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BACKGROUND: Many studies have been performed to identify various genomic loci and genes associated with the meat quality in pigs. However, the full genetic architecture of the trait still remains unclear in part because of the lack of accurate identification of related structural variations (SVs) which resulted from the shortage of target breeds, the limitations of sequencing data, and the incompleteness of genome assemblies. The recent generation of a new pig breed with superior meat quality, called Nanchukmacdon, and its chromosome-level genome assembly (the NCMD assembly) has provided new opportunities. RESULTS: By applying assembly-based SV calling approaches to various genome assemblies of pigs including Nanchukmacdon, the impact of SVs on meat quality was investigated. Especially, by checking the commonality of SVs with other pig breeds, a total of 13,819 Nanchukmacdon-specific SVs (NSVs) were identified, which have a potential effect on the unique meat quality of Nanchukmacdon. The regulatory potentials of NSVs for the expression of nearby genes were further examined using transcriptome- and epigenome-based analyses in different tissues. CONCLUSIONS: Whole-genome comparisons based on chromosome-level genome assemblies have led to the discovery of SVs affecting meat quality in pigs, and their regulatory potentials were analyzed. The identified NSVs will provide new insights regarding genetic architectures underlying the meat quality in pigs. Finally, this study confirms the utility of chromosome-level genome assemblies and multi-omics analysis to enhance the understanding of unique phenotypes.
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Genoma , Genômica , Suínos/genética , Animais , Carne/análise , Fenótipo , CromossomosRESUMO
Photoactivated gas sensors that are fully integrated with micro light-emitting diodes (µLED) have shown great potential to substitute conventional micro/nano-electromechanical (M/NEMS) gas sensors owing to their low power consumption, high mechanical stability, and mass-producibility. Previous photoactivated gas sensors mostly have utilized ultra-violet (UV) light (250-400 nm) for activating high-bandgap metal oxides, although energy conversion efficiencies of gallium nitride (GaN) LEDs are maximized in the blue range (430-470 nm). This study presents a more advanced monolithic photoactivated gas sensor based on a nanowatt-level, ultra-low-power blue (λpeak = 435 nm) µLED platform (µLP). To promote the blue light absorbance of the sensing material, plasmonic silver (Ag) nanoparticles (NPs) are uniformly coated on porous indium oxide (In2 O3 ) thin films. By the plasmonic effect, Ag NPs absorb the blue light and spontaneously transfer excited hot electrons to the surface of In2 O3 . Consequently, high external quantum efficiency (EQE, ≈17.3%) and sensor response (ΔR/R0 (%) = 1319%) to 1 ppm NO2 gas can be achieved with a small power consumption of 63 nW. Therefore, it is highly expected to realize various practical applications of mobile gas sensors such as personal environmental monitoring devices, smart factories, farms, and home appliances.
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Developing high response hydrogen sensors manufacturable in a large scale is desirable in hydrogen industry. In this study, a chromium oxidation-based nanogap formation process was developed to fabricate a hydrogen switch with suspended palladium and gold films having a tens of nanometer-sized gap. The nanogap was formed by using oxidized chromium as a self-alignment shadow mask. The hydrogen switch operates by the principle of volume expansion of palladium upon exposure to the hydrogen gas and the current reading by closing of a nanogap formed between suspended palladium and gold films. Further improvement of the sensor performance was achieved by optimizing the design parameters such as suspended film lengths and thicknesses. The fabricated palladium nanogap hydrogen sensor showed an ultrahigh sensitivity of ΔI/I0 > 108 with a fast response time (22 s) to 4% hydrogen. The complementary metal-oxide-semiconductor-compatible fabrication of the hydrogen switch is easily scalable with low manufacturing cost.
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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.
