Identifying the unique characteristics of the Chinese indigenous pig breeds in the Yangtze River Delta region for precise conservation.

BACKGROUND: China is the country with the most abundant swine genetic resources in the world. Through thousands of years of domestication and natural selection, most of pigs in China have developed unique genetic characteristics. Finding the unique genetic characteristics and modules of each breed is an essential part of their precise conservation. RESULTS: In this study, we used the partial least squares method to identify the significant specific SNPs of 19 local Chinese pig breeds and 5 Western pig breeds. A total of 37,514 significant specific SNPs (p < 0.01) were obtained from these breeds, and the Chinese local pig breed with the most significant SNPs was Hongdenglong (HD), followed by Jiaxing black (JX), Huaibei (HB), Bihu (BH), small Meishan (SMS), Shengxian Hua (SH), Jiangquhai (JQ), Mi (MI), Chunan (CA), Chalu (CL), Jinhualiangtouwu (JHL), Fengjing (FJ), middle Meishan (MMS), Shanzhu (SZ), Pudong white (PD), Dongchuan (DC), Erhualian (EH), Shawutou (SW) and Lanxi Hua (LX) pig. Furthermore, we identified the breeds with the most significant genes, GO terms, pathways, and networks using KOBAS and IPA and then ranked them separately. The results showed that the breeds with the highest number of interaction networks were Hongdenglong (12) and Huaibei (12) pigs. In contrast, the breeds with the lowest interaction networks were Shawutou (4) and Lanxi Hua pigs (3), indicating that Hongdenglong and Huaibei pigs might have the most significant genetic modules in their genome, whereas Shawutou and Lanxi Hua pigs may have the least unique characteristics. To some degree, the identified specific pathways and networks are related to the number of genes and SNPs linked to the specific breeds, but they do not appear to be the same. Most importantly, more significant modules were found to be related to the development and function of the digestive system, regulation of diseases, and metabolism of amino acids in the local Chinese pig breeds, whereas more significant modules were found to be related to the growth rate in the Western pig breeds. CONCLUSION: Our results show that each breed has some relatively unique structural modules and functional characteristics. These modules allow us to better understand the genetic differences among local Chinese and Western pig breeds and therefore implement precise conservation methods. This study could provide a basis for formulating more effective strategies for managing and protecting these genetic resources in the future.

Selection signature reveals genes associated with susceptibility loci affecting respiratory disease due to pleiotropic and hitchhiking effect in Chinese indigenous pigs.

BACKGROUND: Porcine respiratory disease is one of the most important health problems which causes significant economic losses. OBJECTIVE: To understand the genetic basis for susceptibility to swine enzootic pneumonia (EP) in pigs, we detected 102,809 SNPs in a total of 249 individuals based on genome-wide sequencing data. METHODS: Genome comparison of three susceptibility to swine EP pig breeds (Jinhua, Erhualian and Meishan) with two western lines that are considered more resistant (Duroc and Landrace) using XP-EHH and FST statistical approaches identified 691 positively selected genes. Based on QTLs, GO terms and literature search, we selected 14 candidate genes that have convincible biological functions associated with swine EP or human asthma. RESULTS: Most of these genes were tested by several methods including transcription analysis and candidated genes association study. Among these genes: CYP1A1 and CTNNB1 are involved in fertility; TGFBR3 plays a role in meat quality traits; WNT2, CTNNB1 and TCF7 take part in adipogenesis and fat deposition simultaneously; PLAUR (completely linked to AXL, r2=1) plays an essential role in the successful ovulation of matured oocytes in pigs; CLPSL2 (strongly linked to SPDEF, r2=0.848) is involved in male fertility. CONCLUSION: These adverse genes susceptible to swine EP may be selected while selecting for economic traits (especially reproduction traits) due to pleiotropic and hitchhiking effect of linked genes. Our study provided a completely new point of view to understand the genetic basis for susceptibility or resistance to swine EP in pigs thereby, provide insight for designing sustainable breed selection programs. Finally, the candidate genes are crucial due to their potential roles in respiratory diseases in a large number of species, including human.

