Using genomic information to conserve genetic diversity in livestock

Concern about the status of livestock breeds and their conservation has increased as selection and small population sizes caused loss of genetic diversity. Meanwhile, dense SNP chips and whole genome sequences (WGS) became available, providing opportunities to accurately quantify the impact of selection on genetic diversity and develop tools to better preserve such genetic diversity for long-term perspectives. This thesis aimed to infer the impact of selection and mitigate its effects on genetic diversity using genomic information. One of the advantages of WGS information, compared to pedigree and SNP chip information, is that it provides information on all variants, including rare ones, and ‘true’ relationships between individuals may be estimated thus being useful for evaluating genetic diversity. Taking into account rare variants had significant effects on estimated relationships. Moreover, optimal contribution (OC) strategy was used to perform selection either in a breeding program, maximising genetic merit while minimising loss of genetic diversity, or to build a gene bank, only maximising the conserved genetic diversity, with the aim to quantify loss of genetic diversity due to selection decisions. More genetic diversity was conserved when genomic information was used for selection decisions instead of pedigree and WGS information revealed a high loss of genetic diversity due to losing rare variants. Ways to reduce the loss of genetic diversity during a genomic selection program were investigated. The choice of individuals to update the reference population was proposed as a promising way to better conserve genetic diversity in a breeding population. In fact, changes in the reference population will lead to changes in prediction equations and thus ultimately to a shift in long-term selection decisions. Differences between reference population design using either random, truncation or OC selection of individuals, on the breeding population were modest but OC achieved conservation of more genetic diversity in the breeding population with only a small reduction in long-term genetic gain. Finally the potential of gene bank material as additional source of genetic diversity in the breeding population was examined, using the Dutch MRY cattle breed as a case study. Including old bulls, containing more genetic diversity than recent bulls, in the population of fathers for the next generation, selected with OC, resulted in both a slightly higher genetic merit and more genetic diversity conserved. The impact of selection on genetic diversity can be monitored by estimating the loss of rare variants over time. For the long-term perspectives of populations it is important to use specialised methods and genomic information to balance between selection response and conservation of genetic diversity. </p

Aportes a la caracterización de la problemática del uso terapéutico del aceite de Cannabis en Córdoba, Argentina

Informe CIMEFil: Bustos Fierro, Carolina. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas; Argentina.Fil: Uema, Sonia Andrea Naeko. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Departamento de Ciencias Farmacéuticas; Argentina.Fil: Nuñez Montoya, Susana Carolina. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Departamento de Ciencias Farmacéuticas; Argentina.Fil: Nuñez Montoya, Susana Carolina. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto Multidisciplinario de Biología Vegetal; Argentina.Fil : Bertotto, María Eugenia. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas; ArgentinaFil: Eynard, M. Universidad Nacional de Córdoba. Facultad de Ciencias Médicas; Argentina.Fil : Armando, Pedro D. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Departamento de Farmacología; Argentina.Fil : Manzo, Pablo Gabriel Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Centro de Química Aplicada; Argentina.El uso terapéutico del aceite de “cannabis" (AC) es una problemática social que pone en tensión aspectos legales, sanitarios, científicos y culturales. En nuestra legislación nacional, el “cannabis” está clasificado como estupefaciente. Esta situación se traduce, en drogas de uso prohibido y presupuestas de peligrosidad para la salud. En Argentina, no se produce formalmente AC de manufactura de calidad, que asegure la pureza, uniformidad y un contenido estándar de cannabinoides. Sin embargo, una importante cantidad de personas lo emplean para el tratamiento de diversas patologías, los cuales son realizados en un contexto de informalidad terapéutica y donde la provisión del mismo se realiza por canales externos al sistema de salud, desconociendo su composición química, las dosificaciones a utilizar y la forma de realizar el seguimiento clínico de la evolución de la patología abordada.info:eu-repo/semantics/publishedVersionFil: Bustos Fierro, Carolina. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas; Argentina.Fil: Uema, Sonia Andrea Naeko. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Departamento de Ciencias Farmacéuticas; Argentina.Fil: Nuñez Montoya, Susana Carolina. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Departamento de Ciencias Farmacéuticas; Argentina.Fil: Nuñez Montoya, Susana Carolina. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto Multidisciplinario de Biología Vegetal; Argentina.Fil : Bertotto, María Eugenia. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas; ArgentinaFil: Eynard, M. Universidad Nacional de Córdoba. Facultad de Ciencias Médicas; Argentina.Fil : Armando, Pedro D. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Departamento de Farmacología; Argentina.Fil : Manzo, Pablo Gabriel Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Centro de Química Aplicada; Argentina