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Adipogenia/genética , Proteínas do Citoesqueleto/genética , Fibras Musculares Esqueléticas/metabolismo , Músculo Esquelético/crescimento & desenvolvimento , Miosinas/genética , Tecido Adiposo/crescimento & desenvolvimento , Tecido Adiposo/metabolismo , Animais , Cruzamento , Regulação da Expressão Gênica , Estudo de Associação Genômica Ampla , Genótipo , Carne , Camundongos , Camundongos Transgênicos , Músculo Esquelético/metabolismo , Cadeias Pesadas de Miosina/genética , Motivos de Nucleotídeos , Sus scrofa/genética , Sus scrofa/metabolismo , SuínosRESUMO
BACKGROUND: DNA methylation and demethylation at CpG islands is one of the main regulatory factors that allow cells to respond to different stimuli. These regulatory mechanisms help in developing tissue without affecting the genomic composition or undergoing selection. Liver and backfat play important roles in regulating lipid metabolism and control various pathways involved in reproductive performance, meat quality, and immunity. Genes inside these tissue store a plethora of information and an understanding of these genes is required to enhance tissue characteristics in the future generation. RESULTS: A total of 16 CpG islands were identified, and they were involved in differentially methylation regions (DMRs) as well as differentially expressed genes (DEGs) of liver and backfat tissue samples. The genes C7orf50, ACTB and MLC1 in backfat and TNNT3, SIX2, SDK1, CLSTN3, LTBP4, CFAP74, SLC22A23, FOXC1, GMDS, GSC, GATA4, SEMA5A and HOXA5 in the liver, were categorized as differentially-methylated. Subsequently, Motif analysis for DMRs was performed to understand the role of the methylated motif for tissue-specific differentiation. Gene ontology studies revealed association with collagen fibril organization, the Bone Morphogenetic Proteins (BMP) signaling pathway in backfat and cholesterol biosynthesis, bile acid and bile salt transport, and immunity-related pathways in methylated genes expressed in the liver. CONCLUSIONS: In this study, to understand the role of genes in the differentiation process, we have performed whole-genome bisulfite sequencing (WGBS) and RNA-seq analysis of Nanchukmacdon pigs. Methylation and motif analysis reveals the critical role of CpG islands and transcriptional factors binding site (TFBS) in guiding the differential patterns. Our findings could help in understanding how methylation of certain genes plays an important role and can be used as biomarkers to study tissue specific characteristics.
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Metilação de DNA , Genoma , Animais , Ilhas de CpG , Fígado/metabolismo , RNA-Seq , Suínos/genéticaRESUMO
OBJECTIVE: We tried to analyze allele-specific expression in the pig neocortex using bioinformatic analysis of high-throughput sequencing results from the parental genomes and offspring transcriptomes from reciprocal crosses between Korean Native and Landrace pigs. METHODS: We carried out sequencing of parental genomes and offspring transcriptomes using next generation sequencing. We subsequently carried out genome scale identification of SNPs in two different ways using either individual genome mapping or joint genome mapping of the same breed parents that were used for the reciprocal crosses. Using parent-specific SNPs, allele-specifically expressed genes were analyzed. RESULTS: Because of the low genome coverage (~4x) of the sequencing results, most SNPs were non-informative for parental lineage determination of the expressed alleles in the offspring and were thus excluded from our analysis. Consequently, 436 SNPs covering 336 genes were applicable to measure the imbalanced expression of paternal alleles in the offspring. By calculating the read ratios of parental alleles in the offspring, we identified seven genes showing allele-biased expression (P < 0.05) including three previously reported and four newly identified genes in this study. CONCLUSION: The newly identified allele-specifically expressing genes in the neocortex of pigs should contribute to improving our knowledge on genomic imprinting in pigs. To our knowledge, this is the first study of allelic imbalance using high throughput analysis of both parental genomes and offspring transcriptomes of the reciprocal cross in outbred animals. Our study also showed the effect of the number of informative animals on the genome level investigation of allele-specific expression using RNA-seq analysis in livestock species.
