Maternal origins,population structure and demographic history of ten Chinese indigenous goat breeds from Yunnan

Yunnan as a frontier zone that connects China with South and Southeast Asia, has 11 well‐recognized goat breeds. However, the knowledge about maternal origins, population structure and demographic history of Chinese indigenous goats from Yunnan is limited. In this study, we analysed a 481‐bp fragment of first hypervariable segment (HVSI) of the mitochondrial DNA (mtDNA) control region sequences of 749 individuals from 10 Yunnan indigenous goat breeds, of which 556 sequences were newly determined. There were 110 polymorphic sites that defined 158 haplotypes among all sequences. The haplotype and nucleotide diversity of these breeds ranged from 0.782 ± 0.079 to 0.982 ± 0.015 and from 0.028 ± 0.003 to 0.043 ± 0.005, respectively. Phylogenetic analysis identified two lineages A and B, of which the lineage A had higher frequency (68.1%) and distributed in all Yunnan breeds. We combined previously reported sequences with our sequences belonging to the lineage B and detected two subclades B1 and B2, in which the B1 subclade shared individuals from Eastern Asia, Southeast Asia and Southern Asia. Given higher level of diversity and more unique haplotypes, the B2 subclade probably originated from Southwestern China. The haplotype network, analysis of molecular variance (AMOVA) and a Mantel test revealed no significant phylogeographic structuring among Yunnan goat breeds. This can be explained by high gene flow and genetic admixture among these breeds from different geographic regions in Yunnan. Additionally, both the lineages A and B reflected different demographic histories. This study will provide a scientific basis for the conservation and utilization of Yunnan indigenous goats.     

Breeding objectives for indigenous chicken: Model development and application to different production systems

A bio-economic model was developed to evaluate the utilisation of indigenous chickens (IC) under different production systems accounting for the risk attitude of the farmers. The model classified the production systems into three categories based on the level of management: free-range system (FRS), where chickens were left to scavenge for feed resources with no supplementation and healthcare; intensive system (IS), where the chickens were permanently confined and supplied with rationed feed and healthcare; and semi-intensive system (SIS), a hybrid of FRS and IS, where the chickens were partially confined, supplemented with rationed feeds, provided with healthcare and allowed to scavenge within the homestead or in runs. The model allows prediction of the live weights and feed intake at different stages in the life cycle of the IC and can compute the profitability of each production system using both traditional and risk-rated profit models. The input parameters used in the model represent a typical IC production system in developing countries but are flexible and therefore can be modified to suit specific situations and simulate profitability and costs of other poultry species production systems. The model has the capability to derive the economic values as changes in the genetic merit of the biological parameter results in marginal changes in profitability and costs of the production systems. The results suggested that utilisation of IC in their current genetic merit and production environment is more profitable under FRS and SIS but not economically viable under IS.     

Furazolidone in chicken: case study of an incident of widespread contamination

1. Furazolidone, a nitrofuran antibiotic, was prohibited from the use in food-producing animals in the European Union (EU) in 1997. In 2002, the EU restricted the import of poultry meat and aquaculture species from countries where furazolidone residues had been detected.

2. By 2004, however, residues of the side-chain metabolite, 3-amino-2-oxazolidinone (AOZ) of furazolidone, were detected in chicken meat produced in Northern Ireland.

3. With the random spread of positive results across farms of a single integrated organisation, including organically reared flocks, it seemed unlikely that the source of residues was due to illegal use of the drug, but more likely caused by a source of contamination.

4. Potential sources investigated were as follows: furazolidone contamination of feedstuffs, a “hot spot” of furazolidone in poultry houses, contamination occurring within breeding stocks and transferred with the birds to broiler growing houses, and furazolidone contamination of the water supply.

5. Furazolidone contamination was associated with birds reared in houses more than 10 years old.

6. Contamination was traced to the water supply of poultry houses, where un-dissolved furazolidone, legally administered prior to 1997, had settled to the bottom of water storage tanks. It remained un-disturbed until 2004 when the integrator changed the procedure for cleaning water tanks between crops of birds.

