Population genetics reveals new introgression in the nucleus herd of min pigs.

OBJECTIVE: Min pigs are a unique genetic resource among local pig breeds in China. They have more excellent characteristics in cold and stress resistance, good meat quality, and a high reproductive rate. However, the genetic structure and driving factors remain unclear in the nucleus herd. In this study, the genetic diversity of Min pigs was studied to reveal the formation mechanism of its unique genetic structure. We hope to protect and develop the genetic resources of Min pigs. METHODS: We analyzed different types of genes to identify the genetic structure and gene introgression pattern of Min pigs. The nuclear DNA dataset includes information on 21 microsatellite loci and 6 Y-chromosome genes, and the mitochondrial D-loop gene is selected to represent maternal lineages. The above genes are all from the nucleus herd of Min pigs. RESULTS: The results of genetic structure identification and analysis of potential exogenous gene introgression patterns indicate that the nucleus herd of Min pigs maintains a high level of genetic diversity (polymorphism information content = 0.713, expected heterozygosity = 0.662, observed heterozygosity = 0.612). Compared with other Asian pig breeds, the formation of Min pig breeds is more special. Gene introgression from European pig breeds to Min pigs has occurred, which is characterized by complete introgression of paternal genes and incomplete introgression of maternal genes. CONCLUSION: Gene introgression caused by cross-breeding is not the main factor leading to the formation of the current genetic structure of Min pigs, but this process has increased the level of genetic diversity in the nucleus herd. Compared with the influence of gene introgression, our research suggest that artificial selection and environmental adaptive evolution make Min pigs form unique genetic characteristics.

Transcriptomics and Selection Pressure Analysis Reveals the Influence Mechanism of PLIN1 Protein on the Development of Small Size in Min Pigs.

Body size is an important biological phenotypic trait that has attracted substantial attention. Small domestic pigs can serve as excellent animal models for biomedicine and also help meet sacrificial culture needs in human societies. Although the mechanisms underlying vertebral development regulating body size variation in domestic pigs during the embryonic period have been well described, few studies have examined the genetic basis of body size variation in post embryonic developmental stages. In this study, seven candidate genes-PLIN1, LIPE, PNPLA1, SCD, FABP5, KRT10 and IVL-significantly associated with body size were identified in Min pigs, on the basis of weighted gene co-expression network analysis (WGCNA), and most of their functions were found to be associated with lipid deposition. Six candidate genes except for IVL were found to have been subjected to purifying selection. PLIN1 had the lowest ω value (0.139) and showed heterogeneous selective pressure among domestic pig lineages with different body sizes (p < 0.05). These results suggested that PLIN1 is an important genetic factor regulating lipid deposition and consequently affecting body size variation in pigs. The culture of whole pig sacrifice in Manchu during the Qing Dynasty in China might have contributed to the strong artificial domestication and selection of Hebao pigs.

The Effect of Short-term Classical Music stimulus on Behavior and Tonic Immobility Reaction of Pullets.

The purpose of this study was to investigate the effect of short-term stimulation of classical music on the behavior of pullets and to explore whether classical music as an auditory enrichment factor reduces the fear level in pullets. One hundred and twenty 10-weeks'old Roman white pullets were randomly divided into two treatments of which one group was exposed to classic music (M), and another one was the control group (N). The music was played during 8:00-18:00 every day for 7 consecutive days. The behavior of the focal animals was observed from 11:00 to13:00 every day for 7 days. The results showed that during the observation period, the pullets in group M had more comforting (P < .05) and preening (P < .05), but less aggressive (P < .01) and feather-pecking (P < .01) behaviors than those in group N. No significant difference was found in other behaviors and the duration of tonic immobility between the two groups. Therefore, auditory enrichment as a means of environmental enrichment can increase the welfare level of pullets to a certain extent.

Removal of antibiotic resistance genes and mobile genetic elements in a three-stage pig manure management system: The implications of microbial community structure.

