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 Variation

Copy number variants (CNVs) are polymorphisms which influence phenotypic variation and are an important source of genetic variability [1]. In Mexico the backyard poultry population is a unique widespread Creole chicken (Gallus gallus domesticus) population, an undefined cross among different breeds brought to Mexico from Europe and under natural selection for almost 500 years [2-3]. The aim of this study was to investigate genomic variation in the Mexican chicken population using CNVs.A total of 256 DNA samples genotyped with Axiom® Genome-Wide Chicken Genotyping Array were used in the analyses. The individual CNV calling, based on log-R ratio and B-allele frequency values, was performed using the Hidden Markov Model (HMM) of PennCNV software on the autosomes [4-5]. CNVs were summarized to CNV regions (CNVRs) at a population level (i.e. overlapping CNVs), using BEDTools.The HMM detected a total of 1924 CNVs in the genome of 256 samples resulting, at population level, in 1216 CNV regions, of which 959 gains, 226 losses and 31 complex CNVRs (i.e. containing both losses and gains), covering a total of 47 Mb of sequence length corresponding to 5,12 % of the chicken galGal4 assembly autosome. A comparison among this study and 7 previous reports about CNVs in chicken was performed, finding that the 1,216 CNVRs detected in this study overlap with 617 regions (51%) mapped by others studies. 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 never genetically characterized with SNP markers. Based on a cluster analysis (pvclust – R package) on CNV markers the population, even if presenting extreme morphological variation, does not resulted divided in differentiated genetic subpopulations. Finally this study provides a CNV map based on the 600K SNP chip array jointly with a genome-wide gene copy number estimates in Mexican chicken population.

Genomic Diversity Using Copy Number Variations in Worldwide Chicken Populations

Recently, many studies in livestock have focused on the identification of Copy Number Variants (CNVs) using high-density Single Nucleotide Polymorphism (SNP) arrays, but few have focused on studying chicken ecotypes coming from many locations. CNVs are polymorphisms, which may influence phenotype and are an important source of genetic variation in populations. The aim of this study was to explore the genetic difference and structure, using a high density SNP chip in 936 individuals from seven different countries (Brazil, Italy, Egypt, Mexico, Rwanda, Sri Lanka and Uganda). The DNA was genotyped with the Affymetrix Axiom®600k Chicken Genotyping Array and processed with stringent quality controls to obtain 559,201 SNPs in 915 individuals. The Log R Ratio (LRR) and the B Allele Frequency of SNPs were used to perform the CNV calling with PennCNV software based on a Hidden Markov Model analysis and the LRR was used to perform CNV detection with SVS Golden Helix software.After filtering, a total of 19,027 CNVs were detected with the SVS software, while 9,065 CNVs were identified with the Penn CNV software. The CNVs were summarized in 7,001 Copy Number Variant Regions (CNVRs) and 4,414 CNVRs, using the software BedTool.The consensus analysis across the CNVRs allowed the identification of 2,820 consensus CNVR, of which 1,721 were gain, 637 loss and 462 complex, for a total length of 53 Mb corresponding to the 5 % of the GalGal5 chicken autosomes. Only the consensus CNV regions obtained from both detections were considered for further analysis.The intersection analysis performed between the chicken gene database (Gallus_gallus-5.0) and the 1,927 consensus CNVRs allowed the identification (within or partial overlap) of a total of 2,354 unique genes with an official gene ID.  The CNVRs identified here represent the first comprehensive mapping in several worldwide populations, using a high-density SNP chip

The Impact of Different Types of Rice and Cooking on Postprandial Glycemic Trends in Children with Type 1 Diabetes with or without Celiac Disease