Complex population structure and haplotype patterns in the Western European honey bee from sequencing a large panel of haploid drones:Sequencing haploid honey bee drones

International audienceHoney bee subspecies originate from specific geographical areas in Africa, Europe and the Middle East, and beekeepers interested in specific phenotypes have imported genetic material to regions outside of the bees' original range for use either in pure lines or controlled crosses. Moreover, imported drones are present in the environment and mate naturally with queens from the local subspecies. The resulting admixture complicates population genetics analyses, and population stratification can be a major problem for association studies. To better understand Western European honey bee populations, we produced a whole genome sequence and single nucleotide polymorphism (SNP) genotype data set from 870 haploid drones and demonstrate its utility for the identification of nine genetic backgrounds and various degrees of admixture in a subset of 629 samples. Five backgrounds identified correspond to subspecies, two to isolated populations on islands and two to managed populations. We also highlight several large haplotype blocks, some of which coincide with the position of centromeres. The largest is 3.6 Mb long and represents 21% of chromosome 11, with two major haplotypes corresponding to the two dominant genetic backgrounds identified. This large naturally phased data set is available as a single vcf file that can now serve as a reference for subsequent populations genomics studies in the honey bee, such as (i) selecting individuals of verified homogeneous genetic backgrounds as references, (ii) imputing genotypes from a lower-density data set generated by an SNP-chip or by low-pass sequencing, or (iii) selecting SNPs compatible with the requirements of genotyping chips

Complex population structure and haplotype patterns in the Western European honey bee from sequencing a large panel of haploid drones

Honey bee subspecies originate from specific geographical areas in Africa, Europe and the Middle East, and beekeepers interested in specific phenotypes have imported genetic material to regions outside of the bees' original range for use either in pure lines or controlled crosses. Moreover, imported drones are present in the environment and mate naturally with queens from the local subspecies. The resulting admixture complicates population genetics analyses, and population stratification can be a major problem for association studies. To better understand Western European honey bee populations, we produced a whole genome sequence and single nucleotide polymorphism (SNP) genotype data set from 870 haploid drones and demonstrate its utility for the identification of nine genetic backgrounds and various degrees of admixture in a subset of 629 samples. Five backgrounds identified correspond to subspecies, two to isolated populations on islands and two to managed populations. We also highlight several large haplotype blocks, some of which coincide with the position of centromeres. The largest is 3.6 Mb long and represents 21% of chromosome 11, with two major haplotypes corresponding to the two dominant genetic backgrounds identified. This large naturally phased data set is available as a single vcf file that can now serve as a reference for subsequent populations genomics studies in the honey bee, such as (i) selecting individuals of verified homogeneous genetic backgrounds as references, (ii) imputing genotypes from a lower-density data set generated by an SNP-chip or by low-pass sequencing, or (iii) selecting SNPs compatible with the requirements of genotyping chips.This work was performed in collaboration with the GeT platform, Toulouse (France), a partner of the National Infrastructure France Génomique, thanks to support by the Commissariat aux Grands Invetissements (ANR-10-INBS-0009). Bioinformatics analyses were performed on the GenoToul Bioinfo computer cluster. This work was funded by a grant from the INRA Département de Génétique Animale (INRA Animal Genetics division) and by the SeqApiPop programme, funded by the FranceAgriMer grant 14-21-AT. We thank John Kefuss for helpful discussions. We thank Andrew Abrahams for providing honey bee samples from Colonsay (Scotland), the Association Conservatoire de l'Abeille Noire Bretonne (ACANB) for samples from Ouessant (France), CETA de Savoie for sample from Savoie, ADAPI for samples from Porquerolles and all beekeepers and bee breeders who kindly participated in this study by providing samples from their colonies.info:eu-repo/semantics/publishedVersio

Descriptive Analysis of the Varroa Non-Reproduction Trait in Honey Bee Colonies and Association with Other Traits Related to Varroa Resistance