In this work, the removal of antibiotic resistance genes (ARGs) in the industrial-scale pig manure management system has been investigated. Additionally, the implications of mobile genetic elements (MGEs) and microbial community structure have been discussed. During the whole period of manure management, 19 ARGs and 7 MGEs were obtained from the system. The results identified that the 9 ARGs and 2 MGEs were removed from the pig manure-based materials after composting, while 5 ARGs and 2 MGEs were still remained, indicating that the ARGs/MGEs could not be removed completely as contaminants by composting. The pig farm without additional antibiotics in-feed was still faced with the risk of ARGs/MGEs from outside. Microbial community analysis illuminated that a greater decrease in the abundance of norank_f__JG30-KF-CM45, Corynebacterium, Terrisporobacter, Truepera, Salinispora and Clostridium, was responsible for the removal of ARGs/MGEs. The genes, including tnpA-01, tnpA-02, tnpA-05, Tp614, tetQ, tetM-01, tetR-02, tetX, cfxA, floR, dfrA1 and ermF exhibited significantly positive correlation with fungal communities. Fungal community analysis verified that a remarkable decrease in the abundance of Aspergillus and Thermomyces after composting was responsible for the ARGs/MGEs removal. The results elucidated the crucial roles of the related bacterial and fungal communities in the removal of ARGs/MGEs. The compound microbial agent assisted the temperature rise of composting, thereby changing the related microbial community structure and resulting in ARGs/MGEs removal.

Single nucleotide polymorphism-based analysis of the genetic structure of the Min pig conserved population.

OBJECTIVE: The study aims to uncover the genetic diversity and unique genetic structure of the Min pig conserved population, divide the nucleus conservation population, and construct the molecular pedigree. METHODS: We used KPS Porcine Breeding Chip v1 50K for SNP detection of 94 samples (31♂, 63♀) in the Min pig conserved population from Lanxi breeding Farm. RESULTS: The polymorphic marker ratio (PN), the observed heterozygosity (Ho), and the expected heterozygosity (He) were 0.663, 0.335, and 0.330, respectively. The pedigree-based inbreeding coefficients (FPED) was significantly different from those estimated from runs of homozygosity (FROH) and single nucleotide polymorphism (FSNP) based on genome. The Pearson correlation coefficient between FROH and FSNP was significant (p<0.05). The effective population content (Ne) showed a continuously decreasing trend. The rate of decline was the slowest from 200 to 50 generations ago (r = 0.95), then accelerated slightly from 50 to 5 generations ago (1.40

Evolution of toll-like receptor gene family in amphibians.

The evolutionary position and lifestyle of amphibians highlights the important roles of the immune system in adaptive radiation and their adaptation to a complex pathogenic environment. Toll-like receptors (TLRs) are membrane-like sensors that recognize and bind conserved molecular motifs in pathogens to initiate downstream immune responses. To understand the evolutionary patterns of TLRs in amphibians, we analyzed TLR genes from the genomes and transcriptomes of 102 amphibian species. Phylogenetic results showed that 578 intact amphibian TLR sequences belonged to 16 TLR genes and were divided into seven subfamilies. The TLR4 subfamily was only identified in the Anura. Purification selection plays a leading role in amphibian TLR evolution and mean ω (dN/dS) values ranged from 0.252 for TLR7 to 0.381 for TLR19. Furthermore, the ω values of different domains were significantly different. We found positive selection patterns for 141 of 12,690 codons (1.1%) in all amphibian TLRs, most of which were located in leucine-rich repeats (LRRs). We also observed low to moderate levels of single-nucleotide polymorphisms (SNPs) in Pelophylax nigromaculatus and Bombina orientalis. This study provided critical primers, meaningful information regarding TLR gene family evolution in amphibians, and insights into the complex evolutionary patterns and implications of TLR polymorphisms.

Effect of prenatal different auditory environment on learning ability and fearfulness in chicks.

