作者机构：
[Morota, Gota; Spangler, Matthew L.; Lee, Jungjae; He, Jun] Univ Nebraska, Dept Anim Sci, Lincoln, NE 68583 USA.;[He, Jun] Hunan Agr Univ, Coll Anim Sci & Technol, Changsha 410128, Hunan, Peoples R China.;[Bauck, Stewart; He, Jun; Xu, Jiaqi; Wu, Xiao-Lin] Neogen GeneSeek, Biostat & Bioinformat, Lincoln, NE 68504 USA.;[Xu, Jiaqi; Kachman, Stephen D.] Univ Nebraska, Dept Stat, Lincoln, NE 68583 USA.;[Wu, Xiao-Lin] Univ Wisconsin, Dept Anim Sci, Madison, WI 53706 USA.
通讯机构：
[Spangler, Matthew L.; Wu, Xiao-Lin] U;[Wu, Xiao-Lin] N;Univ Nebraska, Dept Anim Sci, Lincoln, NE 68583 USA.;Neogen GeneSeek, Biostat & Bioinformat, Lincoln, NE 68504 USA.;Univ Wisconsin, Dept Anim Sci, Madison, WI 53706 USA.
关键词：
Holstein;Imputation;Genomic prediction;Low-density SNP chips
摘要：
SNP chips are commonly used for genotyping animals in genomic selection but strategies for selecting low-density (LD) SNPs for imputation-mediated genomic selection have not been addressed adequately. The main purpose of the present study was to compare the performance of eight LD (6K) SNP panels, each selected by a different strategy exploiting a combination of three major factors: evenly-spaced SNPs, increased minor allele frequencies, and SNP-trait associations either for single traits independently or for all the three traits jointly. The imputation accuracies from 6K to 80K SNP genotypes were between 96.2 and 98.2%. Genomic prediction accuracies obtained using imputed 80K genotypes were between 0.817 and 0.821 for daughter pregnancy rate, between 0.838 and 0.844 for fat yield, and between 0.850 and 0.863 for milk yield. The two SNP panels optimized on the three major factors had the highest genomic prediction accuracy (0.821–0.863), and these accuracies were very close to those obtained using observed 80K genotypes (0.825–0.868). Further exploration of the underlying relationships showed that genomic prediction accuracies did not respond linearly to imputation accuracies, but were significantly affected by genotype (imputation) errors of SNPs in association with the traits to be predicted. SNPs optimal for map coverage and MAF were favorable for obtaining accurate imputation of genotypes whereas trait-associated SNPs improved genomic prediction accuracies. Thus, optimal LD SNP panels were the ones that combined both strengths. The present results have practical implications on the design of LD SNP chips for imputation-enabled genomic prediction.
通讯机构：
[Xu, DJ; Yang, Q] H;Hunan Agr Univ, Coll Vet Med, Changsha 410128, Hunan, Peoples R China.
摘要：
Colostrum is the main external resource providing piglets with nutrients and maternal immune molecules. Astragalus polysaccharides (APS) have been used as immunopotentiators in vitro and several animal models. This study aimed to determine the effects of APS on immune factors in sow colostrum and milk. The sow diet was supplemented with APS one week before the expected delivery date. Colostrum and milk were collected and designated as 0 h- (onset of parturition), 12 h-, and 24 h-colostrum and 36 h-milk postpartum. Samples were measured using porcine immunoglobulin (Ig) G, IgM, classical swine fever virus antibody (CSFV Ab), epidermal growth factor (EGF), and insulin-like growth factor- (IGF-) 1 ELISA Quantitation Kits. Dietary supplementation of APS significantly enhanced the presence of IgG, IgM, EGF, and IGF-1 in 0 h-colostrum (p < 0.001). The blocking rates of CSFV Ab were increased in samples from APS-supplemented sow when compared to those from the matched samples without APS treatment. The results indicate that supplement of APS could improve the immune components in sow colostrum and/or milk; and status of some specific vaccination could be determined through using colostrum or early milk in sow.
