Additional file 1 of Origin, evolution, and tissue-specific functions of the porcine repetitive element 1

Additional file 1: Figure S1. Nested and tandem PRE1. a Mechanisms of the formation of nested PRE1 and tandem PRE1. b A PRE1 inserted into another PRE1 tail. The target motif is located in the PRE1 tail (chr7:29710723:29711249). The nested PRE1 are actually two new tandem PRE1 with changed tile lengths. The tail of the basal PRE1 at the 5′ end is shortened, but the tail of the embedded PRE1 at the 3′ end is extended. Target site duplications (TSD) are shown in red font. Embedded PRE1 are shown in blue font, and basal PRE1 are shown in green font. c Repeated TSD produce three tandem PRE1 (chr12:33294823-33295640); d A PRE1 inserted into another PRE1 body. The target motif is located in the PRE1 body, which leads to a nested PRE1 (chr14:22207023-22207668); and e A tandem PRE1 inserted into the genome (chr2:80470307-80470742). Figure S2. Internal repeat segments in PRE1. a The consensus sequence of quasi-oligomeric PRE1 including three direct repeats. The black arrows indicate the three direct repeats; b Several rare PRE1 with other direct repeats in the PRE1 body. Four repeat segments of PRE1 (chr15:28050427-28050730, chr6:166491294-166491728, chr7:65896533-65896843; and chr15:77600095-77600373) have been marked in the consensus sequence. The arrows show the duplicated segments in different PRE1; and c The degenerate 46-bp repeat sequence in PRE1. The blue dotted arrows show the degenerate 46-bp repeat sequence, and the green arrows show the direct repeats. Figure S3. Three alternative alignment methods for PRE1d2. The PRE1d2 shows a degenerate 46-bp segment following the splicing model, and PRE1d2(2) and PRE1d2(3) show hypothetically missed whole R or F direct repeats, respectively. Figure S4. Differentially-methylated PRE1 in the promoter regions of the HACD3 and HORMAD1 genes

MOESM9 of Multi-breed genome-wide association study reveals novel loci associated with the weight of internal organs

Additional file 9: Figure S6. Results of the dominance GWAS for kidney weight in the F2 population. In the Manhattan plots, negative log10 P values of the qualified SNPs were plotted against their genomic positions; the red and green dots represent the SNPs that exceeded the genome-wide significance and suggestive significance thresholds, respectively; solid lines indicate the 5 % genome-wide Bonferroni-corrected threshold

DataSheet_1_Rediscover and Refine QTLs for Pig Scrotal Hernia by Increasing a Specially Designed F3 Population and Using Whole-Genome Sequence Imputation Technology.pdf

Pig scrotal hernia is one of the most common congenital defects triggered by both genetic and environmental factors, leading to severe economic loss as well as poor animal welfare in the pig industry. Identification and implementation of genomic regions controlling scrotal hernia in breeding is of great appeal to reduce incidences of hernia in pig production. The aim of this study was to identify such regions or molecular markers affecting scrotal hernia in pigs. First of all, we summarized and analyzed the results of some international teams on scrotal hernia and designed a specially population which contains 246 male individuals. We then performed genome-wide association study (GWAS) in this specially designed population using two scenarios, i.e., the target panel data before and after imputation, which contain 42,365 SNPs and 18,756,672 SNPs, respectively. In addition, a series of methods including genetic differentiation analysis, linkage disequilibrium and linkage analysis (LDLA), and haplotype sharing analysis were appropriate to provide for further analysis to identify the potential gene underlying the QTL. The GWAS in this report detected a highly significant region affecting scrotal hernia within a 24.8Mb region (114.1–138.9Mb) on SSC8. And the result of genetic differentiation analysis also showed a strong genetic differentiation signal between 116.1 and 132.7Mb on SSC8. In addition, the QTL interval was refined to 2.99Mb by combining LDLA and genetic differentiation analysis. Finally, two susceptibility haplotypes were identified through haplotype sharing analysis, with one potential causal gene in it. Our study provided deeper insights into the genetic architecture of pig scrotal hernia and contributed to further fine-mapping and characterize haplotype and gene that influence scrotal hernia in pigs.</p

MOESM2 of Multi-breed genome-wide association study reveals novel loci associated with the weight of internal organs

Additional file 2: Table S2. Suggestive significant SNPs for the weights of four internal organs and carcass in five populations. A total of 248 suggestive significant SNPs were identified in our study, including 91 for heart weight, 125 for liver weight, 6 for spleen weight, 12 for kidney weight and 14 for carcass weight

Genome-Wide Association Study Reveals Constant and Specific Loci for Hematological Traits at Three Time Stages in a White Duroc × Erhualian F₂ Resource Population

<div><p>Hematological traits are important indicators of immune function and have been commonly examined as biomarkers of disease and disease severity in humans. Pig is an ideal biomedical model for human diseases due to its high degree of similarity with human physiological characteristics. Here, we conducted genome-wide association studies (GWAS) for 18 hematological traits at three growth stages (days 18, 46 and 240) in a White Duroc × Erhualian F₂ intercross. In total, we identified 38 genome-wide significant regions containing 185 genome-wide significant SNPs by single-marker GWAS or LONG-GWAS. The significant regions are distributed on pig chromosomes (SSC) 1, 4, 5, 7, 8, 10, 11, 12, 13, 17 and 18, and most of significant SNPs reside on SSC7 and SSC8. Of the 38 significant regions, 7 show constant effects on hematological traits across the whole life stages, and 6 regions have time-specific effects on the measured traits at early or late stages. The most prominent locus is the genomic region between 32.36 and 84.49 Mb on SSC8 that is associated with multiple erythroid traits. The <i>KIT</i> gene in this region appears to be a promising candidate gene. The findings improve our understanding of the genetic architecture of hematological traits in pigs. Further investigations are warranted to characterize the responsible gene(s) and causal variant(s) especially for the major loci on SSC7 and SSC8.</p></div