7. The use of Proxitane, a hydrogen peroxide disinfectant, caused effervescence within the tank such that small quantities of furazolidone were dissolved, delivered to birds via drinkers and subsequently caused residues in the broiler meat.

8. The environmental impact of the contamination was investigated by testing soil and grass from land adjacent to an organic poultry house to which birds had access.

9. Mechanisms of contamination and how residues may be spread throughout a large integrated poultry system are not restricted to furazolidone. Incidents of contamination are even more likely when using licensed drugs where the drugs may be present on-farm in large quantities.     

Lack of association between p53 SNP and FISS in a cat population from Germany

One recent study indicates a significant association between certain single nucleotide polymorphisms (SNPs) in the genomic sequence of feline p53 and feline injection‐site sarcoma (FISS). The aim of this study was to investigate the correlation between a specific nucleotide insertion in p53 gene and FISS in a German cat population. Blood samples from 150 German cats were allocated to a control group consisting of 100 healthy cats and a FISS‐group consisting of 50 cats with FISS. All blood samples were examined for the presence of the SNP in the p53 gene. Results found the T‐insertion at SNP 3 in 20.0% of the cats in the FISS‐group and 19.2% of cats in the control‐group. No statistically significant difference was observed in allelic distribution between the two groups. Further investigations are necessary to determine the association of SNPs in the feline p53 gene and the occurrence of FISS.     

Community-based interventions for the use and conservation of animal genetic resources: the case of indigenous scavenger chicken production in Benin

Scavenging chicken production in Africa is important for the livelihood of the poor. In most countries, these low inputs, low output systems employ local breeds making use of the feeding resources available in the household. However, their replacement with introduced exotic breeds with higher productivities represents a risk for their conservation. Here, we present a simulation model to evaluate the impact of community-based interventions aiming to improve the profitability of local chicken breeds and promote their use and conservation. The results indicate that under the current conditions, farmers producing exotic chicken are able to sell more animals in a one year period; however the market price of local chicken makes their production more profitable. Vaccination campaigns significantly reduce the mortality rate of both breeds, having a positive effect on producers’ income but its impact on animal off-take is larger for exotic breeds, and the availability of feeding resources is the limiting factor as the flock size increases. The results of the intervention are positive in terms of increasing farmers’ income but do not clearly contribute to the conservation of indigenous breeds since after the vaccination campaign, the gap between the profitability of indigenous and exotic breeds is reduced. The simulation model indicates that under the current conditions, the conservation of indigenous chicken breeds in Benin is maintained by the existence of distinct niche markets with consumers able to pay higher prices for indigenous chicken. Policies for the conservation of chicken genetic resources in Benin are discussed.     

Genomewide association study of immune traits in chicken F2 resource population

Immune traits play pivotal roles in animal immune capacity development and disease resistance. Single nucleotide polymorphisms (SNPs) are common forms of genetic variations among individuals, which are thought to account for the majority of inherited phenotypic variations. In this study, we performed genomewide association, using the Illumina 60K SNP BeadChip studies to detect molecular markers and candidate genes associated with immune traits in an F2 population. Sixteen immune traits were measured. We identified 85 significant SNPs (p < 2.98 × 10^?6) with 5% as the genomewide significance threshold, 380 SNPs of suggestive significance (p < 5.96 × 10^?5) from simple model (general linear model, GLM) and 15 SNPs of suggestive significance (p < 5.96 × 10^?5) from the compressed mixed linear model (MLM), which were also found in GLM (six significant SNPs and seven suggestive SNPs). Three significant SNPs (GGaluGA151406, Gga_rs14554319 and Gga_rs13593979) and candidate genes (LYRM4 and KTN1) were found to be associated with avian influenza antibody titres, and the first two SNPs are from the results of two‐model analysis. For the immune organs, through the analysis of GLM, 19 SNPs were found to be significantly associated with the thymus weight, 61 SNPs were significantly associated with the bursa of Fabricius weight, six of which were located within a 34‐Mb region (125 846 474–159 649 698 bp) on chicken chromosome 1 (GGA1). A candidate region relevant to haematological traits from GLM was found in GGA4 and 9 loci were located on it. Three loci (GGaluGA348521, Gga_rs16098446 and GGaluGA348518) within 179 kb (16 286 868–16 466 134 bp) on GGAZ from GLM provided evidence that this genomic segment may be relevant to red blood cell volume distribution width (RDW). Our study provides a list of significant SNPs and candidate genes that will be valuable information for unveiling the underlying molecular mechanism of immune regulation.     