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We report ZnO nanowire- and TiO2 nanotube-based light sensors on flexible polymer substrates fabricated by localized hydrothermal synthesis and liquid phase deposition (LPD). This method realized simple and cost-effective in situ synthesis and integration of one-dimensional ZnO and TiO2 nanomaterials. The fabricated sensor devices with ZnO nanowires and TiO2 nanotubes show very high sensitivity and quick response to the ultraviolet (UV) and ambient light, respectively. In addition, our direct synthesis and integration method result in mechanical robustness under external loading such as static and cyclic bending because of the strong bonding between the nanomaterial and the electrode. By controlling the reaction time of the LPD process, the Ti/Zn ratio could be simply modulated and the spectral sensitivity to the light in the UV to visible range could be controlled.
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Myosin heavy chain (MyHC) isoforms consist of Myh7, Myh2, Myh1, and Myh4, which are expressed in skeletal muscle tissues during postnatal development. These genes influence the contractionâ»relaxation activity in skeletal muscles and are involved in determining muscle composition such as the proportion of fast-to-slow and/or slow-to-fast fiber types. Among them, Myh1 is associated with skeletal muscle contraction and is involved in both slow-to-fast and fast-to-slow transition. However, the muscle transition mechanism is not well understood. For this study, we first produced porcine Myh1 transgenic (TG) mice to study whether the ectopic expressed porcine Myh1 gene had any effects on muscle composition, especially on slow-type muscle components. Our results showed that the factors associated with slow muscles, such as Myh7, Myoglobin, Troponin (slow-type units), and cytochrome C, were highly expressed in the quadriceps muscles of Myh1 transgenic mice. Furthermore, the ectopic porcine MYH1 protein was located only in the slow-type muscle fibers of the quadriceps muscles in Myh1 transgenic mice. In physical endurance tests, Myh1 transgenic mice ran longer and further on a treadmill than wild-type (WT) mice. These data fully supported our hypothesis that Myh1 is associated with slow muscle composition, with overexpression of Myh1 in muscle tissues possibly being a new key in modulating muscle fiber types. Our study provides a better understanding of muscle composition metabolism, physical mobility, and genetic factors in muscle fatigue.
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Fibras Musculares Esqueléticas/metabolismo , Cadeias Pesadas de Miosina/metabolismo , Condicionamento Físico Animal , Resistência Física , Animais , Regulação da Expressão Gênica , Camundongos Endogâmicos C57BL , Camundongos Transgênicos , Cadeias Pesadas de Miosina/genética , SuínosAssuntos
Endofenótipos , Mioglobina , Animais , Músculos/metabolismo , Mioglobina/genética , Mioglobina/metabolismo , Oxirredução , Suínos/genéticaRESUMO
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.
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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.
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Caloric restriction (CR) has been shown to extend the lifespan of many species by improving cellular function and organismal health. Additionally, fat reduction by CR may play an important role in lengthening lifespan and preventing severe age-related diseases. Interestingly, CR induced the greatest transcriptome change in the epididymal fat of mice in our study. In this transcriptome analysis, we identified and categorized 446 genes that correlated with CR level. We observed down-regulation of several signaling pathways, including insulin/insulin-like growth factor 1 (insulin/IGF-1), epidermal growth factor (EGF), transforming growth factor beta (TGF-ß), and canonical wingless-type mouse mammary tumor virus integration site (Wnt). Many genes related to structural features, including extracellular matrix structure, cell adhesion, and the cytoskeleton, were down-regulated, with a strong correlation to the degree of CR. Furthermore, genes related to the cell cycle and adipogenesis were down-regulated. These biological processes are well-identified targets of insulin/IGF-1, EGF, TGF-ß, and Wnt signaling. In contrast, genes involved in specific metabolic processes, including the tricarboxylic acid cycle and the electron transport chain were up-regulated. We performed in silico analysis of the promoter sequences of CR-responsive genes and identified two associated transcription factors, Paired-like homeodomain 2 (Pitx2) and Paired box gene 6 (Pax6). Our results suggest that strict regulation of signaling pathways is critical for creating the optimal energy homeostasis to extend lifespan.