Dihydromyricetin Inhibits Inflammation of Fibroblast-Like Synoviocytes through Regulation of Nuclear Factor-κB Signaling in Rats with Collagen-Induced Arthritis.

Dihydromyricetin (DMY), the main flavonoid of Ampelopsis grossedentata, has potent anti-inflammatory activity. However, the effect of DMY on chronic autoimmune arthritis remains undefined. In this study, we investigated the therapeutic effects of DMY on collagen-induced arthritis (CIA). Wistar rats were immunized with bovine type II collagen to establish CIA and were then administered DMY intraperitoneally (5, 25, and 50 mg/kg) every other day for 5 weeks. Paw swelling, clinical scoring, and histologic analysis were assessed to determine the therapeutic effects of DMY on the development of arthritis in CIA rats. The results showed that treatment with DMY significantly reduced erythema and swelling in the paws of CIA rats. Pathologic analysis of the knee joints and peripheral blood cytokine assay results confirmed the antiarthritic effects of DMY on synovitis and inflammation. Fibroblast-like synoviocytes (FLSs) were isolated from the synovium of CIA rats and treated with 10 ng/ml interleukin (IL)-1ß DMY significantly inhibited the proliferation, migration, and inflammation of IL-1ß-induced FLSs, whereas it significantly increased IL-1ß-induced FLS apoptosis in a dose-dependent manner (6.25-25 µM). Moreover, DMY suppressed phosphorylation of IκB kinase (IKK) and inhibitor of NF-κB α and subsequently reduced the IL-1ß-induced nucleus translocation of NF-κB in FLSs. Through a molecular docking assay, we demonstrated that DMY could directly bind to the Thr9 and Asp88 residues in IKKα and the Asp95, Asn142, and Gln167 residues in IKKß These findings demonstrate that DMY could alleviate inflammation in CIA rats and attenuate IL-1ß-induced activities in FLSs through suppression of NF-κB signaling.

MiR-204/-211 double knockout exacerbates rheumatoid arthritis progression by promoting splenic inflammation.

OBJECTIVE: Collagen-induced arthritis (CIA) model was induced in C57BL/6 wild-type (wt) and C57BL/6 miR-204/-211 double-knockout (dKO) mice to investigate the role of miR-204/-211 in suppressing splenic inflammation in rheumatoid arthritis (RA). METHODS: Differences of miR-204/-211 and structure-specific recognition protein 1 (SSRP1) in the spleen of DBA/1J wt and CIA mice were detected via PCR and immunohistochemistry. CIA was induced in both C57BL/6 wt and C57BL/6 miR-204/-211 dKO mice, and the onset of CIA and disease severity were statistically analyzed. Immunohistochemistry staining of interleukin-1ß (IL-1ß), tumor necrosis factor-α (TNF-α), and SSRP1 in spleen or knee joints was performed and analyzed. In CIA miR-204/-211 dKO mice, AAV-shSSRP1 was intra-articularly injected, with both the AAV-shRNA Ctrl and AAV-shRNA Ctrl CIA groups receiving the same dose of AAV-shRNA. Spleen sections were stained with hematoxylin and eosin (H&E). RESULTS: Compared to wt mouse spleens, aberrant expression of miR-204/-211 and SSRP1 was observed in the spleens of CIA mice. Immunized dKO mice exhibited a higher incidence of CIA onset and a more exacerbated RA disease phenotype, characterized by increased spleen inflammation score and elevated levels of IL-1ß, TNF-α, and SSRP1 expression. AAV-shSSRP1 injection in CIA dKO mice significantly reduced spleen inflammation scores, IL-1ß and TNF-α expression levels, and down-regulated Ki-67 expression compared to CIA dKO mice. CONCLUSION: Knockout of miR-204/-211 exacerbated the onset of CIA in C57BL/6 mice, while miR-204/-211 played a protective role against the progression of splenic inflammatory and proliferative progression in RA by targeting SSRP1.

Mir204 and Mir211 suppress synovial inflammation and proliferation in rheumatoid arthritis by targeting Ssrp1.