Population viability analysis of small population: a case study for Asian elephant in China

Small populations are at risk of extinction from deterministic and stochastic factors. Less than 250 Asian elephants (Elephas maximus) remain in China, and are distributed in a few isolated areas; yet, population viability analyses of this endangered population have not been conducted. Here, the current genetic status of the Pu'Er‐Mengyang Asian elephant populations in China was analyzed, and the risk of extinction was predicted over the next 500 years. Factors affecting the viability of this population were determined through simulations. The genetic diversity of the population was very low (mean allele number: 3.1; expected heterozygosity: 0.463), even though a recent population bottleneck was not detected. The effective population size was approximately 24.1 adult elephants. Enough adult breeding individuals exist to maintain population viability. VORTEX simulation model showed that this population would not go extinct in the next 500 years. However, illegal poaching and harvesting could negatively affect population size. A sensitivity analysis showed that the mean stochastic growth rate of the study population is sensitive to sex ratio, number of breeding females, mortality of females of different age classes, carrying capacity, and lethal equivalents. Based on our results, we suggest that action should be taken to alleviate inbreeding and any further loss of genetic diversity, by connecting fragmented elephant habitat or by translocating individual elephants. In addition, human–elephant conflict should be mitigated using various modern approaches, including crop guarding techniques, and by encouraging farmers to switch to crops and income sources not vulnerable to elephant raids.     

抗鸡柔嫩艾美耳球虫中药复方的筛选(二报)

采用人工感染病理模型对由常山、柴胡、青蒿、地榆、黄芪、绞股蓝等6味中草药组成的抗鸡球虫复方进行了试验研究.结果1%和5%提前3 d给药预防组的抗球虫效果最好,ACI分别达到了144.90和142.70.而该组方用于治疗的效果却较差,即使是5%添加,ACI也只有85.56.     

Culicoides arakawae (Diptera: Ceratopogonidae) population succession in relation to leucocytozoonosis prevalence on a chicken farm in Taiwan

Leucocytozoonosis caused by Leucocytozoon caulleryi is a significant disease prevalent in open chicken houses of southern and eastern Asia. L. caulleryi is transmitted by Culicoides arakawae, a blood-sucking vector. Leucocytozoonosis prevalence is influenced by vector population succession. Thus this examination was performed on a farm to investigate vector population succession and leucocytozoonosis prevalence in experimental chicks and to obtain the ecology data for assessing the prevalence. The findings were as follows: (1) C. arakawae adults might be highly host specific because they were rarely discovered on cattle or pig farms, and none of the experimental chickens were infected by L. caulleryi on those farms. (2) Identifying and counting gorged and gravid C. arakawae to assess leucocytozoonosis prevalence is a practical strategy. The critical vector index should be 5.0 calculated by dividing the smallest vector mean from the prevalent period by the largest vector mean from the population not causing leucotocytozoonosis. (3) Taking vector means from three or more collections each month, should be the best assessment of leucocytozoonosis prevalence because C. arakawae succession appears to have a 3-week periodicity. Hopefully, these findings will contribute to assessing leucocytozoonosis prevalence.     