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Restrição Calórica , Perfilação da Expressão Gênica/métodos , Longevidade/genética , Transcriptoma/genética , Tecido Adiposo/metabolismo , Animais , Fator de Crescimento Epidérmico/biossíntese , Proteínas do Olho/biossíntese , Regulação da Expressão Gênica , Proteínas de Homeodomínio/biossíntese , Fígado/metabolismo , Camundongos , Oxirredução , Fator de Transcrição PAX6 , Fatores de Transcrição Box Pareados/biossíntese , Proteínas Repressoras/biossíntese , Fatores de Transcrição/biossíntese , Fator de Crescimento Transformador beta/biossíntese , Via de Sinalização Wnt , Proteína Homeobox PITX2RESUMO
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
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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.
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Cruzamentos Genéticos , Estudo de Associação Genômica Ampla , Locos de Características Quantitativas , Carne Vermelha , Sus scrofa/genética , Animais , Ligação Genética , Variação Genética/genética , Genótipo , Repetições de Microssatélites/genética , Fenótipo , Sus scrofa/classificaçãoRESUMO
BACKGROUND: Meningocele and meningoencephalocele of the skull are congenital deformities. Various species, such as pigs, dogs, and cats, are susceptible to congenital meningocele and meningoencephalocele and the incidence is higher in large white and landrace pigs. CASE PRESENTATION: In this study, swelling was observed in the fontanel areas of the median planes of the skull cap in two female piglets of the same litter. Gross clinical examination, neurological examination, computed tomography (CT), and magnetic resonance imaging (MRI) were conducted on the symptomatic piglets. The gross clinical and neurological examinations revealed no specific findings, except for the swellings. According to the CT results, the length of the defect on the sagittal section of the skull was 4.7 mm in case 1 and 20.62 mm in case 2. Connected flow between the skull swellings and the cerebrospinal fluid (CSF) of the lateral ventricles was observed, and partial herniation was identified in case 2. On MRI, CSF with high T2 signals was identified in the arachnoid spaces between the cerebrum and the cerebellum in the two cases, which is consistent with intracranial hypertension. The size of the swelling formed in the parietal bones was 1.6 × 1.1 × 1.8 cm(3) (case 1) and 1.2 × 1.38 × 1.7 cm(3) (case 2). The increase in intracranial pressure was more obvious in case 2 than in case 1, and was accompanied by posterior displacements of the mesencephalon and cerebellum. CONCLUSIONS: Case 1 was diagnosed as meningocele resulting from meningeal herniation and case 2 was diagnosed as meningoencephalocele caused by brain tissue herniation.
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Encefalocele/veterinária , Meningocele/patologia , Doenças dos Suínos/congênito , Animais , Encefalocele/patologia , Feminino , República da Coreia , Suínos , Doenças dos Suínos/patologiaRESUMO
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.
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Cruzamento/métodos , Hibridização Genética/genética , Glândulas Mamárias Animais/anatomia & histologia , Polimorfismo de Nucleotídeo Único/genética , Locos de Características Quantitativas/genética , Sus scrofa/genética , Animais , Cruzamentos Genéticos , Feminino , Estudo de Associação Genômica Ampla , Modelos Lineares , Modelos Genéticos , República da Coreia , Sus scrofa/anatomia & histologiaRESUMO
In recent years, 1D nanostructure-based devices have achieved widespread usage in various fields, such as sensors, energy harvesters, transistors, and electrodes owing to their exceptional and distinct properties. The pioneering work of Dr. R. S. Wagner at Bell Laboratories in 1964 introduced the vapor-liquid-solid (VLS) process, a powerful synthesis method. Since then, numerous synthesis techniques, including sol-gel, hydrothermal, chemical vapor deposition (CVD), physical vapor deposition (PVD), and more, have been developed. These methods have enabled researchers to effectively control the shape (length and diameter) and material properties of nanowires. However, it was only about two decades ago that nanowires started to be widely utilized as key components in functional devices, primarily due to the lack of proper integration methods. Although dozens of integration techniques have been developed, none have emerged as a predominant choice, with each method presenting its own set of advantages and limitations. Therefore, this work aims to categorize these methods based on their working principles and provide a comprehensive summary of their pros and cons. Additionally, state-of-the-art devices that capitalize on the integration of 1D nanomaterials are introduced.