Rheumatoid arthritis (RA) is a chronic inflammatory joint disease characterized by synovial hyperplasia. Mir204 and Mir211 are homologous miRNAs with the same gene targeting spectrum. It is known that Mir204/211 play an important role in protecting osteoarthritis development; however, the roles of Mir204/211 in RA disease have not been determined. In the present study, we investigated the effects and molecular mechanisms of Mir204/211 on synovial inflammation and hyperproliferation in RA. The effects of Mir204/211 on the inflammation and abnormal proliferation in primary fibroblast-like synoviocytes (FLSs) were examined by Mir204/211 gain-of-function and loss-of-function approaches in vitro and in vivo. We identified the structure-specific recognition protein 1 (Ssrp1) as a downstream target gene of Mir204/211 based on the bioinformatics analysis. We overexpressed Ssrp1and Mir204/211 in FLS to determine the relationship between Ssrp1 and Mir204/211 and their effects on synovial hyperplasia. We created a collagen-induced arthritis (CIA) model in wild-type as well as Mir204/211 double knockout (dKO) mice to induce RA phenotype and administered adeno-associated virus (AAV)-mediated Ssrp1-shRNA (AAV-shSsrp1) by intra-articular injection into Mir204/211 dKO mice. We found that Mir204/211 attenuated excessive cell proliferation and synovial inflammation in RA. Ssrp1 was the downstream target gene of Mir204/211. Mir204/211 affected synovial proliferation and decelerated RA progression by targeting Ssrp1. CIA mice with Mir204/211 deficiency displayed enhanced synovial hyperplasia and inflammation. RA phenotypes observed in Mir204/211 deficient mice were significantly ameliorated by intra-articular delivery of AAV-shSsrp1, confirming the involvement of Mir204/211-Ssrp1signaling during RA development. In this study, we demonstrated that Mir204/211 antagonize synovial hyperplasia and inflammation in RA by regulation of Ssrp1. Mir204/211 may serve as novel agents to treat RA disease.

Pharmacology and molecular docking study of cartilage protection of Chinese herbal medicine Fufang Shatai Heji (STHJ) by inhibiting the expression of MMPs in collagen-induced arthritis mice.

BACKGROUND: This study aims to explore whether Fufang Shatai Heji (STHJ), as a mixture collected by a decoction of a variety of Chinese herbal medicines for immune system diseases, can improve the cartilage destruction of rheumatoid arthritis (RA). METHODS: The therapeutic effects of STHJ were studied using collagen induced arthritis (CIA) mice. The improvement effect of STHJ on synovitis and cartilage damage caused by arthritis was studied by joint pathological analysis. The inhibitory effect of STHJ on related degradation enzymes in cartilage was studied by immunohistochemistry and real-time polymerase chain reaction (PCR). The specific targets of STHJ were predicted by molecular docking. RESULTS: After successfully inducing CIA, the paws of the mice showed significant swelling, and athological analysis of the ankle and knee joints also showed significant cartilage destruction and synovial hyperplasia. However, synovial hyperplasia and cartilage destruction were markedly alleviated after administration of STHJ. And after STHJ treatment, the expression of ADAMTS-4, ADAMTS-5, MMP-9 and MMP-13, in the cartilage layer of CIA mice was significantly inhibited. Through molecular docking assays, we proved that acteoside in STHJ could directly bind to the Glu111, Phe110 residues in MMP-9 and glycyrrhizic acid in STHJ bind to the Glu382, Asn433 residues in MMP-13. CONCLUSIONS: Our results suggested that STHJ may alleviate synovial hyperplasia and cartilage destruction in CIA mice and protect cartilage by inhibiting the expression of MMP-9 and other enzymes.

Dexamethasone-loaded thermo-sensitive hydrogel attenuates osteoarthritis by protecting cartilage and providing effective pain relief.