Mortality supposedly due to intoxication by pyrrolizidine alkaloids from Heliotropium indicum in a horse population in Costa Rica: a case report.

This article describes a case of massive mortality among horses which was probably due to intoxication by pyrrolizidine alkaloids from Heliotropium indicum. Over 4 years more than 75% of a population of about 110 horses on a farm in Costa Rica died after showing nervous neurological symptoms. Two clinical manifestations were encountered, an acute and a chronic one, both with a fatal outcome. Pathological findings in 2 horses coincided with those reported in the literature for intoxication by pyrrolizidine alkaloids and were not specific for VEE. However Venezuelan equine encephalitis (VEE) was the main differential diagnosis and could not completely be excluded because this disease was endemic in the region and VEE titres were found to be high. Taxonomic and toxicological investigations implicated Heliotropium indicum as the most probable principal cause of the intoxication.     

Pacheco's disease in a Hungarian zoo bird population: a case report

An epizootic of Pacheco's disease is reported from a zoo bird population. The infection was introduced by wild-captured Patagonian conures (Cyanoliseus patagonus) despite 61 days of quarantine. The disease affected several parrot species and, interestingly, three out of seven bearded barbets (Lybius dubius). The mortality rate was 30.93%. Autopsy revealed abdominal hyperaemia with liver haemorrhages and, in less rapid cases, yellowish discoloration and fragility of the liver. Death was caused by the collapse of circulation. Histopathology demonstrated liver cell necrosis, disintegration of the lobular structure, and a few intranuclear inclusion bodies. Icosahedral virions were detected by electron microscopy. The virus was isolated in the allantoic cavity of embryonated chicken eggs as well as in chicken embryo fibroblast cell culture. A 281-bp-long fragment of psittacid herpesvirus DNA was detected by PCR in cell culture material and liver samples of the affected birds. To our knowledge this is the first report of Pacheco's disease in bearded barbets as well as the first occurrence of Pacheco's disease in Hungary.     

Detection of protein binding to a glucocorticoid response element-like sequence in a chicken major histocompatibility complex class II promoter

The glucocorticoid response element in gene promoters mediates regulation of gene expression by glucocorticoids. The major histocompatibility (MHC) class II genes, crucial for immunoresponsiveness, are among those modulated by glucocorticoids. A GRE-like sequence has been located in the promoter of a chicken MHC class II promoter. DNase footprinting revealed protein binding by the GRE-like sequence when nuclear extract from chicken T or B cell lines were used. Gel shift assays detected multiple binding activities in the lymphocyte cell lines, but little binding in the macrophage cell line. Relative band intensity differed among the lymphocyte cell lines. By using a mutant GRE oligonucleotide, most of the binding activities were demonstrated to be specific to the GRE. This study suggests a role of the GRE-like sequence in regulating chicken MHC class II genes and provides further evidence for the previously reported influence of glucocorticoids on chicken MHC class II expression which may be the molecular basis of glucocorticoid immunomodulation.     

Use of factor scores for predicting body weight from linear body measurements in three South African indigenous chicken breeds

Body weight and weight of body parts are of economic importance. It is difficult to directly predict body weight from highly correlated morphological traits through multiple regression. Factor analysis was carried out to examine the relationship between body weight and five linear body measurements (body length, body girth, wing length, shank thickness, and shank length) in South African Venda (VN), Naked neck (NN), and Potchefstroom koekoek (PK) indigenous chicken breeds, with a view to identify those factors that define body conformation. Multiple regression was subsequently performed to predict body weight, using orthogonal traits derived from the factor analysis. Measurements were obtained from 210 chickens, 22 weeks of age, 70 chickens per breed. High correlations were obtained between body weight and all body measurements except for wing length in PK. Two factors extracted after varimax rotation explained 91, 95, and 83 % of total variation in VN, NN, and PK, respectively. Factor 1 explained 73, 90, and 64 % in VN, NN, and PK, respectively, and was loaded on all body measurements except for wing length in VN and PK. In a multiple regression, these two factors accounted for 72 % variation in body weight in VN, while only factor 1 accounted for 83 and 74 % variation in body weight in NN and PK, respectively. The two factors could be used to define body size and conformation of these breeds. Factor 1 could predict body weight in all three breeds. Body measurements can be better selected jointly to improve body weight in these breeds.     

