Looking at genetic structure and selection signatures of the Mexican chicken population using single nucleotide polymorphism markers

Genetic variation enables both adaptive evolutionary changes and artificial selection. Genetic makeup of populations is the result of a long-term process of selection and adaptation to specific environments and ecosystems. The aim of this study was to characterize the genetic variability of México's chicken population to reveal any underlying population structure. A total of 213 chickens were sampled in different rural production units located in 25 states of México. Genotypes were obtained using the Affymetrix Axiom® 600 K Chicken Genotyping Array. The Identity by Descent (IBD) and the principal components analysis (PCA) were performed by SVS software on pruned single nucleotide polymorphisms (SNPs).ADMIXTURE analyses identified 3 ancestors and the proportion of the genetic contribution of each of them has been determined in each individual. The results of the Neighbor-Joining (NJ) analysis resulted consistent with those obtained by the PCA. All methods utilized in this study did not allow a classification of Mexican chicken in distinct clusters or groups. A total of 3,059 run of homozygosity (ROH) were identified and, being mainly short in length (<4 Mb), these regions are indicative of a low inbreeding level in the population. Finally, findings from the ROH analysis indicated the presence of natural selective pressure in the population of Mexican chicken.The study indicates that the Mexican chicken clearly appear to be a unique creole chicken population that was not subjected to a specific artificial selection. Results provide a genetic knowledge that can be used as a basis for the genetic management of a unique and very large creole population, especially in the view of using it in production of hybrids to increase the productivity and economic revenue of family farming agriculture, which is widely present in México.

Genomic variability in Mexican chicken population using copy number variants

BACKGROUND

Copy number variations are genome polymorphism that influence phenotypic variation and are an important source of genetic variation in populations. The aim of this study was to investigate genetic variability in the Mexican Creole chicken population using CNVs.

RESULTS

The Hidden Markov Model of the PennCNV software detected a total of 1924 CNVs in the genome of the 256 samples processed with Axiom® Genome-Wide Chicken Genotyping Array (Affymetrix). The mapped CNVs comprised 1538 gains and 386 losses, resulting at population level in 1216 CNV regions (CNVRs), of which 959 gains, 226 losses and 31 complex (i.e. containing both losses and gains). The CNVRs covered a total of 47 Mb of the whole genome sequence length, corresponding to 5.12% of the chicken galGal4 autosome assembly.

CONCLUSIONS

This study allowed a deep insight into the structural variation in the genome of unselected Mexican chicken population, which up to now has not been genetically characterized. The genomic study disclosed that the population, even if presenting extreme morphological variation, cannot be organized in differentiated genetic subpopulations. Finally this study provides a chicken CNV map based on the 600 K SNP chip array jointly with a genome-wide gene copy number estimates in a native unselected for more than 500 years chicken population.

Genome-wide association study for milk somatic cell score in holstein cattle using copy number variation as markers

Mastitis, the most common and expensive disease in dairy cows, implies significant losses in the dairy industry worldwide. Many efforts have been made to improve genetic mastitis resistance in dairy populations, but low heritability of this trait made this process not as effective as desired. The purpose of this study was to identify genomic regions explaining genetic variation of somatic cell count using copy number variations (CNVs) as markers in the Holstein population, genotyped with the Illumina BovineHD BeadChip. We found 24 and 47 copy number variation regions significantly associated with estimated breeding values for somatic cell score (SCS_EBVs) using SVS 8.3.1 and PennCNV-CNVRuler software, respectively. The association analysis performed with these two software allowed the identification of 18 candidate genes (TERT, NOTCH1, SLC6A3, CLPTM1L, PPARα, BCL-2, ABO, VAV2, CACNA1S, TRAF2, RELA, ELF3, DBH, CDK5, NF2, FASN, EWSR1 and MAP3K11) that result classified in the same functional cluster. These genes are also part of two gene networks, whose genes share the 'stress', 'cell death', 'inflammation' and 'immune response' GO terms. Combining CNV detection/association analysis based on two different algorithms helps towards a more complete identification of genes linked to phenotypic variation of the somatic cell count.

[Tuberculosis in the area of Lorca: to adapt or resist]

OBJECTIVE

We studied the epidemiological characteristic of tuberculosis in Lorca area, drug resistant and the effect of the immigration population (Ecuador) in this area.

PATIENTS AND METHODS

A retrospective study for six years ago (1999, January to 2004, December) was realized. Epidemiological data, initial diagnostic probability, mycobacteria stain and cultive, drug resistance, treatment response, and epidemiological differences between immigrants and spain population were compared.

RESULTS

Within 158 cases registered, 41.7 percent were immigrants with less than one year in Spain, the most part Ecuador population. We observed that extrapulmonar tuberculosis was lower initial diagnostic probability than pleural disease as well too haemoptisis, pleural pain and weight loss. It was identified positive micobacterial stain in 35.4 percent of respiratory samples. It was successfully results in 74 percent of cases and 13.9 percent of patients were lost, this result was frequently registered in immigrants, The isoniazide resistant in patients with not previous treatment was 5.3 percent and it was 9.5 percent in immigrants and 10.8 percent in Ecuador population.

CONCLUSION

It is necessary improve: the diagnostic of extrapulmonar tuberculosis and avoid loss patient by programs of capture and then the successfully treatments raise. The isoniazide resistant in this area suggest that we must use initial four drug than tree and this manner not raise the drug resistant in the area.

[Repeated hemoptysis for foreign body bronchial aspiration: presentation of a case and review of literature]

The foreign body aspiration is more frequent in children. The most usual etiology is the foreign bodies of vegetable nature, which can not be observed in the chest radiograph. The clinic signs are varied, including shortness of breath, cough and wheezing. Hemoptysis is a rare symptom, whose arising is generally connected with the existence of bronchiectasis. We present the case of a child who showed repeated hemoptysis and focal neumonitis due to Eikenelle corrodens three years after the aspiration of a spike. The diagnosis of the bronchial aspiration obtained after The most unusual in this case is the clinic manifestation of repeated hemoptysis, together with the long connected to the existence of foreign body inside the bronchus.

[Listeria monocytogenes pneumonia: a severe complication in a patient with neoplasia]

Listeriosis is a infectious disease which can affect to immunosuppressed patients. We report a case of pneumonia by Listeria monocytogenes as unusual presentation, because the central nervous system infections are the most common clinical entities. Many cases reported had a underlying disease, most commonly Hodgkin's disease, and had received immunosuppressive therapy. In our case the patient was considered to be immunosuppressed by had received corticosteroids and had been diagnosed of stage IIIa squamous cell carcinoma 3 years ago. The illness began 48 hours before the admission to hospital, he had fever, mental confusion and the location of pneumonia was right lower lobe, 24 hours later the patient die.

[Lesions of the tracheobronchial tree after the aspiration of a tablet of ferrous sulfate]

Foreign body aspiration requires emergency bronchoscopic examination when the product is chemically active. We describe the case of a female patient who aspirated a ferrous sulfate tablet that, in spite of being extracted immediately, caused lesions that persisted in the bronchial tree for 6 weeks. We then discuss the potential of ferrous sulfate substance to cause damage to the tracheobronchial tree.