Genomic selection for meat quality traits in Pekin duck.

Genomic selection uses genome-wide molecular marker data to predict an animal's genetic value in the breeding program. This study's objective was to present heritability estimates and accuracy of genomic prediction using different methods for meat quality traits in Pekin duck. There were two kinds of ducks in the genomic selection training population: 639 fat-type ducks and 540 lean-type ducks. A single-trait animal model was used to estimate heritability and adjust the phenotype. GBLUP and BayesR methods were performed to estimate the SNP effects. The accuracy of genomic prediction was calculated using 5-fold cross-validation. The accuracy varied from 0.235 to 0.501 with the lowest accuracy estimated for traits associated with abdominal fat weight in the combined population and the most remarkable accuracy observed for abdominal fat percentage traits in the lean-type duck population. Overall, BayesR can achieve the highest prediction accuracy, while the combined population strategy could be used to increase the accuracy of prediction only when the two populations have the same breeding aim for a certain trait.

[Characteristics and related factors of plantar pressure in the chronic ankle instability individuals].

OBJECTIVE: To analyze characteristics and related factors of the plantar pressure during the level walking and single leg standing in the chronic ankle instability (CAI) individuals. METHODS: From April 2019, 75 CAI individuals and 40 healthy individuals were enrolled in this study. Both of the static and dynamic plantar pressure were measured during six times level walking and three times single leg standing testing. The data including peak force, time to peak force in various foot contact areas and the time to boundary (TTB) and velocity of center of pressure (COP) were measured and compared between the affected side and the unaffected side and between the CAI cases and the healthy individuals. The correlations between the plantar pressure and the gender, Beighton score, affected side and body mass index (BMI) were analyzed. RESULTS: The characteristics of plantar pressure distribution in the CAI individuals included: (1) During the level walking, the affected side showed the similar pressure contribution as the unaffected side (P>0.05). While compared with healthy individuals, there was a significantly higher peak force in the 5th metatarsal area (t=-3.86, P=0.03) of the affected side, lower peak force in the 1st (t=2.99, P=0.02), 2nd metatarsal head areas (t=2.09, P=0.01) of the affected side, medial hindfoot areas of both sides (affected, t=2.33, P=0.01; unaffected, t=3.74, P=0.02) and toes areass of both sides (affected, t=2.23, P=0.01; unaffected, t=3.28, P=0.02) and a delay to peak force in the 4th metatarsal head area (t=3.33, P=0.01) of the affected side. (2) During the single leg standing, the CAI individuals showed significantly worse balance control in the anterior/posterior direction (P < 0.05) and lateral/medial direction (P < 0.05) compared with the healthy controls, and the affected side had more severe balance control deficit in the lateral/medial direction (P < 0.05). (3) The women (P < 0.05) and the individuals with higher Beighton scores (P < 0.05) showed worse balance control deficit in the lateral/medial direction. CONCLUSION: CAI individuals showed significantly a more lateral shifted plantar distribution during the level walking compared with the healthy individuals and the tendency was worse on the affected sides, and showed worse balance control in the anterior/posterior direction and lateral/medial direction during the single leg standing. The women and those with generalized ligament laxity showed significantly worse balance control.

Genome-wide association study reveals novel loci associated with fat-deposition and meat-quality traits in Pekin ducks.

Meat-quality traits play an essential role in meat poultry production. To determine the genetic mechanisms of meat quality in Pekin ducks, we performed a large-scale GWAS to identify quantitative trait loci affecting meat quality in Pekin ducks. We measured 10 traits in 542 Pekin ducks and genotyped each duck using genotyping-by-sequencing. The genetic parameters (genomic heritability, genetic correlation) for 10 meat-quality related traits were evaluated. Based on the large genotype-phenotype dataset, we performed GWASs for all of these traits. A total of 33 significant QTL (P < 3.03 × 10-5 ) across 13 chromosomes were identified by loci-based analysis. Some newly identified candidate genes were discovered for fat-deposition and meat-quality traits, including PAG1 for body weight and eviscerated weight, INTU and NUP35 for abdominal fat weight and ratio, NUP3 and ARHGDIB for skin fat weight and ratio, GOLGA5 for breast muscle toughness and breast tenderness, and CTDSPL and PKP1 for breast muscle thickness. The current study is the first systematic report regarding duck meat quality.

Avian sarcoma and leukosis virus gag gene in the Anser anser domesticus genome.