BACKGROUND: We utilized the destabilization of medial meniscus (DMM)-induced mice to illustrate the osteoarthritis (OA) suppressing and pain-relieving effects of a novel prolonged-release intra-articular (IA)-dexamethasone-loaded thermo-sensitive hydrogel (DLTH). METHODS: The effects of temperature and pH on DLTH formation and in vitro DLTH release profile were assessed. C57BL/6J mice were randomly divided into three groups: Ctrl group, Model group and DLTH group. The DLTH group received joint injections of 10 µL DLTH (1 mg/kg) into the right knee once a week from week 2 to week 11. We performed micro-computed tomography (Micro-CT) and histological analyses of safranin O-fast green, hematoxylin and eosin, and tartrate-resistant acid phosphatase in knee joints. We also carried out immunohistochemical (IHC) staining for matrix metalloproteinase-9 (MMP-9), MMP-13, and a disintegrin and metalloproteinase with thrombospondin motifs-5 (ADAMTS-5) in cartilage and Ki-67 in synovia. Pain behavioral testing was carried out in all mice. The serum content of prostaglandin E2 (PGE2) and real-time polymerase chain reaction (PCR) of inflammatory cytokines and pain-related factors in dorsal root ganglia (DRGs) were evaluated. RESULTS: It took 20 minutes to form DLTH at pH 7.0 and 37 °C. The cumulative release profiles of dexamethasone (Dex) from DLTH at 37 °C revealed a rapid release in the first 24 h and a sustained slow release for 7 days. In vivo study illustrated that DLTH attenuated OA bone destruction and ameliorated synovitis and progression of OA in DMM-induced mice. The chondroprotective effects of DLTH were mediated by decreased expressions of MMP-9, MMP-13, and ADAMTS-5. The results showed that IA-DLTH exerted pain-relieving effects in OA mice. Upregulation of nociceptive response time (NRT) and downregulations of serum PGE2, inflammatory factors, and pain-related mediators in DRGs of mice in the DLTH group were recorded. CONCLUSIONS: Data presented in this study elucidated that DLTH exhibited a long and lasting Dex release and it is a potential sustainable drug delivery system (DDS) to treat OA locally. IA-DLTH injection exerted chondroprotective and pain-relieving effects in DMM-induced arthritis. The involvement of MMP-9, MMP-13, ADAMTS-5, and inflammatory and pain-related factors, may account for the suppression of OA progression and pain.

Conservation Priorities Analysis of Chinese Indigenous Pig Breeds in the Taihu Lake Region.

Most indigenous pig resources are known to originate from China. Thus, establishing conservation priorities for these local breeds is very essential, especially in the case of limited conservation funds. Therefore, in this study, we analyzed 445 individuals belonging to six indigenous breeds from the Taihu Lake Region, using a total of 131,300 SNPs. In order to determine the long-term guidelines for the management of these breeds, we analyzed the level of diversity in the metapopulation following a partition of diversity within and between breed subpopulations, using both measures of genic and allelic diversity. From the study, we found that the middle Meishan (MMS) pig population contributes the most (22%) to the total gene diversity while the Jiaxing black (JX) pig population contributes the most (27%) to the gene diversity between subpopulations. Most importantly, when we consider one breed is removed from the meta-population, the first two breeds prioritized should be JX pig breed and Fengjing pig breed followed by small Meishan (SMS), Mizhu (MI), and Erhualian (EH) if we pay more attention to the gene diversity between subpopulations. However, if the priority focus is on the total gene diversity, then the first breed to be prioritized would be the Shawutou (SW) pig breed followed by JX, MI, EH, and Fengjing (FJ). Furthermore, we noted that if conservation priority is to be based on the allelic diversity between subpopulations, then the MI breed should be the most prioritized breed followed by SW, Erhuanlian, and MMS. Summarily, our data show that different breeds have different contributions to the gene and allelic diversity within subpopulations as well as between subpopulations. Our study provides a basis for setting conservation priorities for indigenous pig breeds with a focus on different priority criteria.

[Study on regulatory mechanism of bovine early embryos development based on the analysis of gene expression data].

The death of early embryo development will bring huge economic losses in animal husbandry, especially for dairy production of cattle. Thus, it has an extremely important value to study the process of early embryonic development. In our study, one dataset of gene expression was chosen from the public database of GEO, which was related to bovine preimplantation development. Significance and clustering analyses were used to study the genome expression patterns of each stage during bovine preimplantation development. The whole process was assigned to three main groups. The waves of significant gene expression in each stage indicated that both 8-cell and 16-cell stages played an important role during the process of bovine preimplantation development. Further functional analysis and pathway analysis revealed that some major factors and related pathways are required for distinctive developmental stages.