In the current context of worldwide honey bee colony losses, among which the varroa mite plays a major role, the hope to improve honey bee health lies in part in the breeding of varroa resistant colonies. To do so, methods used to evaluate varroa resistance need better understanding. Repeatability and correlations between traits such as mite non-reproduction (MNR), varroa sensitive hygiene (VSH), and hygienic behavior are poorly known, due to practical limitations and to their underlying complexity. We investigate (i) the variability, (ii) the repeatability of the MNR score, and (iii) its correlation with other resistance traits. To reduce the inherent variability of MNR scores, we propose to apply an empirical Bayes correction. In the short-term (ten days), MNR had a modest repeatability of 0.4, whereas in the long-term (a month), it had a low repeatability of 0.2, similar to other resistance traits. Within our dataset, there was no correlation between MNR and VSH. Although MNR is amongst the most popular varroa resistance estimates in field studies, its underlying complex mechanism is not fully understood. Its lack of correlation with better described resistance traits and low repeatability suggest that MNR needs to be interpreted cautiously, especially when used for selection

Identification of runs of homozygosity in Western honey bees (<i>Apis mellifera</i>) using whole‐genome sequencing data

Runs of homozygosity (ROH) are continuous homozygous segments that arise through the transmission of haplotypes that are identical by descent. The length and distribution of ROH segments provide insights into the genetic diversity of populations and can be associated with selection signatures. Here, we analyzed reconstructed whole‐genome queen genotypes, from a pool‐seq data experiment including 265 Western honeybee colonies from Apis mellifera mellifera and Apis mellifera carnica. Integrating individual ROH patterns and admixture levels in a dynamic population network visualization allowed us to ascertain major differences between the two subspecies. Within A. m. mellifera, we identified well‐defined substructures according to the genetic origin of the queens. Despite the current applied conservation efforts, we pinpointed 79 admixed queens. Genomic inbreeding (F$_{ROH}$) strongly varied within and between the identified subpopulations. Conserved A. m. mellifera from Switzerland had the highest mean F$_{ROH}$ (3.39%), while queens originating from a conservation area in France, which were also highly admixed, showed significantly lower F$_{ROH}$ (0.45%). The majority of A. m. carnica queens were also highly admixed, except 12 purebred queens with a mean F$_{ROH}$ of 2.33%. Within the breed‐specific ROH islands, we identified 14 coding genes for A. m. mellifera and five for A. m. carnica, respectively. Local adaption of A. m. mellifera could be suggested by the identification of genes involved in the response to ultraviolet light (Crh‐BP, Uvop) and body size (Hex70a, Hex70b), while the A. m. carnica specific genes Cpr3 and Cpr4 are most likely associated with the lighter striping pattern, a morphological phenotype expected in this subspecies. We demonstrated that queen genotypes derived from pooled workers are useful tool to unravel the population dynamics in A. mellifera and provide fundamental information to conserve native honey bees

Dietary patterns and risk of urinary tract tumors: a multilevel analysis of individuals in rural and urban contexts

Introduction: Bladder cancer is the fourth most frequently diagnosed malignancy in males in Córdoba, Argentina. The evidence regarding an association between urinary tract tumors and dietary factors still remains controversial. Argentina has particular dietary habits, which have already been associated with cancer occurrence. Purposes: (a) To estimate the association of typical dietary patterns in Argentina on the occurrence of urinary tract tumors and (b) to assess the urban–rural context of residence and cancer occurrence dependency. Methods A case–control study of urinary tract tumors (n = 123, 41/82 cases/controls) was performed in Co´rdoba Province (Argentina), 2006–2011. A two-level logistic regression model was fitted, taking into account rural– urban residence. An exhaustive probabilistic sensitivity analysis (bias analysis) was performed. Results: Southern Cone pattern, characterized by red meat, starchy vegetables and wine consumptions (OR 1.75 high versus low level of adherence to the pattern), and a medium adherence to a high-sugar drinks pattern, with high loadings for soft drinks (OR 2.55), were associated with increasing risk of urinary tract tumors. High adherence to the latter pattern was inversely associated (OR 0.72). The occurrence of urinary tract tumors was also linked to place of residence (urban–rural), explaining more than 20 % of outcome variability and improving the above risk estimations. Conclusions: A high intake of red meat, starchy vegetables and wine, and a moderate intake of high-sugar drinks seem to be associated with increased risk of urinary tract tumors, with differences related to the context of residence.Fil: Pou, Sonia Alejandra. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Cordoba. Facultad de Medicina. Escuela de Nutricion. Cat.de Estadistica y Bioestasdística; ArgentinaFil: Niclis, Camila. Universidad Nacional de Cordoba. Facultad de Medicina. Escuela de Nutricion. Cat.de Estadistica y Bioestasdística; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Eynard, Aldo Renato. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Cordoba. Instituto de Investigaciones en Ciencias de la Salud; Argentina. Universidad Nacional de Córdoba. Facultad de Ciencias Médicas; ArgentinaFil: Diaz, Maria del Pilar. Universidad Nacional de Cordoba. Facultad de Medicina. Escuela de Nutricion. Cat.de Estadistica y Bioestasdística; Argentina. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Cordoba. Instituto de Investigaciones en Ciencias de la Salud; Argentin