Endogenous retroviruses are regarded as ideal genetic markers for evolutionary analyses. Birds were some of the initial vertebrates found to contain endogenous retroviruses. However, few studies have investigated the presence and distribution of endogenous retroviruses in goose. In this study, we detected the avian sarcoma and leukosis virus gag gene in the genomic DNA of 8 Chinese native breeds using polymerase chain reaction method. The results indicated that a 1.2-kb avian sarcoma and leukosis virus gag sequence was integrated into all 8 goose breeds. The mean genetic pairwise distance was 0.918% among the investigated geese. To the best of our knowledge, this is the first report demonstrating the presence of the endogenous retroviruses in the domestic goose genome. The genetic structure should be further examined in the domestic goose.

Detection of autoantibodies to a panel of tumor-associated antigens for the diagnosis values of gastric cardia adenocarcinoma.

To evaluate the diagnostic values of using autoantibodies in sera to a panel of eight tumor-associated antigens (TAAs) of P53, Koc, P62, C-myc, IMP1, Survivn, P16 and Cyclin B1 full-length recombinant proteins for early detection of patients with gastric cardia adenocarcinoma (GCA) and high-risk subjects screening. Enzyme-linked immunosorbent assay was used to detect autoantibodies against the eight selected TAAs in 383 sera samples from four groups, including 140 subjects with normal gastric cardia epithelia (NOR), 76 patients with chronic atrophic gastritis (CAG), 79 patients with gastric cardia dysplasia (DYS) and 88 patients with GCA. In addition, the expression of the eight antigens was analyzed in gastric cardia tissues by immunohistochemical method. The individual autoantibodies to six TAAs (P53, P62, IMP1, Survivn P16 and Cyclin B1) were significantly higher in sera from patients with GCA than that in normal subjects (P < 0.05). When autoantibody assay successively accumulated to seven TAAs (P53, Koc, P62, C-myc, IMP1, Survivn and P16), a stepwise increased detection frequency of autoantibodies was found in the four sera groups (13% in NOR, 39% in CAG, 46% in DYS, and 64% in GCA, respectively), the risks to CAG, DYS and GCA steadily increased about 4.4-, 5.7- and 12.0-fold. The sensitivity and the specificity for autoantibodies against the seven TAAs in diagnosing GCA reached up to 64% and 87%, respectively. The area under the receiver operating characteristic curve for the seven anti-TAA autoantibodies was 0.73 (95%CI: 0.68-0.78) No more increase in sensitivity was found with the addition of new anti-TAA autoantibodies. A combination detection of autoantibodies to TAAs might be helpful to distinguish GCA patients from normal subjects and the patients with gastric cardia precancerous lesions. In addition, further studies in patients with GCA and precancerous lesions using enlarged TAA panels might improve the sensitivity and specificity of cancer detection and high-risk subjects screening.

Differential expression of Toll-like receptor genes in lymphoid tissues between Marek's disease virus-infected and noninfected chickens.

Toll-like receptors (TLR) are trans-membrane sensors recognizing invading microbes. Toll-like receptors play a central role in initiating immune responses against several pathogens. In this study, we investigated the response of TLR and downstream genes to Marek's disease virus (MDV) infection. Forty 1-d-old chicks were randomly divided into 2 groups, with 20 chicks infected with MDV and 20 chicks mock-infected. Four chickens were euthanized respectively from infected and age-matched noninfected groups at 4, 7, 14, 21, and 28 d postinfection (dpi). Bursas, spleens, and thymuses were removed. The differential expression of TLR genes, including TLR3, TLR5, TLR7, TLR15, and TLR21, and downstream genes of TLR7, including MyD88, TRAF3, TRAF6, IFNA, IFNB, and IL6, in lymphoid tissues of MDV-infected and noninfected chickens was determined by real-time PCR. The results showed that the change of TLR genes was different in 3 lymphoid tissues. Expression of TLR7 and MyD88 was upregulated at 14 dpi and downregulated at 28 dpi in MDV-infected compared with noninfected spleens. The TRAF6 and IFNB were upregulated, and TRAF3, IFNA, and IL6 genes showed increasing trends in MDV-infected compared with noninfected spleens at 14 dpi. The expression of TLR3 and TLR15 genes was downregulated in MDV-infected compared with noninfected spleens at 28 dpi. The results indicated that TLR7 and its downstream genes were a response to MDV infection at 14 dpi. However, the function of TLR was impaired when the infection entered the tumor transformation phase. In bursas, TLR3 and TLR15 genes were upregulated at 7 and 4 dpi, respectively. It indicated that TLR3 and TLR15 might be involved in response to MDV infection in bursa at early phases. However, no differential expression of TLR genes was observed between MDV-infected and noninfected thymuses, which indicated that the thymus had little response to MDV infection mediated by TLR.