MOESM8 of Multi-breed genome-wide association study reveals novel loci associated with the weight of internal organs

Additional file 8: Table S3. Suggestive significant SNPs for the traits studied in the meta-analysis of GWAS datasets. A total of 148 suggestive significant SNPs were identified. Most of these SNPs were within the QTL regions that were identified by single-population GWAS. Four novel QTL associated with carcass weight were identified in the meta-analysis, which are highlighted in yellow. ** = genome-wide significance level and * = suggestive significance level

DataSheet_2_Rediscover and Refine QTLs for Pig Scrotal Hernia by Increasing a Specially Designed F3 Population and Using Whole-Genome Sequence Imputation Technology.docx

Pig scrotal hernia is one of the most common congenital defects triggered by both genetic and environmental factors, leading to severe economic loss as well as poor animal welfare in the pig industry. Identification and implementation of genomic regions controlling scrotal hernia in breeding is of great appeal to reduce incidences of hernia in pig production. The aim of this study was to identify such regions or molecular markers affecting scrotal hernia in pigs. First of all, we summarized and analyzed the results of some international teams on scrotal hernia and designed a specially population which contains 246 male individuals. We then performed genome-wide association study (GWAS) in this specially designed population using two scenarios, i.e., the target panel data before and after imputation, which contain 42,365 SNPs and 18,756,672 SNPs, respectively. In addition, a series of methods including genetic differentiation analysis, linkage disequilibrium and linkage analysis (LDLA), and haplotype sharing analysis were appropriate to provide for further analysis to identify the potential gene underlying the QTL. The GWAS in this report detected a highly significant region affecting scrotal hernia within a 24.8Mb region (114.1–138.9Mb) on SSC8. And the result of genetic differentiation analysis also showed a strong genetic differentiation signal between 116.1 and 132.7Mb on SSC8. In addition, the QTL interval was refined to 2.99Mb by combining LDLA and genetic differentiation analysis. Finally, two susceptibility haplotypes were identified through haplotype sharing analysis, with one potential causal gene in it. Our study provided deeper insights into the genetic architecture of pig scrotal hernia and contributed to further fine-mapping and characterize haplotype and gene that influence scrotal hernia in pigs.</p

Pressure Dependence of Superconductivity in a Charge-Density-Wave Superconductor Bi₂Rh₃Se₂

The structural and superconducting properties of a Bi-based compound, Bi2Rh3Se2, are investigated over a wide pressure range. Bi2Rh3Se2 is a superconductor with a superconducting transition temperature, Tc, of 0.7 K. This compound is in a charge-density-wave (CDW) state below 240 K, which implies the coexistence of superconducting and CDW states at low temperatures. Here, the superconducting properties of Bi2Rh3Se2 are studied from the perspective of the temperature dependence of electrical resistance (R) at high pressures (p’s). The pressure dependence of Tc of Bi2Rh3Se2 shows a slow increase in Tc at 0–15.5 GPa, and the Tc slowly decreases with pressure above 15.5 GPa, which is markedly different from that of normal superconductors because the value of Tc should simply decrease owing to the decrease in density of states (DOS) on the Fermi level, N(εF), driven by a simple shrinkage of the lattice under pressure. To ascertain the origin of such a dome-like Tc–p behavior, the crystal structure of Bi2Rh3Se2 was explored over a wide pressure range of 0–20 GPa on the basis of powder X-ray diffraction; no structural phase transitions or simple shrinkage of the lattice was observed. This result implies that the increase in Tc against pressure cannot simply be explained from a structural point of view. In other words, a direct relation between superconductivity and crystal structure was not found. On the other hand, the CDW transition became ambiguous at pressures higher than 3.8 GPa, suggesting that the Tc had been suppressed by the CDW transition in a low pressure range. Thus, the findings suggest that for Bi2Rh3Se2, Tc is enhanced through the suppression of CDW transition, which may be reasonable because the CDW-ordered state restrains the charge fluctuation to weaken the electron–phonon coupling and opens the gap to decrease the density of states on the Fermi level. The obtained dome-like Tc–p behavior indicates the possibility of Bi2Rh3Se2 being an exotic superconductor

MOESM2 of Copy number variation in the MSRB3 gene enlarges porcine ear size through a mechanism involving miR-584-5p

Additional file 2: Table S1. The sample size and final set of informative SNPs for each population

MOESM5 of Multi-breed genome-wide association study reveals novel loci associated with the weight of internal organs

Additional file 5: Figure S3. Single-population GWAS results for spleen weight. Manhattan plots of GWAS results for spleen weight in F2 pigs (A), Sutai pigs (B), Erhualian pigs (C) and Laiwu pigs (D) and commercial pigs (E). In the Manhattan plots, negative log10 P values of the qualified SNPs were plotted against their genomic positions. Green dots are SNPs that surpass the suggestive significance level; red dots are the SNPs that surpass the genome-wide significance level; solid lines indicate the 5 % genome-wide Bonferroni-corrected threshold