Assembly of novel sequences for Chinese domestic pigs reveals new genes and regulatory variants providing new insights into their diversity.

There is an increasing understanding that a reference genome representing an individual cannot capture all the gene repertoire of a species. Here, we conduct a population-scale missing sequences detection of Chinese domestic pigs using whole-genome sequencing data from 534 individuals. We identify 132.41 Mb of sequences absent in the reference assembly, including eight novel genes. In particular, the breeds spread in Chinese high-altitude regions perform significantly different frequencies of new sequences in promoters than other breeds. Furthermore, we dissect the role of non-coding variants and identify a novel sequence inserted in the 3'UTR of the FMO3 gene, which may be associated with the intramuscular fat phenotype. This novel sequence could be a candidate marker for meat quality. Our study provides a comprehensive overview of the missing sequences in Chinese domestic pigs and indicates that this dataset is a valuable resource for understanding the diversity and biology of pigs.

MAGE: metafounders-assisted genomic estimation of breeding value, a novel additive-dominance single-step model in crossbreeding systems.

MOTIVATION: Utilizing both purebred and crossbred data in animal genetics is widely recognized as an optimal strategy for enhancing the predictive accuracy of breeding values. Practically, the different genetic background among several purebred populations and their crossbred offspring populations limits the application of traditional prediction methods. Several studies endeavor to predict the crossbred performance via the partial relationship, which divides the data into distinct sub-populations based on the common genetic background, such as one single purebred population and its corresponding crossbred descendant. However, this strategy makes prediction inaccurate due to ignoring half of the parental information of crossbreed animals. Furthermore, dominance effects, although playing a significant role in crossbreeding systems, cannot be modeled under such a prediction model. RESULTS: To overcome this weakness, we developed a novel multi-breed single-step model using metafounders to assess ancestral relationships across diverse breeds under a unified framework. We proposed to use multi-breed dominance combined relationship matrices to model additive and dominance effects simultaneously. Our method provides a straightforward way to evaluate the heterosis of crossbreeds and the breeding values of purebred parents efficiently and accurately. We performed simulation and real data analyses to verify the potential of our proposed method. Our proposed model improved prediction accuracy under all scenarios considered compared to commonly used methods. AVAILABILITY AND IMPLEMENTATION: The software for implementing our method is available at https://github.com/CAU-TeamLiuJF/MAGE.

Comparative Genomic Analysis of Warthog and Sus Scrofa Identifies Adaptive Genes Associated with African Swine Fever.

BACKGROUND: As warthogs (Phacochoerus africanus) have innate immunity against African swine fever (ASF), it is critical to understand the evolutionary novelty of warthogs to explain their specific ASF resistance. METHODS: Here, we present two completed new genomes of one warthog and one Kenyan domestic pig as fundamental genomic references to elucidate the genetic mechanisms of ASF tolerance. RESULTS: Multiple genomic variations, including gene losses, independent contraction, and the expansion of specific gene families, likely molded the warthog genome to adapt to the environment. Importantly, the analysis of the presence and absence of genomic sequences revealed that the DNA sequence of the warthog genome had an absence of the gene lactate dehydrogenase B (LDHB) on chromosome 2 compared with the reference genome. The overexpression and siRNA of LDHB inhibited the replication of the African swine fever virus. Combined with large-scale sequencing data from 42 pigs worldwide, the contraction and expansion of tripartite motif-containing (TRIM) gene families revealed that TRIM family genes in the warthog genome are potentially responsible for its tolerance to ASF. CONCLUSION: Our results will help improve the understanding of genetic resistance to ASF in pigs.

Mining Unknown Porcine Protein Isoforms by Tissue-based Map of Proteome Enhances Pig Genome Annotation.

A lack of the complete pig proteome has left a gap in our knowledge of the pig genome and has restricted the feasibility of using pigs as a biomedical model. In this study, we developed a tissue-based proteome map using 34 major normal pig tissues. A total of 5841 unknown protein isoforms were identified and systematically characterized, including 2225 novel protein isoforms, 669 protein isoforms from 460 genes symbolized beginning with LOC, and 2947 protein isoforms without clear NCBI annotation in the current pig reference genome. These newly identified protein isoforms were functionally annotated through profiling the pig transcriptome with high-throughput RNA sequencing of the same pig tissues, further improving the genome annotation of the corresponding protein-coding genes. Combining the well-annotated genes that have parallel expression pattern and subcellular witness, we predicted the tissue-related subcellularlocations and potential functions for these unknown proteins. Finally, we mined 3081 orthologous genes for 52.7% of unknown protein isoforms across multiple species, referring to 68 KEGG pathways as well as 23 disease signaling pathways. These findings provide valuable insights and a rich resource for enhancing studies of pig genomics and biology, as well as biomedical model application to human medicine.