摘要：
Abstract Dahuabai pig is one of the most important indigenous breed of the Guangzhou province of China. It is the first time that the complete mitochondrial genome sequence of Dahuabai pig is reported in this work, which is determined through the PCR-based method. The total length of the mitognome is 16,709 bp, which contains a control region (D-loop region), 2 ribosomal RNA genes, 13 protein-coding genes and 22 tRNA genes. The total base composition of Dahuabai pig mitochondrial genome is 34.68% for A, 26.20% for C, 25.81% for T and 13.32% for G, in the order A > C > T > G. The complete mitochondrial genome of Dahuabai pig provides an important data in studying mitochondrial DNA's role in the process of metabolism and programmed cell death.
摘要：
Luchuan pig is one of the famous native breeds in China. In this study, we report the complete mitochondrial genome sequence of Luchuan pig for the first time, which is determined through the PCR-based method. The total length of the mitogenome is 16,710 bp with the base composition of 34.67% A, 13.33% G, 25.82% T and 26.18% C, and an A + T (60.48%)-rich feature is detected, which contains 1 control region (D-loop region), 2 ribosomal RNA genes, 13 PCGs and 22 tRNA genes. The complete mitochondrial genome of Luchuan pig provides an important data in genetic mechanism and the evolution genomes.
作者：
Wu, Xiao-Lin*;Xu, Jiaqi;Feng, Guofei;Wiggans, George R.;Taylor, Jeremy F.;...
期刊：
PLOS ONE,2016年11(9):e0161719 ISSN：1932-6203
通讯作者：
Wu, Xiao-Lin
作者机构：
[Bauck, Stewart; Walker, Jeremy; Xu, Jiaqi; Feng, Guofei; Wu, Xiao-Lin; Simpson, Barry; Qiu, Jiansheng] GeneSeek, Bioinformat & Biostat, Lincoln, NE USA.;[Xu, Jiaqi; Feng, Guofei] Univ Nebraska, Dept Stat, Lincoln, NE USA.;[Wiggans, George R.] USDA ARS, Anim Genom & Improvement Lab, Beltsville, MD USA.;[Taylor, Jeremy F.] Univ Missouri, Div Anim Sci, Columbia, MO USA.;[He, Jun] Hunan Agr Univ, Coll Anim Sci & Technol, Changsha, Hunan, Peoples R China.
通讯机构：
[Wu, Xiao-Lin] G;GeneSeek, Bioinformat & Biostat, Lincoln, NE USA.
关键词：
Single nucleotide polymorphisms;Genomics;Chromosome mapping;Variant genotypes;Optimization;Cattle;Animal genomics;Haplotypes
摘要：
Low-density (LD) single nucleotide polymorphism (SNP) arrays provide a cost-effective solution for genomic prediction and selection, but algorithms and computational tools are needed for the optimal design of LD SNP chips. A multiple-objective, local optimization (MOLO) algorithm was developed for design of optimal LD SNP chips that can be imputed accurately to medium-density (MD) or high-density (HD) SNP genotypes for genomic prediction. The objective function facilitates maximization of non-gap map length and system information for the SNP chip, and the latter is computed either as locus-averaged (LASE) or haplotype-averaged Shannon entropy (HASE) and adjusted for uniformity of the SNP distribution. HASE performed better than LASE with ≤1,000 SNPs, but required considerably more computing time. Nevertheless, the differences diminished when >5,000 SNPs were selected. Optimization was accomplished conditionally on the presence of SNPs that were obligated to each chromosome. The frame location of SNPs on a chip can be either uniform (evenly spaced) or non-uniform. For the latter design, a tunable empirical Beta distribution was used to guide location distribution of frame SNPs such that both ends of each chromosome were enriched with SNPs. The SNP distribution on each chromosome was finalized through the objective function that was locally and empirically maximized. This MOLO algorithm was capable of selecting a set of approximately evenly-spaced and highly-informative SNPs, which in turn led to increased imputation accuracy compared with selection solely of evenly-spaced SNPs. Imputation accuracy increased with LD chip size, and imputation error rate was extremely low for chips with ≥3,000 SNPs. Assuming that genotyping or imputation error occurs at random, imputation error rate can be viewed as the upper limit for genomic prediction error. Our results show that about 25% of imputation error rate was propagated to genomic prediction in an Angus population. The utility of this MOLO algorithm was also demonstrated in a real application, in which a 6K SNP panel was optimized conditional on 5,260 obligatory SNP selected based on SNP-trait association in U.S. Holstein animals. With this MOLO algorithm, both imputation error rate and genomic prediction error rate were minimal.