DMY protects the knee joints of rats with collagen-induced arthritis by inhibition of NF-κB signaling and osteoclastic bone resorption.

Collagen-induced arthritis (CIA) is a widely used animal model for studying rheumatoid arthritis (RA), which manifests serious joint dysfunction, progressive bone erosion and articular cartilage destruction. Considering that joint damage in RA is caused by systemic inflammation and dihydromyricetin (DMY), the main flavonoid of Ampelopsis Michx, possesses anti-inflammatory properties, in the present study we have investigated the potential capability of DMY to inhibit inflammation-mediated joint damage and explore the underlying mechanisms. A rat model of RA induced by CIA was administered with DMY for 5 weeks. Prior to histological analysis, the knee joints were scanned by microcomputed tomography (µCT) to detect bone damage. Articular cartilage destruction was assessed by Alcian blue and Toluidine blue staining and the pathological alteration of osteoblasts and osteoclasts in joints was evaluated by hematoxylin-eosin (H&E) and tartrate-resistant acid phosphatase (TRAP) staining, respectively. The effects of DMY on osteoblast differentiation and osteoclast formation in vitro were investigated. Consistent with the in vivo results, DMY had no significant effect on osteoblast differentiation but an inhibitory effect on osteoclast formation. Furthermore, we determined that the mechanism of the DMY-suppressed osteoclast formation was blocking the phosphorylation of I-κB kinase (IKK) so as to hinder the activation of nuclear factor-κB (NF-κB). Collectively, DMY could ameliorate knee joint damage, especially in articular cartilage, which is the weight-bearing region, by inhibiting osteoclast formation through NF-κB signaling.

Dexamethasone-Loaded Thermosensitive Hydrogel Suppresses Inflammation and Pain in Collagen-Induced Arthritis Rats.

PURPOSE: To overcome negative adverse effects and improve therapeutic index of dexamethasone (Dex) in rheumatoid arthritis (RA), we developed a novel sustained release formulation-intra-articular injectable dexamethasone-loaded thermosensitive hydrogel (DLTH) with chitosan-glycerin-borax as carrier for the remission of inflammation and pain. The focus of this article is to explore both anti-inflammatory and pain-relieving effects of DLTH joint injection in bovine type-II collagen-induced arthritis (CIA) rats. METHODS: Wistar rats were randomized into three groups, including the normal group (n=6), the model group (n=6) and the DLTH group (n=10). Joint injection of DLTH (1mg/kg Dex per rat) was injected on day 12 in the DLTH group twice a week for three weeks. Clinical signs of body weight, paw swelling and arthritis scores, histologic analysis, hind paw mechanical withdrawal threshold (MWT), plantar pressure pain threshold (PPT) were taken into consideration. Serum contents of IL-17A, prostaglandin E2 (PGE2), prostacyclin 2 (PGI2) and prostaglandin D2 (PGD2), real-time polymerase chain reaction (PCR) analysis of inflammatory factors and pain-related mediators in synovium and dorsal root ganglia (DRG), Western blotting of NF-κB in synovium were all evaluated. RESULTS: Paw swelling, arthritis scores and joint inflammation destruction were all attenuated in the DLTH-treated group. Results showed that DLTH not only down-regulated serum IL-17A, but also mRNA levels of inflammatory factors and NGF, and key proteins contents of the NF-κB pathway in synovium. Increases of MWT and PPT in DLTH-treated rats elucidated pain-reducing effects of DLTH. Elevated serum PGD2 levels and declines of serum PGE2 and PGI2, and inflammatory and pain-related genes in DRGs in the DLTH group were also recorded. CONCLUSION: These data elucidated that DLTH joint injection impeded synovial inflammation processes through down-regulating transcription activity of NF-κB pathway, and intra-articular DLTH may aid in the regulation of RA pain through regulating inflammation and pain conduction process.