Polymorphisms in Wnt signaling pathway genes are significantly associated with chicken carcass traits.

The Wnt signaling pathway plays a crucial role during embryogenesis in vertebrates. In this study, 124 SNP in 31 Wnt signaling pathway genes were selected to genotype 764 individuals in an F(2) resource population by reciprocally crossing Silkie fowls and Cornish broilers, and 102 SNP were polymorphic. Pairwise linkage disequilibrium among the SNP within each gene was calculated. Haplotypes were reconstructed from the SNP in strong linkage disequilibrium. The associations of SNP and haplotypes with carcass traits were analyzed respectively, and the SNP contributions to phenotypic variance were estimated. The present study showed that 58 SNP in 24 genes and 8 haplotype blocks within 7 genes were significantly (P < 0.05) associated with at least one carcass trait. Fourteen SNP (among the 58 SNP) explained >2% phenotypic variance, 12 of which had significantly (P < 0.01) additive or dominant effects. Furthermore, both rs15865526 (Wnt9A) and rs14066777 (MAPK9) as well as their corresponding haplotype blocks were significantly associated with shank circumference and wing weight, respectively. In addition, 5 muscle-weight-related SNP explained >7% phenotypic variance, which was much higher than those of others. It was found that the Wnt signaling pathway was strongly associated with chicken carcass traits, and 7 genes were particularly important, namely RHOA and CHP for breast muscle weight, Wnt3A for breast muscle weight percentage over carcass weight, RAC1 for thigh weight percentage and thigh muscle weight percentage over carcass weight, Wnt11 for thigh weight percentage over carcass weight, Wnt9A for shank length, and MAPK9 for shank circumference. It is evident that Wnt signaling plays a major role in regulating carcass characteristics important for production traits in chickens.

Genetic structure of Eurasian and North American mallard ducks based on mtDNA data.

To elucidate the origin and genetic structure of the domesticated duck in Eurasia and North America, we sequenced 114 duck D-loop sequences and retrieved 489 D-loop sequences from GenBank. In total, 603 ducks including 50 duck breeds/populations from eight countries (China, France, Russia, India, Kazakhstan, Mongolia, Thailand and USA) were used in this study. One hundred and thirty-four haplotypes and 81 variable sites were detected. H49 was the predominant haplotype, which was considered to be the same dominant haplotype found in the previous studies, and was found in 309 birds. The smallest values for both genetic differentiation index (F(ST), 0.04156) and the number of the net nucleotide substitutions between two populations (D(A), 0.00018) were observed between Eurasian domestic ducks and Eurasian mallards. No geography, breed or population clusters were observed in the Eurasian domestic ducks and mallards. Five haplotypes were shared by USA mallards and Eurasian domestic duck/Eurasian mallards. Only one haplotype (H49) was shared by Eurasian domestic ducks and China spot-billed ducks. By combining phylogenetic analyses, haplotype network profile, genetic distances and shared haplotypes, we can draw two major conclusions: (i) Eurasian and North American mallards show a clear geographic distribution pattern; (ii) Eurasian domestic ducks are derived from the Eurasian mallards, not from the spot-billed ducks.

Low-density lipoprotein receptor-related protein 2 gene is associated with egg-quality traits in dwarf layers.

Some members of the low-density lipoprotein receptor (LDLR) family play important roles in the regulation of lipoprotein metabolism and egg quality traits. Low-density lipoprotein receptor-related protein 2 (LRP2) gene belongs to the LDLR super family, and widely expresses in many tissues. This work identified and genotyped 1 single-nucleotide polymorphism (SNP), T14347C, at 3'-UTR of the LRP2 using matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS), and analyzed the effects of the SNP (T14347C) on egg-quality traits in 544 dwarf hens from 44 sire families. Frequencies of this SNP in the studied population did not agree with the Hardy-Weinberg equilibrium (P < 0.0001). Egg weight, albumen weight, albumen height, and albumen ratio of the TT genotype were significantly higher than those of the CC genotype (P < 0.05), whereas eggshell ratio of the TT genotype was significantly lower than that of the CC genotype (P < 0.05). The relative expression level of the LRP2 gene in the magnum was determined by real-time quantitative PCR. The gene expression of genotype CC individuals was significantly higher than that of TT and CT birds (P < 0.05). By combining both genetic effects and expression analyses results, we propose that the LRP2 gene is a good candidate gene, exhibiting a key role in albumen formation processes.

Genomic structure and diversity of the chicken Mx gene.

