Retroviral Insertion Polymorphism (RIP) of Porcine Endogenous Retroviruses (PERVs) in Pig Genomes

Endogenous retroviruses (ERVs) are one of the superfamilies of long terminal repeat retrotransposons (LTRs) in mice and humans. Approximately 8% of the pig genome is composed of sequences derived from LTRs. While the majority of ERVs in pigs have decayed, a small number of full-length copies can still mobilize within the genome. This study investigated the unexplored retroviral insertion polymorphisms (RIPs) generated by the mobilization of full-length ERVs (Fl-ERVs), and evaluated their impact on phenotypic variation to gain insights into the biological role of Fl-ERVs in pigs. Overall, 39 RIPs (insertions or deletions relative to the pig reference genome) generated by Fl-ERVs were predicted by comparative genomic analysis, and 18 of them were confirmed by PCR detection. Four RIP sites (D5, D14, D15, and D18) were further evaluated by population analysis, and all of them displayed polymorphisms in multiple breeds. The RIP site of ERV-D14, which is a Fl-ERV inserted in the STAB2-like gene, was further confirmed by sequencing. Population analysis of the polymorphic site of ERV-D14 reveals that it presents moderate polymorphism information in the Large White pig breed, and the association analysis reveals that the RIP of ERV-D14 is associated with age variations at 30 kg body weight (p p N = 480). Furthermore, the ERV-D14 RIP is associated with changes in the expression of the target gene STAB2-like in the liver, backfat, and leaf fat in Sushan pigs. These data suggest that some Fl-ERVs are still mobilizing in the pig’s genome, and contribute to genomic and phenotypic variations

Retrotransposon Insertion Polymorphisms (RIPs) in Pig Coat Color Candidate Genes

The diversity of livestock coat color results from human positive selection and represents an indispensable part of breed identity. As an important biodiversity resource, pigs have many special characteristics, including the most visualized feature, coat color, and excellent adaptation, and the coat color represents an important phenotypic characteristic of the pig breed. Exploring the genetic mechanisms of phenotypic characteristics and the melanocortin system is of considerable interest in domestic animals because their energy metabolism and pigmentation have been under strong selection. In this study, 20 genes related to coat color in mammals were selected, and the structural variations (SVs) in these genic regions were identified by sequence alignment across 17 assembled pig genomes, from representing different types of pigs (miniature, lean, and fat type). A total of 167 large structural variations (>50 bp) of coat-color genes, which overlap with retrotransposon insertions (>50 bp), were obtained and designated as putative RIPs. Finally, 42 RIPs were confirmed by PCR detection. Additionally, eleven RIP sites were further evaluated for their genotypic distributions by PCR in more individuals of eleven domesticated breeds representing different coat color groups. Differential distributions of these RIPs were observed across populations, and some RIPs may be associated with breed differences

Retrotransposon Insertion Polymorphisms (RIPs) in Pig Coat Color Candidate Genes

The diversity of livestock coat color results from human positive selection and represents an indispensable part of breed identity. As an important biodiversity resource, pigs have many special characteristics, including the most visualized feature, coat color, and excellent adaptation, and the coat color represents an important phenotypic characteristic of the pig breed. Exploring the genetic mechanisms of phenotypic characteristics and the melanocortin system is of considerable interest in domestic animals because their energy metabolism and pigmentation have been under strong selection. In this study, 20 genes related to coat color in mammals were selected, and the structural variations (SVs) in these genic regions were identified by sequence alignment across 17 assembled pig genomes, from representing different types of pigs (miniature, lean, and fat type). A total of 167 large structural variations (>50 bp) of coat-color genes, which overlap with retrotransposon insertions (>50 bp), were obtained and designated as putative RIPs. Finally, 42 RIPs were confirmed by PCR detection. Additionally, eleven RIP sites were further evaluated for their genotypic distributions by PCR in more individuals of eleven domesticated breeds representing different coat color groups. Differential distributions of these RIPs were observed across populations, and some RIPs may be associated with breed differences

Hidden Markov Model-Based Dynamic Hard Shoulders Running Strategy in Hybrid Network Environments

With the development of vehicle-road network technologies, the future traffic flow will appear in the form of hybrid network traffic flow for a long time. Due to the change in traffic characteristics, the current hard shoulder running strategy based on traditional traffic characteristics cannot effectively serve the hybrid network traffic flow scenario, and will even lead to the further deterioration of traffic congestion. In order to propose a hard shoulder running strategy suitable for a hybrid network environment, a traffic breakdown prediction method based on a hidden Markov model was established. Secondly, the characteristics of traffic breakdown in a hybrid network environment were analyzed. Finally, based on the traffic breakdown characteristics in a hybrid network environment, a dynamic hard shoulder running method based on the hidden Markov model was proposed. The effectiveness of HMMD-HSR was verified by simulation and comparison with HMM-HSR, LMD-HSR, and N-HSR. The simulation results show that the HMMD-HSR proposed in this paper can improve operation efficiency and reduce travel time in a congested expressway

Topographic Effects on Stratiform Precipitation Observed by Vertically Pointing Micro Rain Radars at Ridge and Valley Sites in the Liupan Mountains Area, Northwest China

To investigate the topographic effects on precipitation in the Liupan Mountains Area of Northwest China, three micro rain radars, located at a ridge, west valley, and east valley in the area, respectively, were used to observe precipitation processes. By comparing the characteristics of stratiform precipitation at three sites, it was found that (i) the effective radar reflectivity and characteristic falling velocity of hydrometeors at the ridge and east valley were larger than those at the west valley; (ii) the diameter and density of solid hydrometeors at the ridge and east valley were slightly larger than those at the west valley; and (iii) there was also a higher occurrence frequency of larger graupel at the ridge. It is inferred that the precipitable water vapor at the ridge and east valley is richer than at the west valley, which leads to a larger aggregation efficiency and degrees of riming at the former than the latter. Besides, forced uplifting of water vapor over the mountain area around the ridge may play a part in topographic supercooling, which leads to enhanced riming of supercooled liquid water. The conclusions will contribute to a better understanding of the mechanisms of precipitation–terrain interactions in the area

Review of Advances in Precipitation Enhancement Research

International audienceThis paper provides a summary of the assessment report of the WorldMeteorological Organization (WMO) Expert Team on Weather Modificationthat discusses recent progress on precipitation enhancement research.The progress has been underpinned by advances in our understanding ofcloud processes and interactions between clouds and their environmentwhich, in turn, have been enabled by substantial developments intechnical capabilities to both observe and simulate clouds from themicrophysical to the mesoscale.We focus on the two cloud types most seeded in the past: winterorographic cloud systems and convective cloud systems. A key issue forcloud seeding is the extension from cloud-scale research to watercatchment-scale impacts on precipitation on the ground. Consequently,the requirements for the design, implementation and evaluation of acatchment-scale precipitation enhancement campaign are discussed.The paper concludes by indicating the most important gaps in ourknowledge. Some recommendations regarding the most urgent researchtopics are given to stimulate further research