OBJECTIVE: Early environmental enrichment in life can improve cognition in animals. The effect of prenatal auditory stimulation on learning ability and fear level in chick embryos remained unexplored. Therefore, this study investigated the effect of prenatal auditory stimulation on the learning ability and fear level of chicks. METHODS: A total of 450 fertilized eggs were randomly divided into 5 groups, including control group (C), low-sound intensity music group (LM), low-sound intensity noise group (LN), high-sound intensity noise group (HN) and high-sound intensity music group (HM). From the 10th day of embryonic development until hatching, group LM and group LN received 65 to 75 dB of music and noise stimulation. Group HN and group HM received 85 to 95 dB of noise and music stimulation, and group C received no additional sound. At the end of incubation, the one-trial passive avoidance learning (PAL) task and tonic immobility (TI) tests were carried out, and the serum corticosterone (CORT) and serotonin (5-HT) concentrations were determined. RESULTS: The results showed that compared with the group C, 65 to 75 dB of music and noise stimulation did not affect the PAL avoidance rate (p>0.05), duration of TI (p>0.05) and the concentration of CORT (p>0.05) and 5-HT (p>0.05) in chicks. However, 85 to 95 dB of music and noise stimulation could reduce duration of TI (p<0.05) and the concentration of CORT (p<0.05), but no significant effect was observed on the concentration of 5-HT (p>0.05) and PAL avoidance rate (p>0.05). CONCLUSION: Therefore, the prenatal auditory stimulation of 85 to 95 dB can effectively reduce the fear level of chicks while it does not affect the learning ability.

Dispersal and mating patterns determine the fate of naturally dispersed populations: evidence from Bombina orientalis.

BACKGROUND: In contrast to the explosive increase of a population following biological invasion, natural dispersal, i.e., when a population disperses from its original range into a new range, is a passive process that is affected by resources, the environment, and other factors. Natural dispersal is also negatively impacted by genetic drift and the founder effect. Although the fates of naturally dispersed populations are unknown, they can adapt evolutionarily over time to the new environment. Can naturally dispersed populations evolve beneficial adaptive strategies to offset these negative effects to maintain their population in a stable state? RESULTS: The current study addressed this question by focusing on the toad Bombina orientalis, the population of which underwent natural dispersal following the Last Glacial Maximum in Northeast Asia. Population genetic approaches were used to determine the genetic structure, dispersal pattern, and mating system of the population of B. orientalis in northeast China (Northern population). The results showed that this northern population of B. orientalis is a typical naturally dispersed population, in which the stable genetic structure and high level of genetic diversity of the population have been maintained through the long-distance biased dispersal behavior of males and the pattern of promiscuity within the population. CONCLUSIONS: Our findings suggest that naturally dispersed populations can evolve effective adaptive strategies to maintain a stable population. Different species may have different strategies. The relevance of these maintenance mechanisms for naturally dispersed populations provide a new perspective for further understanding the processes of speciation and evolution.

Evolutionary history of the oriental fire-bellied toad (Bombina orientalis) in Northeast China.

The evolutionary history of a species is generally affected by the combination of geological events and climate fluctuations. By analyzing the population features, genetic structure and the effective population historical dynamics of existing species, the population evolutionary history can be reestablished. In recent years, geological evidence shows that the Yilan-Yitong fault zone located in Northeast Asia experienced strong and frequent geological changes in the late Quaternary period. Species population history has been shaped by the combination of the complex climatic conditions of the Quaternary and Pleistocene glacial interglacial cycles and palaeogeological events in Northeast Asia and it has become a research focus for evolutionary biology researchers. In this study, mitochondrial and microsatellite molecular markers were used to reveal the population features, genetic structure, and the effective population historical dynamics of the Oriental fire-bellied toad (Bombina orientalis). The results showed that the strong seismic activity of the Yilan-Yitong fault zone in the late Quaternary period was the main reason for the population differentiation of Oriental fire-bellied toad in northeast China. The Quaternary Pleistocene glacial interglacial cycles led to the significant bottleneck effect of the western population located in the Maoer mountain area. As a result, the western population has low genetic diversity. Recent gene flow between eastern and western populations and historical evidence of population expansion proved that the dispersal behavior of the western populations was the main cause of the low genetic diversity and mitochondrial and nuclear discordance. Human economic activity may be the mainly driving factor. These evidences showed that the comprehensive influence of geology, climate, human activities and other factors should be considered in the process of exploring the evolutionary history of species.