Whole-genome sequence data uncover loss of genetic diversity due to selection

Background: Whole-genome sequence (WGS) data give access to more complete structural genetic information of individuals, including rare variants, not fully covered by single nucleotide polymorphism chips. We used WGS to investigate the amount of genetic diversity remaining after selection using optimal contribution (OC), considering different methods to estimate the relationships used in OC. OC was applied to minimise average relatedness of the selection candidates and thus miminise the loss of genetic diversity in a conservation strategy, e.g. for establishment of gene bank collections. Furthermore, OC was used to maximise average genetic merit of the selection candidates at a given level of relatedness, similar to a genetic improvement strategy. In this study, we used data from 277 bulls from the 1000 bull genomes project. We measured genetic diversity as the number of variants still segregating after selection using WGS data, and compared strategies that targeted conservation of rare (minor allele frequenc

Cancer Mortality in Córdoba, Argentina, 1986–2006: An Age-Period-Cohort Analysis

Aims and background. Cancer is the second main cause of death in Argentina, surpassed only by cardiovascular disease. However, analytical approaches isolating some of the known effects, such as age at death, period of death and birth cohort, have never been performed in cancer mortality studies in Argentina. The aim of this study was to analyze cancer mortality trends in a representative region of the country, the Córdoba province (1986-2006). Methods and study design. Overall age-standardized (world population) mortality rates for cancer (all sites) were computed by a direct method. Joinpoint regression was fitted to the age-standardized mortality rates for both sexes to provide estimated and 95% confidence intervals of the annual percentage changes. The effects of age (15 age groups), period of death (1986-90, 1991-95, 1996-00 or 2001-06), and birth cohort (18 overlapping 10-year birth cohorts) covariates on mortality rates were estimated using a sequentially fitted Poisson regression model. Results. During the study period, 102,737 people died of cancer in Córdoba, with the age-standardized mortality rates decreasing from 139.3 to 118.7/100,000 personyears. Although this reduction was more noticeable in men, the joinpoint regression model showed a significant change of the age-standardized mortality rates after 1996 in both sexes. Age-period-cohort analysis suggested that the cancer mortality trends may be linked with a strong age effect and a moderate or mild period and cohort effect, related to sex and place of residence. Conclusions.Based on the observed cohort effect, it may be argued that there has been a lower exposure level to some risk factors, such as diet and other environmental factors, in Cordoba over the last decades. Free full text available at www.tumorionline.itFil: Pou, Sonia Alejandra. Universidad Nacional de Córdoba. Facultad de Matemática, Astronomía y Física; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; ArgentinaFil: Osella, Alberto Rubén. Istituto Nazionale Di Ricovero E Cura A Carattere Scientifico "saverio de Bellis". Laboratorio Di Epidemiologia E Biostatistica.; ItaliaFil: Eynard, Aldo Renato. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Cátedra de Biología Celular; Argentina. Universidad Nacional de Córdoba. Facultad de Medicina. Instituto de Biología Celular; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; ArgentinaFil: Diaz, Maria del Pilar. Universidad Nacional de Córdoba. Facultad de Medicina. Escuela de Nutrición. Cátedra de Estadística y Bioestadística; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; Argentin

MOESM2 of Whole-genome sequence data uncover loss of genetic diversity due to selection

Additional file 2. Pedigree subsets. Impact of using different pedigree subsets that are defined based on depth and completeness on genetic diversity conservation