Metformin inhibits inflammation and bone destruction in collagen-induced arthritis in rats.

BACKGROUND: Metformin (MF) is a widely used biguanide oral hypoglycemic agent, which has obvious anti-inflammatory and immunomodulatory effects. However, the mechanism of MF on rheumatoid arthritis (RA) remains uncertain. In this study, we investigated the therapeutic effects of MF on collagen-induced arthritis (CIA). METHODS: CIA was induced in rats by intradermal injection of a mixture of bovine type II collagen and incomplete Freund's adjuvant (IFA) on day 0 and day 7 through the base of the tail. Intraperitoneal injection of MF (100 mg/kg) was given every 3 days, from day 14 for 3 weeks. The effects of MF on arthritis-induced systemic inflammation and synovitis were studied by pathological analysis of the knee joint and serological examination of peripheral blood in CIA rats. The bone protection effect of MF was studied by microscopic computed tomography (micro-CT) and histological analysis of the knee joint. The effects of MF on chondrocytes in CIA rats were studied by detecting the relevant pro-apoptotic mediators in the chondrocytes. RESULTS: After administration of MF in CIA rats, systemic inflammation and synovitis caused by arthritis were significantly suppressed. Histomorphometry and micro-CT analysis of the knee joint revealed that MF can protect bone by inhibiting the changes of trabecular bone in CIA rats. Histological analysis of the knee joint found that MF can inhibit osteoclast formation and degradation of the cartilage layer matrix. Detection of the relevant pro-apoptotic mediators in chondrocytes revealed that MF can significantly inhibit the apoptosis of chondrocytes in CIA rats. CONCLUSIONS: Our study showed that MF can inhibit systemic inflammation and synovitis and plays a role in bone protection by inhibiting cartilage layer matrix degradation, osteoclast formation, and chondrocyte apoptosis.

The Traditional Chinese Medicine Fufang Shatai Heji (STHJ) Enhances Immune Function in Cyclophosphamide-Treated Mice.

Fufang Shatai Heji (STHJ) is a mixture of traditional Chinese medicines, such as Radix Adenophorae, Radix Pseudostellariae, and Radix Astragali. STHJ is commonly used to treat diseases caused by low immune function, for example, Sjögren's syndrome (SS). The primary objective of this study was to assess the immunopotentiating effect of STHJ using an immunosuppressive mouse model receiving cyclophosphamide (CTX). Following CTX treatment, STHJ was administered by oral gavage for 30 consecutive days. The percentage of specific lymphocyte subpopulations in the spleen was measured by flow cytometry. Levels of inflammatory factors in serum were detected by enzyme-linked immunosorbent assays (ELISAs). The administration of STHJ significantly elevated thymus and spleen indices, increased B cell and natural killer (NK) cell activities, and decreased CD8+ T, CD8+CD122+ T, NKT, and γδT cell activities in the CTX-treated mice. In addition, STHJ upregulated the expression of interleukin- (IL-) 2, IL-6, and tumor necrosis factor-α (TNF-α) and downregulated IL-10 expression in CTX-treated mice. In conclusion, STHJ effectively remitted CTX-induced immunosuppression by modulating the balance of lymphocyte subsets and cytokines. Our results suggest STHJ treatment could be used as an effective therapeutic approach to improve immune function in patients with low immunity.

Exploring the Structure of Haplotype Blocks and Genetic Diversity in Chinese Indigenous Pig Populations for Conservation Purpose.