Integrated hybrid de novo assembly technologies to obtain high-quality pig genome using short and long reads.

With the rapid progress of sequencing technologies, various types of sequencing reads and assembly algorithms have been designed to construct genome assemblies. Although recent studies have attempted to evaluate the appropriate type of sequencing reads and algorithms for assembling high-quality genomes, it is still a challenge to set the correct combination for constructing animal genomes. Here, we present a comparative performance assessment of 14 assembly combinations-9 software programs with different short and long reads of Duroc pig. Based on the results of the optimization process for genome construction, we designed an integrated hybrid de novo assembly pipeline, HSCG, and constructed a draft genome for Duroc pig. Comparison between the new genome and Sus scrofa 11.1 revealed important breakpoints in two S. scrofa 11.1 genes. Our findings may provide new insights into the pan-genome analysis studies of agricultural animals, and the integrated assembly pipeline may serve as a guide for the assembly of other animal genomes.

A Random Regression Model Based on a Single-Step Method for Improving the Genomic Prediction Accuracy of Residual Feed Intake in Pigs.

Residual feed intake (RFI) is considered as a measurement of feed efficiency, which is greatly related to the growth performance in pigs. Daily feeding records can be obtained from automatic feeders. In general, RFI is usually calculated from the total measurement records during the whole test period. This measurement cannot reflect genetic changes in different growth periods during the test. A random regression model (RRM) provides a method to model such type of longitudinal data. To improve the accuracy of genetic prediction for RFI, the RRM and regular animal models were applied in this study, and their prediction performances were compared. Both traditional pedigree-based relationship matrix (A matrix) and pedigree and genomic information-based relationship matrix (H matrix) were applied for these two models. The results showed that, the prediction accuracy of the RRM was higher than that of the animal model, increasing 24.2% with A matrix and 40.9% with H matrix. Furthermore, genomic information constantly improved the accuracy of evaluation under each evaluation model. In conclusion, longitudinal traits such as RFI can describe feed efficiency better, and the RRM with both pedigree and genetic information was superior to the animal model. These results provide a feasible method of genomic prediction using longitudinal data in animal breeding.

PRE-1 Revealed Previous Unknown Introgression Events in Eurasian Boars during the Middle Pleistocene.

Introgression events and population admixture occurred among Sus species across the Eurasian mainland in the Middle Pleistocene, which reflects the local adaption of different populations and contributes to evolutionary novelty. Previous findings on these population introgressions were largely based on extensive genome-wide single-nucleotide polymorphism information, ignoring structural variants (SVs) as an important alternative resource of genetic variations. Here, we profiled the genome-wide SVs and explored the formation of pattern-related SVs, indicating that PRE1-SS is a recently active subfamily that was strongly associated with introgression events in multiple Asian and European pig populations. As reflected by the three different combination haplotypes from two specific patterns and known phylogenetic relationships in Eurasian boars, we identified the Asian Northern wild pigs as having experienced introgression from European wild boars around 0.5-0.2 Ma and having received latitude-related selection. During further exploration of the influence of pattern-related SVs on gene functions, we found substantial sequence changes in 199 intron regions of 54 genes and 3 exon regions of 3 genes (HDX, TRO, and SMIM1), implying that the pattern-related SVs were highly related to positive selection and adaption of pigs. Our findings revealed novel introgression events in Eurasian wild boars, providing a timeline of population admixture and divergence across the Eurasian mainland in the Middle Pleistocene.

Parametric study of blade tip clearance, flow rate, and impeller speed on blood damage in rotary blood pump.

Phenomenological studies on mechanical hemolysis in rotary blood pumps have provided empirical relationships that predict hemoglobin release as an exponential function of shear rate and time. However, these relations are not universally valid in all flow circumstances, particularly in small gap clearances. The experiments in this study were conducted at multiple operating points based on flow rate, impeller speed, and tip gap clearance. Fresh bovine red blood cells were resuspended in phosphate-buffered saline at about 30% hematocrit, and circulated for 30 min in a centrifugal blood pump with a variable tip gap, designed specifically for these studies. Blood damage indices were found to increase with increased impeller speed or decreased flow rate. The hemolysis index for 50-microm tip gap was found to be less than 200-microm gap, despite increased shear rate. This is explained by a cell screening effect that prevents cells from entering the smaller gap. It is suggested that these parameters should be reflected in the hemolysis model not only for the design, but for the practical use of rotary blood pumps, and that further investigation is needed to explore other possible factors contributing to hemolysis.