摘要：
This study was conducted to explore the effect of chitosan supplementation on mouse intestinal microbiota and interleukin-17 (IL-17) expression. Chitosan supplementation reduced mouse body weight, associating with change of intestinal microbiota (i.e. lowering the ratio of Firmicutes: Bacteroidetes). In antibiotics treated mice, chitosan supplementation had little effect on mouse body weight. Chitosan supplementation decreased expression of IL-17 in mouse jejunum and inhibited the mTOR pathway. In antibiotics treated mice, chitosan also reduced expression of IL-17 in the jejunum. Activation of mTOR signalling in mouse increased expression of IL-17 in the jejunum in the context of chitosan supplementation. We conclude that chitosan supplementation reduces mouse body weight through the intestinal microbiota, and inhibits intestinal IL-17 expression through the mTOR signalling. The discovery of this study suggests the potentials of chitosan as a functional supplement in intestinal health.
摘要：
The objective of the study was to determine the role of vitamin D3（VD3） in regulating adaptation and mechanism of rats to low-phosphorus（P） diets. Rats were assigned to 4 diets containing 0.2%, 0.4%, 0.6%,or 0.8% P consisting of 5 replicate cages with 6 rats per replicate cage and fed for 7 days. Four rats from each replicate cage were treated with ethane-1-hydroxy-1,1-diphosphonicacid, tetrasodium salt（EHDP）and 2 rats remained untreated. Twelve hours prior to preparation on d 7, two of the EHDP-treated rats received an intraperitoneal injection of VD3 [1,25-（OH）2 D3] at 600 ng per kg body weight, while two rats did not receive the injection. Rats that did not receive VD3 injection had decreased（P < 0.001） P absorption, but injection of VD3 resulted in increased（P < 0.001） absorption. The effect of VD3 injection was greater（P < 0.001） for rats fed 0.2% P diet than rats fed 0.8% P diet in ileum. Sodium dependent phosphate cotransporter type IIb（Na/Pi-IIb） and 25-hydroxyvitamin D 1-α hydroxylase（CYP27 B1） mRNA level showed the same trend with P absorption. Serum concentration of VD3 and la-hydroxylase activity in rats fed 0.2% P diet were lower than those fed 0.8% P diet. The injection of VD3 increased（P < 0.001）serum concentration of VD3 and la-hydroxylase activity. Thus, VD3 increased Na/Pi-Ⅱb and CYP27 B1 mRNA level and improved serum concentration of VD3 and la-hydroxylase activity in rats fed low-P diets.
关键词：
D x LY pig;genome composition;mitochondrial DNA
摘要：
Duroc (male symbol) x [Landrace (male symbol) x Yorshire (female symbol)] (D x LY) pig is the popular hybrid pigs in order to make the most use of the heterosis in the world. In this study, the complete nucleotide sequence of D x LY pig mitochondrial genome was determined for the first time. Sequence analysis showed that the genome structure was in accordance with other pig breeds. It contained 22 tRNA genes, 2 ribosomal RNA genes, 13 protein-coding genes and 1 control region (D-loop region). The complete mitochondrial genome sequence of the D x LY pig provides an important data set for further study in genetic mechanism.