The complete mitochondrial genome of Min pig (Hebao) and a phylogenetic analysis.

The complete mitochondrial genomes of Min pig (Hebao) are published in this paper. The full length of mtDNA is 16,719 bp and contained 13 PCGs, 2 rRNA and 22 tRNA, and 1D-loop(MN258706). A phylogenetic tree with the 13 protein-coding genes sequences of Min pig (Hebao) together with 45 other Chinese pig breeds and 7 foreign pig breeds was constructed. The results can be subsequently used to provide information for pig phylogenetic and insights into the evolution of genomes. The result of phylogenetic analysis showed that the genetic relationship of Min pig (Hebao) is closer to that of Dapulian pigs.

Development of 12 microsatellite markers for Bombina orientails based on RNA-Seq and their usefulness in population genetic diversity.

Bombina orientalis is widely used due to bombesin which isolated from its skin. But in recent years, the population of B. orientalis has become declining distinctly because of human activities, environmental pollution, drought climatic conditions and other factors. In order to provide the molecular basis for the proposal of biodiversity conservation, we report the development of 12 microsatellite markers for B. orientalis based on RNA-Seq. We test polymorphism against in 48 B. orientalis individuals which randomly selected from 182 individuals take advantage of polyacrylamide gel electrophoresis (PAGE). These markers will be useful in the research on the genetic diversity, population genetic structure and other studies. For B. orientalis, all of these loci showed polymorphism, and in line with the H-W equilibrium law. The number of alleles per locus ranged from 3 to 21. The observed and expected heterozygosities ranged from 0.0118 to 0.7795 and from 0.1612 to 0.8703, respectively. The polymorphism information content ranged from 0.153 to 0.857. And the genetic diversity of B. orientalis in Lushui Rivers is significantly higher than that in the Maoer Mountains.

Revealing the complete mitogenome sequence of Hypsugo alaschanicus based on next generation sequencing.

Hypsugo alaschanicus belong to Chiroptera, which is the only type of mammals with the real ability to fly. The complete mitochondrial genome of H. alaschanicus based on next generation sequencing data thus determined had 37 genes for 13 proteins, 22 tRNAs, and 2 rRNAs together with a major non-coding region in a typical gene arrangement of vertebrate mitogenomes. Phylogenetic analysis shows that Pipistrellini is multiline origin, Pipistrellus-like bats can be divided into three groups: Pipistrellini-Nyctalini, Vespertilionini-Eptesicini, and Asian Pipistrelles. Hypsugo alone become a clade, Vespertilio and Eptesicus phylogenetic relationship are closer, Pipistrellus and Nyctalus have a close phylogenetic relationship.

The complete mitochondrial genome of Cherskii's sculpin (Cottus czerskii) (Scorpaeniformes: Cottidae).

The complete mitogenome sequence of Cherskii's sculpin (Cottus czerskii) is determined using long PCR. The genome is 16,534 bp in length and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region. The overall base composition of the heavy strand is A (26.4%), C (30.1%), T (26.1%) and G (17.5%). The control region is 857 bp in length and the A + T content of the region is 61.5%. The extended termination-associated sequence domain, the central conserved domain and the conserved sequence block domain are defined in the mitochondrial genome control region of Cherskii's sculpin. Mitochondrial genome analyses based on MP, NJ and Bayesian analyses yielded identical phylogenetic trees, indicating a close phylogenetic affinity of the 21 Actinopterygii species. It appears that no less than two major phyletic lineages were present in Actinopterygii. The main clades within the Perciformes and Scorpaeniformes supported are: a clade including the Scombridae, Kyphosidae and Percichthyidae; a clade (Cottidae) with the Trichodontidae as the sister taxon to Pholidae, Anarhichadidae and Zoarcidae, which was supported by bootstrap values of 92%. The five Cottus species formed a paraphyletic group with the high bootstrap value (100%) in all examinations.

