closely related to Jejuia pallidilutea EM39(T) (96.5 % sequence similarity). Based on the polyphasic analysis, strain JH03(T) is a novel species of the genus Jejuia, for which the name Jejuia marina sp. nov. is proposed. The type strain is JH03(T) (= KCTC 42342(T) = JCM 30601(T)).

Genome-wide QTL analysis of meat quality-related traits in a large F2 intercross between Landrace and Korean native pigs.

BACKGROUND: We conducted a genome-wide linkage analysis to identify quantitative trait loci (QTL) that influence meat quality-related traits in a large F2 intercross between Landrace and Korean native pigs. Thirteen meat quality-related traits of the m. longissimus lumborum et thoracis were measured in more than 830 F2 progeny. All these animals were genotyped with 173 microsatellite markers located throughout the pig genome, and the GridQTL program based on the least squares regression model was used to perform the QTL analysis. RESULTS: We identified 23 genome-wide significant QTL in eight chromosome regions (SSC1, 2, 6, 7, 9, 12, 13, and 16) (SSC for Sus Scrofa) and detected 51 suggestive QTL in the 17 chromosome regions. QTL that affect 10 meat quality traits were detected on SSC12 and were highly significant at the genome-wide level. In particular, the QTL with the largest effect affected crude fat percentage and explained 22.5% of the phenotypic variance (F-ratio = 278.0 under the additive model, nominal P = 5.5 × 10(-55)). Interestingly, the QTL on SSC12 that influenced meat quality traits showed an obvious trend for co-localization. CONCLUSIONS: Our results confirm several previously reported QTL. In addition, we identified novel QTL for meat quality traits, which together with the associated positional candidate genes improve the knowledge on the genetic structure that underlies genetic variation for meat quality traits in pigs.

Hyunsoonleella udoensis sp. nov., isolated from a gravel sample from a beach of Udo island, Korea.

A Gram-stain negative, non-motile, rod-shaped and aerobic bacterial strain, designated JG48(T), was isolated from a gravel sample taken from a beach adjacent to Udo island, South Korea. Strain JG48(T) was found to grow optimally at 25 °C, at pH 7.0-8.0 and in the presence of 2.0 % (w/v) NaCl. The 16S rRNA gene sequence of strain JG48(T) exhibited sequence similarities of 96.67 % to Hyunsoonleella jejuensis CNU004(T). The major fatty acids present in the strain JG48(T) were identified as iso-C15:0, iso-C15:1 G, iso-C17:0 3-OH and iso-C15:0 3-OH. The predominant isoprenoid quinone was identified as MK-6. The polar lipids profile of strain JG48(T) was found to consist of phosphatidylethanolamine, three unidentified amino lipids and four unidentified lipids. The DNA G+C content of strain JG48(T) was determined to be 34 mol%. Based on the morphological and physiological properties, and the results of phylogenetic analyses, the strain is considered to represent a novel species of the genus Hyunsoonleella, for which the name Hyunsoonleella udoensis sp. nov. is proposed. The type strain is JG48(T) (=KCTC 42341(T)=JCM 30600(T)).

Transcriptome Characterization for Non-Model Endangered Lycaenids, Protantigius superans and Spindasis takanosis, Using Illumina HiSeq 2500 Sequencing.

The Lycaenidae butterflies, Protantigius superans and Spindasis takanosis, are endangered insects in Korea known for their symbiotic association with ants. However, necessary genomic and transcriptomics data are lacking in these species, limiting conservation efforts. In this study, the P. superans and S. takanosis transcriptomes were deciphered using Illumina HiSeq 2500 sequencing. The P. superans and S. takanosis transcriptome data included a total of 254,340,693 and 245,110,582 clean reads assembled into 159,074 and 170,449 contigs and 107,950 and 121,140 unigenes, respectively. BLASTX hits (E-value of 1.0 × 10(-5)) against the known protein databases annotated a total of 46,754 and 51,908 transcripts for P. superans and S. takanosis. Approximately 41.25% and 38.68% of the unigenes for P. superans and S. takanosis found homologous sequences in Protostome DB (PANM-DB). BLAST2GO analysis confirmed 18,611 unigenes representing Gene Ontology (GO) terms and a total of 5259 unigenes assigned to 116 pathways for P. superans. For S. takanosis, a total of 6697 unigenes were assigned to 119 pathways using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database. Additionally, 382,164 and 390,516 Simple Sequence Repeats (SSRs) were compiled from the unigenes of P. superans and S. takanosis, respectively. This is the first report to record new genes and their utilization for conservation of lycaenid species population and as a reference information for closely related species.

Genome-wide association analysis to identify SNP markers affecting teat numbers in an F2 intercross population between Landrace and Korean native pigs.

Most reproductive traits have low heritability and are greatly affected by environmental factors. Teat number and litter size are traits related to the reproduction ability of pigs. To identify quantitative trait loci (QTLs) for teat number traits, a genome-wide association study (GWAS) was conducted using an F2 intercross between Landrace and Korean native pigs. Genotype analysis was performed using the porcine SNP 60 K beadchip. The GWAS was performed using a mixed-effects model and linear regression approach. When a genome-wide threshold was determined using the Bonferroni method (P = 1.61 × 10(-6)), 38 single nucleotide polymorphism (SNP) markers in pig chromosome 7 (SSC7) were significantly associated with three teat number traits (total teat number, left teat number, and right teat number). Among these, SNPs in 5 genes (HDDC3, LOC100156276, LOC100155863, ANPEP, SCAMP2) were selected for further study based primarily on their statistical significance. A significant association was detected in SCAMP2 g.25280 G>A for total teat number (P = 2.0 × 10(-12)), HDDC3 g.1319 G>A SNP for left teat number (P = 2.3 × 10(-7)), and SCAMP2 g.14198 G>A for right teat number (P = 4.7 × 10(-12)). These results provide valuable information about the selective breeding for desirable teat numbers in pigs.

Pseudoruegeria limi sp. nov. isolated from mud flats in the Yellow Sea in Korea.

A Gram-negative, aerobic, non-motile and rod-shaped bacterial strain, D-17(T), was isolated from mud flats in the Yellow Sea in Korea. Phylogenetic trees based on the 16S rRNA gene sequence showed that strain D-17(T) belongs to the genus Pseudoruegeria and it shared 97.5 % similarity with the type strain of Pseudoruegeria haliotis WM67(T). The sequence similarities with Pseudoruegeria litimaris HD-43(T) and Pseudoruegeria aquimaris SW-255(T) were 96.9 and 96.1 %, respectively. Strain D-17(T) was found to grow with 0.5-6 % (w/v) NaCl, at 20-30 °C, and at pH 6.5-8.0. Strain D-17(T) was determined to contain Q-10 as the predominant ubiquinone and summed feature 8 (C18:1 ω7c and/or C18:1 ω6c, as defined by the MIDI system) as the major fatty acids. The major polar lipids were identified as phosphatidylglycerol, diphosphatidylglycerol, an unidentified aminolipid, an unidentified glycolipid, an unidentified lipid and four unidentified phospholipids. The DNA G+C content was determined to be 63.6 mol%. The DNA-DNA relatedness with P. haliotis WM67(T) was 32.5 %. The differential phenotypic properties revealed that strain D-17(T) can be separated from other Pseudoruegeria species. Based on the data presented in this study, strain D-17(T) represents a novel species, for which the name Pseudoruegeria limi sp. nov. is proposed. The type strain is D-17(T) (=KCTC 32460(T) =JCM 19487(T)).