The Identification of Runs of Homozygosity Gives a Focus on the Genetic Diversity and Adaptation of the “Charolais de Cuba” Cattle

Inbreeding and effective population size (Ne) are fundamental indicators for the management and conservation of genetic diversity in populations. Genomic inbreeding gives accurate estimates of inbreeding, and the Ne determines the rate of the loss of genetic variation. The objective of this work was to study the distribution of runs of homozygosity (ROHs) in order to estimate genomic inbreeding (FROH) and an effective population size using 38,789 Single Nucleotide Polymorphisms (SNPs) from the Illumina Bovine 50K BeadChip in 86 samples from populations of Charolais de Cuba (n = 40) cattle and to compare this information with French (n = 20) and British Charolais (n = 26) populations. In the Cuban, French, and British Charolais populations, the average estimated genomic inbreeding values using the FROH statistics were 5.7%, 3.4%, and 4%, respectively. The dispersion measured by variation coefficient was high at 43.9%, 37.0%, and 54.2%, respectively. The effective population size experienced a very similar decline during the last century in Charolais de Cuba (from 139 to 23 individuals), in French Charolais (from 142 to 12), and in British Charolais (from 145 to 14) for the ~20 last generations. However, the high variability found in the ROH indicators and FROH reveals an opportunity for maintaining the genetic diversity of this breed with an adequate mating strategy, which can be favored with the use of molecular markers. Moreover, the detected ROH were compared to previous results obtained on the detection of signatures of selection in the same breed. Some of the observed signatures were confirmed by the ROHs, emphasizing the process of adaptation to tropical climate experienced by the Charolais de Cuba population.info:eu-repo/semantics/publishedVersio

Whole-genome sequencing reveals insights into the adaptation of French Charolais cattle to Cuban tropical conditions

Background: In the early 20th century, Cuban farmers imported Charolais cattle (CHFR) directly from France. These animals are now known as Chacuba (CHCU) and have become adapted to the rough environmental tropical condi‑ tions in Cuba. These conditions include long periods of drought and food shortage with extreme temperatures that European taurine cattle have difculty coping with. Results: In this study, we used whole-genome sequence data from 12 CHCU individuals together with 60 wholegenome sequences from six additional taurine, indicus and crossed breeds to estimate the genetic diversity, structure and accurate ancestral origin of the CHCU animals. Although CHCU animals are assumed to form a closed population, the results of our admixture analysis indicate a limited introgression of Bos indicus. We used the extended haplotype homozygosity (EHH) approach to identify regions in the genome that may have had an important role in the adapta‑ tion of CHCU to tropical conditions. Putative selection events occurred in genomic regions with a high proportion of Bos indicus, but they were not sufcient to explain adaptation of CHCU to tropical conditions by Bos indicus introgres‑ sion only. EHH suggested signals of potential adaptation in genomic windows that include genes of taurine origin involved in thermogenesis (ATP9A, GABBR1, PGR, PTPN1 and UCP1) and hair development (CCHCR1 and CDSN). Within these genes, we identifed single nucleotide polymorphisms (SNPs) that may have a functional impact and contribute to some of the observed phenotypic diferences between CHCU and CHFR animals. Conclusions: Whole-genome data confrm that CHCU cattle are closely related to Charolais from France (CHFR) and Canada, but also reveal a limited introgression of Bos indicus genes in CHCU. We observed possible signals of recent adaptation to tropical conditions between CHCU and CHFR founder populations, which were largely independent of the Bos indicus introgression. Finally, we report candidate genes and variants that may have a functional impact and explain some of the phenotypic diferences observed between CHCU and CHFR cattle.info:eu-repo/semantics/publishedVersio

Seguimiento de las recomendaciones sobre psicofarmacología y su repercusión conductual en la discapacidad intelectual