Chinese indigenous pigs in the Taihu Lake region are well known for their high fecundity and other excellent characteristics. To better understand the characteristics of these breeds in this area as well as to provide the government and breeders the molecular basis for formulating a reasonable conservation policy, we explored the structure of haplotype blocks and genetic diversity of the 7 populations which is relevant for the management and conservation of these important genetic resources using next-generation sequencing data. In this study, a total of 131 300 single-nucleotide polymorphisms with minor allele frequencies ⩾0.05 were obtained for further analysis. In general, there are similar within-breed genetic diversities (He, Ho, Pn, Ar) among these 7 pig populations in the Taihu Lake region. Average values for the inbreeding coefficients estimates in the 7 populations are 0.110 (F1), 0.056 (F2), and 0.078 (F3). All the breeds have seen a continuous decline in Ne estimates over time with FJ and SW populations having a very similar curve. Moreover, the Ne of SMS pig breeds were smaller than other Chinese pig breeds, indicating that SMS pig breeds underwent stronger selection pressure than other Chinese pig breeds. The average genetic distances among the 7 populations in the Taihu Lake region were 0.235 (MMS), 0.240 (SMS), 0.269 (EH), 0.248 (MI), 0.221 (FJ), 0.254 (JX), and 0.212 (SW). A summary of the number of haplotype blocks and haplotype diversity was also presented. This study provide a deep understanding of the current situation of conservation in this region, thereby uncovering the pertinent insight to better formulate more reasonable preservation policies for the government departments and breeding planners to follow-up.

The genetic connectedness calculated from genomic information and its effect on the accuracy of genomic prediction.

The magnitude of connectedness among management units (e.g., flocks and herds) gives a reliable estimate of genetic evaluation across these units. Traditionally, pedigree-based methods have been used to evaluate the genetic connectedness in China. However, these methods have not been able to yield a substantial outcome due to the lack of accuracy and integrity of pedigree data. Therefore, it is necessary to ascertain genetic connectedness using genomic information (i.e., genome-based genetic connectedness). Moreover, the effects of various levels of genome-based genetic connectedness on the accuracy of genomic prediction still remain poorly understood. A simulation study was performed to evaluate the genome-based genetic connectedness across herds by applying prediction error variance of difference (PEVD), coefficient of determination (CD) and prediction error correlation (r). Genomic estimated breeding values (GEBV) were predicted using a GBLUP model from a single and joint reference population. Overall, a continued increase in CD and r with a corresponding decrease in PEVD was observed as the number of common sires varies from 0 to 19 regardless of heritability levels, indicating increasing genetic connectedness between herds. Higher heritability tends to obtain stronger genetic connectedness. Compared to pedigree information, genomic relatedness inferred from genomic information increased the estimates of genetic connectedness across herds. Genomic prediction using the joint versus single reference population increased the accuracy of genomic prediction by 25% and lower heritability benefited more. Moreover, the largest benefits were observed as the number of common sires equals 0, and the gain of accuracy decreased as the number of common sires increased. We confirmed that genome-based genetic connectedness enhanced the estimates of genetic connectedness across management units. Additionally, using the combined reference population substantially increased accuracy of genomic prediction. However, care should be taken when combining reference data for closely related populations, which may give less reliable prediction results.

Identifying Genetic Differences Between Dongxiang Blue-Shelled and White Leghorn Chickens Using Sequencing Data.

The Dongxiang Blue-shelled chicken is one of the most valuable Chinese indigenous poultry breeds. However, compared to the Italian native White Leghorn, although this Chinese breed possesses numerous favorable characteristics, it also exhibits lower growth performance and fertility. Here, we utilized genotyping sequencing data obtained via genome reduction on a sequencing platform to detect 100,114 single nucleotide polymorphisms and perform further biological analysis and functional annotation. We employed cross-population extended haplotype homozygosity, eigenvector decomposition combined with genome-wide association studies (EigenGWAS), and efficient mixed-model association expedited methods to detect areas of the genome that are potential selected regions (PSR) in both chicken breeds, and performed gene ontology (GO) enrichment and quantitative trait loci (QTL) analyses annotating using the Kyoto Encyclopedia of Genes and Genomes. The results of this study revealed a total of 2424 outlier loci (p-value <0.01), of which 2144 occur in the White Leghorn breed and 280 occur in the Dongxiang Blue-shelled chicken. These correspond to 327 and 94 PSRs containing 297 and 54 genes, respectively. The most significantly selected genes in Blue-shelled chicken are TMEM141 and CLIC3, while the SLCO1B3 gene, related to eggshell color, was identified via EigenGWAS. We show that the White Leghorn genes JARID2, RBMS3, GPC3, TRIB2, ROBO1, SAMSN1, OSBP2, and IGFALS are involved in immunity, reproduction, and growth, and thus might represent footprints of the selection process. In contrast, we identified six significantly enriched pathways in the Dongxiang Blue-shelled chicken that are related to amino acid and lipid metabolism as well as signal transduction. Our results also reveal the presence of a GO term associated with cell metabolism that occurs mainly in the White Leghorn breed, while the most significant QTL regions mapped to the Chicken QTL Database (GG_4.0) for the Dongxiang Blue-shelled breed are predominantly related to lesions, bone mineral content, and other related traits compared to tibia length and body weight (i.e., at 14, 28, 42, and 70 d) in the White Leghorn. The results of this study highlight differences in growth, immunity, and egg quality traits between the two breeds, and provide a foundation for the exploration of their genetic mechanisms.