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Recent advancements in sequencing and genome assembly technologies have led to rapid generation of high-quality genome assemblies for various species and breeds. Despite the importance as minipigs an animal model in biomedical research, the construction of high-quality genome assemblies of minipigs still lags behind other pig breeds. To address this problem, we constructed a high-quality chromosome-level genome assembly of the Korean minipig (KMP) utilizing multiple different types of sequencing reads and reference genomes. The KMP assembly included 19 chromosome-level sequences with a total length of 2.52 Gb and N50 of 137 Mb. Comparative analyses with the pig reference genome (Sscrofa11.1) demonstrated comparable contiguity and completeness of the KMP assembly. Additionally, genome annotation analyses identified 22,666 protein-coding genes and repetitive elements occupying 40.10% of the genome. The KMP assembly and genome annotation provide valuable resources that can contribute to various future research on minipig and other pig breeds.
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Genoma , Porco Miniatura , Animais , Porco Miniatura/genética , Suínos/genética , Sus scrofa/genética , Anotação de Sequência Molecular , CromossomosRESUMO
Fatty acid (FA) composition is one of the most important parameters for the evaluation of meat quality. The stearoyl-CoA desaturase (SCD) gene is considered a positional candidate gene affecting FA composition in SSC14, based on previous quantitative trait loci studies. To evaluate the association of the SCD gene with FA composition in a Korean native pig × Landrace F(2) intercross population, we genotyped six single nucleotide polymorphisms (SNPs) of the SCD gene located in promoter region [2 SNPs (g.-353T>C, g.-233T>C)], exonic region [1 SNP (g.817C>T) in exon 2] and 3' UTR [3 SNPs (g.13311C>G, g.14384G>A, and g.14424C>T)] identified by massively parallel sequencing technology. Eighteen FA composition traits were measured in more than the 950 F(2) animals. A mixed-effect model was used to evaluate associations between these SNPs and FA composition traits in the F(2) intercross population. A detailed investigation detected that the five FA composition traits [palmitoleic acid (C16:1), stearic acid (C18:0), arachidic acid (C20:0), saturated FA, and unsaturated FA] were highly significant (P < 4.7 × 10(-5); C20:0) in association with the SNP g.-233T>C, SNP g.817C>T, SNP g.13311C>G and SNP g.14384G>A in the SCD gene, whereas SNP g.14424C>T was only significantly associated with palmitoleic acid (C16:1, P = 1.4 × 10(-3)). No significant association of FA composition traits with SNP g.-353T>C was detected. In particular, the SNP g.14384G>A accounted for 30.6 % of the additive genetic variance of palmitoleic acid (P = 1.9 × 10(-10)). These results suggest the SCD gene has a strong effect on FA composition in the crossbred pig population.
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Cruzamentos Genéticos , Ácidos Graxos/metabolismo , Estearoil-CoA Dessaturase/genética , Suínos/genética , Alelos , Animais , Feminino , Frequência do Gene , Ordem dos Genes , Genótipo , Masculino , Fenótipo , Polimorfismo de Nucleotídeo ÚnicoRESUMO
Using a methyl-DNA immunoprecipitation technique in combination with next-generation deep sequencing, we conducted comprehensive DNA methylation profiling of liver genomes from three pig breeds: Berkshire, Duroc and Landrace. The profiles revealed that the distribution patterns of methylation signals along the genome are conserved among the three pig breeds. Specifically, many signals in coding genes were found in introns, and most signals in the repetitive elements were identified in non-long terminal repeat (LTR) retrotransposons such as long and short interspersed repetitive elements, implying a significant association with alternative splicing and expression of retrotransposable elements respectively. Differentially methylated regions among the three pig breeds were identified in the non-LTR retrotransposons, suggesting that they may lead to differential retrotransposable element activity. Altogether, this study provides advanced swine methylome data and valuable resources for understanding the function of DNA methylation in the evolutionary divergence of different pig breeds.