En la población con discapacidad intelectual -DI- hay una elevada morbilidad psiquiátricaconductual. Se estima que por este motivo entre un tercio y tres cuartos de estas personas reciben antipsicóticos. Existe un consenso de expertos para guiar la toma de decisiones farmacoterapéuticas en estos casos. Su aplicación conseguiría una mayor eficacia del tratamiento, reduciendo los problemas conductuales, mejorando las habilidades adaptativas. El ICAP Inventory for client and agency planning es un instrumento para valoración y evaluación de servicios para personas con DI, que incluye escalas para puntuación de problemas conductuales y de conductas adaptativas. Para determinar la asociación entre el seguimiento de las recomendaciones farmacoterapeuticas de los expertos y las puntuaciones de los problemas conductuales y las habilidades adaptativas en un grupo de sujetos con DI, se realizó un estudio observación transversal. El tratamiento farmacológico recibido por cada sujeto de un colectivo de sujetos diagnosticados de DI -CIE-10- se clasificó como conforme o no con las recomendaciones de la guía en lo referente a los criterios de indicación, dosis, duración y polifarmacia. Se compararon las puntuaciones de conducta adaptativa y de problemas de conducta del ICAP en función de la conformidad del tratamiento con los criterios. El cumplimiento del criterio de dosis se asoció con mejor conducta adaptativa -p menor que 0,05-, el cumplimiento de los criterios de duración y polifarmacia se asociaron con menores problemas de conducta -p menor que 0,05-. No hubo asociación entre cumplimiento del criterio de indicación con la puntuación de problemas de conducta, ni de las habilidades adaptativas

Polyclonality of Concurrent Natural Populations of Alteromonas macleodii

We have analyzed a natural population of the marine bacterium, Alteromonas macleodii, from a single sample of seawater to evaluate the genomic diversity present. We performed full genome sequencing of four isolates and 161 metagenomic fosmid clones, all of which were assigned to A. macleodii by sequence similarity. Out of the four strain genomes, A. macleodii deep ecotype (AltDE1) represented a different genome, whereas AltDE2 and AltDE3 were identical to the previously described AltDE. Although the core genome (∼80%) had an average nucleotide identity of 98.51%, both AltDE and AltDE1 contained flexible genomic islands (fGIs), that is, genomic islands present in both genomes in the same genomic context but having different gene content. Some of the fGIs encode cell surface receptors known to be phage recognition targets, such as the O-chain of the lipopolysaccharide, whereas others have genes involved in physiological traits (e.g., nutrient transport, degradation, and metal resistance) denoting microniche specialization. The presence in metagenomic fosmids of genomic fragments differing from the sequenced strain genomes, together with the presence of new fGIs, indicates that there are at least two more A. macleodii clones present. The availability of three or more sequences overlapping the same genomic region also allowed us to estimate the frequency and distribution of recombination events among these different clones, indicating that these clustered near the genomic islands. The results indicate that this natural A. macleodii population has multiple clones with a potential for different phage susceptibility and exploitation of resources, within a seemingly unstructured habitat

Association of a single nucleotide polymorphism combination pattern of the Klotho gene with non-cardiovascular death in patients with chronic kidney disease

Chronic kidney disease (CKD) is associated with an elevated risk of all-cause mortality, with cardiovascular death being extensively investigated. However, non-cardiovascular mortality represents the biggest percentage, showing an evident increase in recent years. Klotho is a gene highly expressed in the kidney, with a clear influence on lifespan. Low levels of Klotho have been linked to CKD progression and adverse outcomes. Single nucleotide polymorphisms (SNPs) of the Klotho gene have been associated with several diseases, but studies investigating the association of Klotho SNPs with noncardiovascular death in CKD populations are lacking. The main aim of this study was to assess whether 11 Klotho SNPs were associated with non-cardiovascular death in a subpopulation of the National Observatory of Atherosclerosis in Nephrology (NEFRONA) study (n ¼ 2185 CKD patients). After 48 months of follow-up, 62 cardiovascular deaths and 108 non-cardiovascular deaths were recorded. We identified a high non-cardiovascular death risk combination of SNPs corresponding to individuals carrying the most frequent allele (G) at rs562020, the rare allele (C) at rs2283368 and homozygotes for the rare allele (G) at rs2320762 (rs562020 GG/AG þ rs2283368 CC/CT þ rs2320762 GG). Among the patients with the three SNPs genotyped (n ¼ 1016), 75 (7.4%) showed this combination. Furthermore, 95 (9.3%) patients showed a low-risk combination carrying all the opposite genotypes (rs562020 AA þ rs2283368 TT þ rs2320762 GT/TT). All the other combinations [n ¼ 846 (83.3%)] were considered as normal risk. Using competing risk regression analysis, we confirmed that the proposed combinations are independently associated with a higher fhazard ratio [HR] 3.28 [confidence interval (CI) 1.51-7.12]g and lower [HR 6 × 10- (95% CI 3.3 × 10--1.1 × 10-)] risk of suffering a non-cardiovascular death in the CKD population of the NEFRONA cohort compared with patients with the normal-risk combination. Determination of three SNPs of the Klotho gene could help in the prediction of non-cardiovascular death in CKD