Sequence and organization of the complete mitochondrial genome of the Ussuri mamushi (Gloydius ussuriensis).

The mitochondrial genome sequence of Ussuri mamushi is analyzed and presented publically for the first time. The genome is 17,208 bp in length and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 2 control regions. The overall base composition is A (32.4%), C (28.4%), T (26.3%) and G (12.9%). The base compositions clearly presented the A-C skew, which is the most obvious in the protein-coding genes. Mitochondrial genome analyses based on MP, ML, NJ and Bayesian analyses yielded identical phylogenetic trees, indicating a close phylogenetic affinity of the 13 Crotalinae species. It appeared that no less than two major phyletic lineages were present in Crotalinae. The main clades within the Crotalinae include Protobothrops. A clade (G. brevicaudus, G. ussuriensis, G. intermedius, and G. sahatilis) with the Ovophis as the sister taxon to Protobothrops was supported by bootstrap values of 88%. The four Gloydius species formed a paraphyletic group with the high bootstrap value (100%) in all examinations.

Sequence and organization of the complete mitochondrial genome of Hebius vibakari ruthveni from China.

The mitochondrial genome sequence of Hebius vibakari ruthveni is analyzed and presented for the public for the first time. The genome was 17,259 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 2 control regions. The overall base composition is A (33.9%), C (26.5%), T (26.5%), and G (13.1%). Mitochondrial genomes analyses based on maximum parsimony (MP), neighbor-joining (NJ), and Bayesian analyses yielded identical phylogenetic trees, indicating a close phylogenetic affinity of the 24 Colubridae species. It shows that two major phyletic lineages were present in Colubridae: Hebius and Thamnophis. Hebius comprised 16 species and was supported by bootstrap values of 99%. A clade (H. craspedogaster, H. metusium, H. johannis, H. bitaeniatum and H. octolineatum) as the sister taxon to another clade (H. parallelum, H. khasiense, H. Boulengeri and H. popei) was supported by bootstrap values of 66%. This clade with the H. Atemporale is the sister taxon to H. optatum, H. sauteri, and H. v. ruthveni.

Sequencing and analysis of the complete mitochondrial genome of Amur minnow from China.

The complete mitogenome sequence of Amur minnow (Rhynchocypris lagowskii) was determined using long PCR. The genome was 16,594 bp in length and contained 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one control region. The overall base composition of the heavy strand is A (28.60%), C (26.32%), T (27.40%), and G (17.68%). The control region was 927 bp in length and the A + T content of the region was 63.32%. The extended termination-associated sequence domain, the central conserved domain, and the conserved sequence block domain are defined in the mitochondrial genome control region of Amur minnow. Mitochondrial genomes analyses based on maximum parsimony (MP), neighbor-joining (NJ), and Bayesian analyses yielded identical phylogenetic trees, indicating a close phylogenetic affinity of the 15 Cyprinidae species. It appeared that no less than two major phyletic lineages were present in Leuciscinae. The main clades within the Leuciscinae supported are: A clade is the Tribolodon. A clade (Rhynchocypris) with the Oreoleuciscus as the sister taxon to Tribolodon was supported by bootstrap values of 49%. The five different geographical populations of the R. lagowskii formed a paraphyletic group with the high bootstrap value (45%) in all examinations.

The complete mitochondrial genome of Eurasian water shrew (Neomys fodiens).