一起无检疫证明运输鸡产品案件的查处及启示

2004年9月2日中午1时,我所接到举报电话,在南宁国际机场高速公路收费站有一车可疑无正常手续的动物产品.我所派出两名执法人员前往,到场后向货主出示监督员证,经调查发现该车运载为冷冻鸡产品,数量约为5 t,货主吴某只能提供防城港市工商局出具的《工商局处罚决定书》,该处罚决定书提到该冷冻鸡产品是尹某在东兴市收购后被防城港市工商局以“无证（营业执照）收购”予以查扣,经防城港市海关查验确认其为国内鸡产品,由防城港市工商局对尹某处罚后卖给吴某的.由于案值较大,不适合当场处理,即要求货主将该批鸡产品运回所里作进一步调查.经请示领导,我所立即对此事进行立案.     

Genomic prediction in a numerically small breed population using prioritized genetic markers from whole-genome sequence data

The objective of this study was to investigate the accuracy of genomic prediction of body weight and eating quality traits in a numerically small sheep population (Dorper sheep). Prediction was based on a large multi-breed/admixed reference population and using (a) 50k or 500k single nucleotide polymorphism (SNP) genotypes, (b) imputed whole-genome sequencing data (~31 million), (c) selected SNPs from whole genome sequence data and (d) 50k SNP genotypes plus selected SNPs from whole-genome sequence data. Furthermore, the impact of using a breed-adjusted genomic relationship matrix on accuracy of genomic breeding value was assessed. The selection of genetic variants was based on an association study performed on imputed whole-genome sequence data in an independent population, which was chosen either randomly from the base population or according to higher genetic proximity to the target population. Genomic prediction was based on genomic best linear unbiased prediction (GBLUP), and the accuracy of genomic prediction was assessed according to the correlation between genomic breeding value and corrected phenotypes divided by the square root of trait heritability. The accuracy of genomic prediction was between 0.20 and 0.30 across different traits based on common 50k SNP genotypes, which improved on average by 0.06 (absolute value) on average based on using prioritized genetic markers from whole-genome sequence data. Using prioritized genetic markers from a genetically more related GWAS population resulted in slightly higher prediction accuracy (0.02 absolute value) compared to genetic markers derived from a random GWAS population. Using high-density SNP genotypes or imputed whole-genome sequence data in GBLUP showed almost no improvement in genomic prediction accuracy however, accounting for different marker allele frequencies in reference population according to a breed-adjusted GRM resulted to on average 0.024 (absolute value) increase in accuracy of genomic prediction.     

Development of SNP markers for individual identification and parentage test in a Japanese Black cattle population

This study describes the development of efficient single nucleotide polymorphism (SNP) markers for individual identification and parentage tests in a Japanese Black cattle population. An amplified fragment length polymorphism method was employed to detect informative candidate markers, and yielded 44 SNP markers from 220 primer combinations. 29 unlinked SNPs were finally selected as diagnostic markers. The allelic frequencies for each marker were estimated by using PCR‐RFLP in the Japanese Black population. Based on the frequency data, the estimated identity power of these markers was 2.73 × 10^?12. Parentage exclusion probabilities, when both suspected parents' genotypes were known and when only one suspected parent was genotyped, were estimated as 0.96929 and 0.99693, respectively. This panel of SNP markers is theoretically sufficient for individual identification, and would also be a powerful tool for a parentage test in Japanese Black cattle. The markers could contribute to the management of the beef industry in Japan.