Genomic analysis reveals genes affecting distinct phenotypes among different Chinese and western pig breeds.

The differences in artificial and natural selection have been some of the factors contributing to phenotypic diversity between Chinese and western pigs. Here, 830 individuals from western and Chinese pig breeds were genotyped using the reduced-representation genotyping method. First, we identified the selection signatures for different pig breeds. By comparing Chinese pigs and western pigs along the first principal component, the growth gene IGF1R; the immune genes IL1R1, IL1RL1, DUSP10, RAC3 and SWAP70; the meat quality-related gene SNORA50 and the olfactory gene OR1F1 were identified as candidate differentiated targets. Further, along a principal component separating Pudong White pigs from others, a potential causal gene for coat colour (EDNRB) was discovered. In addition, the divergent signatures evaluated by Fst within Chinese pig breeds found genes associated with the phenotypic features of coat colour, meat quality and feed efficiency among these indigenous pigs. Second, admixture and genomic introgression analysis were performed. Shan pigs have introgressed genes from Berkshire, Yorkshire and Hongdenglong pigs. The results of introgression mapping showed that this introgression conferred adaption to the local environment and coat colour of Chinese pigs and the superior productivity of western pigs.

Degradation of microcystin-RR by UV radiation in the presence of hydrogen peroxide.

Experiments were conducted to investigate the degradation of microcystin-RR in order to assess the effectiveness and feasibility of the combined UV/H(2)O(2) catalytic system for purification of water polluted by microcystins. The operating parameters such as hydrogen peroxide dosage, pH value, UV light intensity, initial concentration of microcystin-RR and reaction time were evaluated, respectively. The degradation efficiency increased nonlinearly with increasing UV light intensity and hydrogen peroxide dosage, respectively. There existed an optimal hydrogen peroxide dosage, beyond which the reagent exhibited an inhibitory effect, for degrading microcystin-RR. The degradation process could be fitted by both of the pseudo-first-order and second-order kinetics well and primarily followed a mechanism of both direct photolysis and hydroxyl radical oxidation. Compared with the treatment using UV radiation and hydrogen peroxide individually, the combined UV/H(2)O(2) system could significantly enhance the degradation efficiency due to the synergetic effect between UV radiation and hydrogen peroxide oxidation. The observed rate constants decreased and the corresponding half-lives prolonged as the concentrations of microcystin-RR increased. The combined UV/H(2)O(2) process provides an effective technology for the removal of microcystins from drinking water supplies.

Qualitative analysis and quantitative simulation on Yin-Huang water salinization mechanism in Bei-Da-Gang Reservoir.

Yellow River water transfer for Tianjin is important in solving the water shortage in Tianjin, which facilitate economic development and social progress for many years. Fresh water drawn from Yellow River (i.e., Yin-Huang water) becomes saltier and saltier when being stored in the Bei-Da-Gang reservoir. We qualitatively analyze the water salinization mechanism based on mass transfer theory. The main factors are salinity transfer of saline soil, evaporation concentrating, and the agitation of wind. A simulative experimental pond and an evaporation pond were built beside the Bei-Da-Gang reservoir to quantitatively investigate the water salinization based on water and solute balance in the simulative pond. 80% of increased [Cl-] is due to the salinity transfer of the saline soil and the other 20% is due to evaporation concentrating, so the former is the most important factor. We found that the salinization of Yin-Huang water can be described with a zero-dimension linear model.