The Mx protein, which confers resistance to orthomyxovirus, has been detected in several organisms, and one nonsynonymous substitution (S631N) of the chicken Mx protein has been shown to affect resistant activities to the avian influenza virus in vitro. In the current study, the genomic sequence and polymorphism of the chicken Mx gene are reported. The full length of the chicken Mx gene spans about 21 kb, with 13 exons on chromosome 1 of the chicken genome. A total of 237 single nucleotide polymorphisms were found in the chicken Mx gene by comparison among 4 directly sequenced Mx genomic DNA sequences, and the reference sequence was inferred from the chicken genome project. The genomic diversity of the chicken Mx gene showed large variation in different regions, with the highest diversity in the 5' untranslated region and the lowest in the 3' untranslated region. The genomic structure and variation of sequences gathered here will allow an extensive analysis of the gene function with the aim of improving the antiviral resistance activities of chickens.

Molecular cloning and expression of the duplicated thyroid hormone responsive spot 14 (THRSP) genes in ducks.

Thyroid hormone responsive Spot 14 (THRSP) is suggested as a transcription factor involved in the regulation of adipogenic enzymes by 3 thyroid response elements in the promoter region. In the chicken genome, THRSP gene was identified to duplicate into 2 paralogs, THRSPalpha and THRSPbeta. In the current study, cDNA sequences of the duplicated duck THRSP genes were cloned by real-time PCR and rapid amplification of cDNA ends. Duck THRSPalpha and THRSPbeta were predicted to encode peptides with 133 amino acids, which had 74 and 68% sequence identity at cDNA level, 78 and 74% identity at amino acid level to the chicken counterparts, respectively. A high percentage (73.1%) of G and C nucleotides were found in the 3' untranslated region of duck THRSPbeta cDNA. Although a low similarity of peptide composition was shared between ducks and mammals, and a moderate similarity was shared between ducks and chickens, many predicted properties of THRSP, including the pI, subcellular localization and functional domains seemed to be highly conserved. The present study demonstrated that the duck THRSP gene duplicates into the 2 paralogs as in chickens. Phylogenetic analysis indicated that the duplication for THRSP paralogs appeared to have taken place preceding the chicken-duck split, and the diverging rate between THRSP paralogs seemed faster in the chicken genome than that in the duck genome. Expression analysis by real-time quantitative PCR showed that THRSP paralogs in ducks were more actively transcribed in fat tissues (i.e., s.c. fat and abdominal fat) than in liver, and the mRNA concentrations of THRSPbeta were higher than that of THRSPalpha in liver and s.c. fat.

Heritabilities and genetic and phenotypic correlations of egg quality traits in brown-egg dwarf layers.

Albumen height, albumen weight (AW), eggshell color (ESC), eggshell index, eggshell strength, eggshell thickness, eggshell weight (ESW), egg weight (EW), Haugh units, and yolk weight (YW) were measured in 2,272 eggs collected 3 d sequentially from 920 brown-egg dwarf layers caged individually. The restricted maximum likelihood procedure was applied to estimate heritabilities and genotypic and phenotypic correlations for these egg quality traits. Heritabilities of albumen height, AW, ESC, eggshell index, eggshell strength, eggshell thickness, ESW, EW, Haugh units, and YW were 0.51, 0.59, 0.46, 0.40, 0.24, 0.34, 0.64, 0.63, 0.41, and 0.45, respectively. The genetic correlations between EW and AW, YW, and ESW were high ranging from 0.67 to 0.97, whereas those for ESC with external and internal egg quality traits were low ranging from -0.23 to 0.13. Thus although heritabilities for these traits were moderate to high, genetic correlations with ESC were low, suggesting a minor relationship between shell color and physical attributes of the shell as well as internal egg quality in brown-egg dwarf layers.

Bundling and cross-linking of intermediate filaments of the nervous system.

Ultrastructural studies have shown that neurons and glia in the mammalian nervous system contain bundles of often hundreds or more individual intermediate filaments. The means by which these bundles are formed and maintained has not been examined. We describe a series of simple experiments indicating that intermediate filament bundles derived from neuronal and glial processes are extremely stable, being resistant to a variety of extreme conditions. Furthermore, a preliminary examination of the mechanism of bundling for both types of filaments rules out several models for the production and control of cross-linking. We conclude that the long processes of both neurons and glia are stabilized by bundled intermediate filaments exhibiting strong interfilament interactions. We present a reconciliation these findings with previous data suggesting that neurofilaments are not actively cross-linked. We also describe a novel detergent-insoluble annular cytoskeletal structure, which appears to constrict bundles of axonal neurofilaments locally.