The complete mitogenome sequence of Eurasian water shrew (Neomys fodiens) was determined using long PCR. The genome was 17,260 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 1 control region. The overall base composition of the heavy strand is A (33.0%), C (23.2%), T (30.9%) and G (12.9%). The base compositions present clearly the A-T skew, which is most obviously in the control region and protein-coding genes. The extended termination-associated sequence domain, the central conserved domain and the conserved sequence block domain are defined in the mitochondrial genome control region of Eurasian water shrew. Mitochondrial genomes analyses based on MP, ML, NJ and Bayesian analyses yielded identical phylogenetic trees. Neomys elegans, Soriculus fumidus, and N. fodiens formed a monophyletic group with the high bootstrap value (100%) in all examinations. This clade with the Anourosorex squamipes as the sister taxon to Sorex.

The complete mitochondrial genome of Amur bitterling (Rhodeus sericeus) from China.

The complete mitogenome sequence of Amur bitterling (Rhodeus sericeus) was determined using long PCR. The genome was 16,581 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, 1 origin of L strand replication and 1 control region. The overall base composition of the heavy strand was A (28.9%), C (27.2%), T (26.6%), and G (17.3%). The control region was 925 bp in length and the A + T content of the region was 63.5%. The extended termination-associated sequence domain, the central conserved domain and the conserved sequence block domain are defined in the mitochondrial genome control region of Amur bitterling. Mitochondrial genome analyses based on MP, ML, NJ and Bayesian analyses yielded identical phylogenetic trees, indicating a close phylogenetic affinity to the 13 Cyprinidae species. It appeared that no less than three major phyletic lineages were present in Cyprinidae. A clade (Rhodeus and Tanakia) with the R. lighti and R. Sinensis as the sister taxon to Acheilognathus was supported by bootstrap values of 100%. The close relationship of Amur bitterling to other Rhodeus species, especially R. pseudosericeus, is consistent with the results confirmed using morphology analysis.

The complete mitochondrial genome of Gloydius intermedius (Squamata: Viperidae: Crotalinae) from China.

The mitochondrial genome sequence of Gloydius intermedius is analyzed and presented for the first time. The genome was 17, 226 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 2 control region. The overall base composition was A (32.4%), C (28.8%), T (25.9%), and G (12.9%). The base compositions clearly presented the A-C skew, which was most obvious in the protein-coding genes. The extended termination-associated sequence domain, the central conserved domain and the conserved sequence block domain are defined in the mitochondrial genome control region of G. intermedius. Mitochondrial genome analyses based on MP, ML, NJ and Bayesian analyses yielded identical phylogenetic trees, indicating a close phylogenetic affinity of the 13 Crotalinae species. It appeared that no less than two major phyletic lineages were present in Crotalinae. The main clades within the Crotalinae supported are: A clade including the Protobothrops. A clade (G. brevicaudus, G. ussuriensis, G. intermedius, G. saxatilis) with the Ovophis appeared as the sister taxon to Protobothrops and was supported by bootstrap values of 88%. The four Gloydius species formed a paraphyletic group with the high bootstrap value (100 %) in all examinations.

Sequencing and analysis of the complete mitochondrial genome of Elaphe davidi (Squamata: Colubridae).

The mitochondrial genome sequence of Elaphe davidi is analyzed and presented for the first time in this work. The genome was 17,117 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 2 control region. The overall base composition is A (35.4%), C (25.2%), T (27.0%), and G (12.4%). The base compositions present clearly the A-T skew, which was most obviously in the control region and protein-coding genes. Mitochondrial genomes analyses based on MP, ML, NJ and Bayesian analyses yielded identical phylogenetic trees, indicating a close phylogenetic affinity of the 12 Colubridae species. Two major phyletic lineages were present in Colubridae. A clade included the six species (Dinodon semicarinatus, E. poryphyracea, Oocatochus rufodorsatus, Orthriophis taeniurus, E. bimaculata and E. davidi) of subfamily Colubrinae except for Oligodon ningshaanensis. Another clade (Hypsiglena chlorophaea, H. unaocularus, H. torquata and Imantodes cenchoa) included Thermophis zhaoermii and O. ningshaanensis as the sister taxon to Colubrinae. The genus Elaphe, Dinodon, Oocatochus and Orthriophis formed a monophyletic group with the high bootstrap value (100 %) in all examinations.