The aims of this study were to evaluate: (i) the chemical and nutritional composition of rice before and after cooking and (ii) postprandial glycemic impacts in children and adolescents with type 1 diabetes (T1D) after eating two different types of rice (“Gigante Vercelli” white rice and “Artemide” black rice) or white rice cooked “risotto” style or boiled using an advanced hybrid closed loop (AHCL) system (Tandem Control-IQTM). General composition and spectrophotometric analyses of raw and cooked rice were performed. Eight T1D subjects (four males and four females, aged 11 ± 1.4 years), two with celiac disease (CD), using an AHCL system were enrolled. “Gigante Vercelli” white rice cooked as risotto or boiled and boiled “Artemide” rice were prepared by the same cook on two evenings. Continuous glucose monitoring metrics were evaluated for 12 h after meal consumption. Total dietary fiber was higher for both rice types after cooking compared with raw rice. Cooking as risotto increased polyphenols and antioxidants (p p p < 0.05), while the mean glycemic peak remained <180 mg/dL in individuals eating boiled Artemide rice. There were no significant differences in automatic basal or auto-bolus insulin deliveries by the AHCL according to different types of rice or cooking method. Our findings suggest that glycemic trends are impacted by the different chemical and nutritional profiles of rice but are nevertheless well controlled by AHCL systems

Mitochondrial DNA genetic diversity in six Italian donkey breeds (<i>Equus asinus</i>)

<p>Donkeys have played an important role in agricultural land practices and in human historical periods of recent past and, still today, are used as a working power in several world areas. The objective of this study was to identify genetic variability in six Italian donkey breeds using mtDNA D-loop. Fifteen haplotypes, grouped in three haplogroups, were identified. The genetic indices were informative and showed a high population genetic variability. The results of AMOVA analyses based on geographic structuring of Italian populations highlighted that the majority of the observed variance is due to differences among samples within breeds. Comparison among Italian haplotypes and mtDNA D-loop sequences belonging to European domestic and Ethiopian donkeys and wild asses, clearly define two clades referred to Nubian lineage. The results can be useful to complement safeguard planes for donkey breeds that are considered to extinction endangered.</p

Transcatheter aortic valve replacement with the self-expanding ACURATE Neo2 in patients with horizontal aorta: Insights from the ITAL-neo registry

Background: Horizontal aorta (HA), defined by an aortic angulation (AA) >= 48 degrees, is associated with worse outcomes particularly after self-expanding (SE) trans-catheter heart valve (THV) implantation. Although the SE ACURATE Neo THV demonstrated favorable procedural success rates in patients with HA, it remains associated with a non-negligible rate of moderate or greater paravalvular leak (PVL).Objectives: Aim of the study was to assess the performance of ACURATE Neo2 in the setting of HA.Methods: We performed a multicenter cohort analysis on patients with severe aortic valve stenosis and HA undergoing transcatheter aortic valve replacement (TAVR) with the Neo or Neo2 THV enrolled in the ITAL-neo registry. The primary endpoint was a composite of early safety and clinical efficacy at 30 days according to the Valve Academic Research Consortium-3 (VARC-3). Secondary endpoints included the occurrence of moderate or severe PVL and 90-day clinical outcomes.Results: Among 900 patients included in the ITAL-neo registry, 407 exhibited HA; of these, 300 received a Neo THV and 107 a Neo2 THV. HA, irrespective of the THV implanted, emerged as an independent risk factor for developing >= moderate PVL. Technical and device success at 30-day follow-up was comparable between groups. However, Neo2 was associated with a significantly lower rate of >= moderate PVL vs. Neo: (5% vs. 15%; p = moderate PVL and AA in the Neo2 group, while PVL degree increased proportionally to the AA in the Neo cohort.Conclusion: In patients with HA, the new generation Acurate Neo2 THV was associated with a comparable device success rate and a significantly lower rate of >= moderate PVL, when compared with its predecessor

Transcatheter Aortic Valve Replacement With Self-Expanding ACURATE neo2: Postprocedural&nbsp;Hemodynamic and Short-Term Clinical&nbsp;Outcomes

The first-generation ACURATE neo transcatheter heart valve (THV) (Boston Scientific) was associated with a non-negligible occurrence of moderate or greater paravalvular aortic regurgitation (AR) following transcatheter aortic valve replacement. To overcome this issue, the ACURATE neo2 iteration, which incorporates a taller outer skirt aimed at reducing the occurrence of paravalvular AR, has recently been developed

MARE, Microcalorimeter Arrays for a Rhenium Experiment: A detector overview.

status: publishe

MARE, Microcalorimeter Arrays for a Rhenium Experiment: A detector overview.

status: publishe