Temperature distribution and blood perfusion response in rat brain during selective brain cooling.

A rat model was used in this study to examine the transient temperature distribution and blood flow response in the brain during selective brain cooling (SBC) and rewarming. SBC was induced by a head cooling helmet with circulating water of 18 degrees C or 0 degrees C. It has been shown that the brain temperature reductions were 1.7+/-0.2 degrees C (5 mm beneath the brain surface) and 3.2+/-1.1 degrees C (2 mm beneath the brain surface) when the temperature of the water was 18 degrees C (moderate cooling). The cooling of the brain tissue was more evident when the circulating water was colder (0 degrees C, deep cooling). The characteristic time that it took for the tissue temperatures to reach a new steady state after the initiation of cooling varied from 5 to more than 35 min and it depended strongly on the blood flow response to the cooling. We used an ultrasound flow meter to measure continuously the blood flow rate in the common carotid artery during the cooling and rewarming. The blood flow rate dropped by up to 22% and 44% during the cooling from its baseline in the moderate cooling group and in the deep cooling group, respectively. Although all brain temperatures recovered to their baseline values 50 min after the helmet was removed, the blood flow rate only recovered to 92% and 77% of its baseline values after the moderate and deep cooling, respectively, implying a possible mismatch between the blood perfusion and metabolism in the brain. The current experimental results can be used to study the feasibility of inducing brain hypothermia by SBC if the blood flow responses in the rat are applicable to humans. The simultaneous recordings of temperature and blood flow rate in the rat brain can be used in the future to validate the theoretical model developed previously.

Towards the development of a pediatric ventricular assist device.

The very limited options available to treat ventricular failure in children with congenital and acquired heart diseases have motivated the development of a pediatric ventricular assist device at the University of Pittsburgh (UoP) and University of Pittsburgh Medical Center (UPMC). Our effort involves a consortium consisting of UoP, Children's Hospital of Pittsburgh (CHP), Carnegie Mellon University, World Heart Corporation, and LaunchPoint Technologies, Inc. The overall aim of our program is to develop a highly reliable, biocompatible ventricular assist device (VAD) for chronic support (6 months) of the unique and high-risk population of children between 3 and 15 kg (patients from birth to 2 years of age). The innovative pediatric ventricular assist device we are developing is based on a miniature mixed flow turbodynamic pump featuring magnetic levitation, to assure minimal blood trauma and risk of thrombosis. This review article discusses the limitations of current pediatric cardiac assist treatment options and the work to date by our consortium toward the development of a pediatric VAD.

The PediaFlow pediatric ventricular assist device.

The very limited options available to treat ventricular failure in patients with congenital and acquired heart diseases have motivated the development of a pediatric ventricular assist device (VAD). Our effort involves a consortium consisting of the University of Pittsburgh, Carnegie Mellon University, Children's Hospital of Pittsburgh, World Heart Corporation, and LaunchPoint Technologies, LLC. The overall aim of our program is to develop a highly reliable, biocompatible VAD for chronic support (6 months) of the unique and high-risk population of children between 3 kg and 15 kg (patients from birth to 2 years of age). The innovative pediatric VAD we are developing (PediaFlow) is based on a miniature mixed-flow turbodynamic pump featuring magnetic levitation, with the design goal being to assure minimal blood trauma and risk of thrombosis. This article discusses the limitations of current pediatric cardiac assist treatment options and the work to date by our consortium toward the development of a pediatric VAD.

Cooling and rewarming for brain ischemia or injury: theoretical analysis.

A three-dimensional model is developed in this study to examine the transient and steady state temperature distribution in the brain during selective brain cooling (SBC) and subsequent rewarming. Selective brain cooling is induced through either wearing a cooling helmet or packing the head with ice. The ischemic region of the brain is simulated through reducing the blood perfusion rate to 20% of its normal value. The geometric and thermal properties and physiological characteristics for each layer, as well as the arterial blood temperature, are used as the input to the Pennes bioheat equation. Our data suggest that rapid cooling of the brain gray matter can be achieved by SBC on the head surface (26 min for adults versus 15 min for infants). Suboptimal thermal contact between the head surface and the coolant in most commercially available cooling helmets is suspected to be the main reason for delayed cooling in SBC as compared to the ice packing. The study has also demonstrated that the simulated 3 degrees C/h passive rewarming rate by exposing the head to room temperature after removing the source of cooling may be too rapid.