Genomic selection analysis of morphological and adaptation traits in Chinese indigenous dog breeds

The significant morphological differences and abundant germplasm resources of Chinese indigenous dog breeds can be attributed to the diverse geographical environment, including plateaus, mountains, and a long history of raising dogs. The combination of both natural and artificial selection during the past several thousand years has led to hundreds of dog breeds with distinct morphological traits and environmental adaptations. China is one of the earliest countries to domesticate dogs and there are more than 50 ancient indigenous dog breeds. In this study, the run of homozygosity (ROH) and proportion of the autosomal genome covered by ROHs (FROH) were calculated for 10 dog breeds that are the most representative Chinese indigenous dogs based on 170K SNP microarray. The results of FROH showed that the Chuandong hound dogs (HCSSC) have the highest level of inbreeding among the tested breeds. The inbreeding in HCSSC occurred more recently than the Liangshan dogs (SCLSQ) dogs because of more numbers of long ROHs in HCSSC dogs, and the former also have higher inbreeding degree. In addition, there are significant differences in the inbreeding degree among different subpopulations of the same breed, such as the Thin dogs from Shaanxi and Shandong province. To explore genome-wide selection signatures among different breeds, including coat color, ear shape, and altitude adaptability, we performed genome selection analyses of FST and cross population extended haplotype homozygosity (XP-EHH). For the coat color, the FST analysis between Xiasi dogs (XSGZ) and HCSSC dogs was performed and identified multiple genes involved in coat color, hair follicle, and bone development, including MC1R, KITLG, SOX5, RSPO2, and TBX15. For the plateau adaptability, we performed FST and XP-EHH analyses between dogs from Tibet (Tibetan Mastiffs and Nyingchi dogs) and plain regions (Guangxi Biwei dogs GXBWQ and Guandong Sharpei dogs). The results showed the EPAS1 gene in dogs from Tibet undergo strong selection. Multiple genes identified for selection signals based on different usage of dogs. Furthermore, the results of ear shape analyses showed that MSRB3 was likely to be the main gene causing the drop ear of domestic dogs. Our study provides new insights into further understanding of Chinese indigenous dogs

Muon neutrinos and the cosmological abundance of primordial black holes

In the mixed dark matter scenarios consisting of primordial black holes (PBHs) and particle dark matter (DM), PBHs can accrete surrounding DM particles to form ultracompact minihalos (UCMHs or clothed PBHs) even at an early epoch of the Universe. The distribution of DM particles in a UCMH follows a steeper density profile compared with a classical DM halo. It is expected that the DM annihilation rate is very large in UCMHs, resulting in a contribution to, e.g., the extragalactic neutrino flux. In this work, we investigate the extragalactic neutrino flux from clothed PBHs due to DM annihilation, and then the muon flux for neutrino detection. Compared with the atmospheric neutrino flux, we derive the upper limits on the cosmological abundance of PBHs for 10 years of exposure time of, e.g., the IceCube experiment. Compared with other constraints, although the upper limits obtained by us are not the strongest, it is a different way to study the cosmological abundance of PBHs.7 pages, 3 figures. comments welcome. Accepted for publication in Physical Review

Elastoplastic constitutive model considering the filling and cementation effects for gas hydrate-bearing sediments: development and finite element implementation

Dynamic evolution of hydrate filling and cementation effects significantly affects the mechanical behavior of gas hydrate-bearing sediments (GHBS). To analyze the strength and deformation characteristics of GHBS under varying effective confining pressures and hydrate saturations, we use the unified hardening model for clays and sands (CSUH model) as a framework. A compressive hardening parameter is introduced to describe the isotropic compression behavior. Additionally, cementation strength is incorporated to adjust the yield function, while state parameters are used to modify the potential strength. An elastoplastic constitutive model is developed to capture the strength, stiffness, dilatancy, and softening of GHBS. Based on the user-defined subroutine interface provided by ABAQUS and the modified Euler integral algorithm with error control, the user-defined subroutine (UMAT) is embedded in ABAQUS to implement the finite element model. Numerical solutions are obtained, and the accuracy of the model is verified by comparing theoretical solutions with experimental data, showing good agreement. The results demonstrate that the model accurately represents the stress-strain relations and shear dilatancy characteristics of GHBS under various conditions. Furthermore, the model effectively evaluates the mechanical responses of GHBS with different hydrate formation behaviors under various environmental loads. These findings provide a foundation for further engineering applications