A SNP based linkage map of the turkey genome reveals multiple intrachromosomal rearrangements between the Turkey and Chicken genomes

<p>Abstract</p> <p>Background</p> <p>The turkey (<it>Meleagris gallopavo</it>) is an important agricultural species that is the second largest contributor to the world's poultry meat production. The genomic resources of turkey provide turkey breeders with tools needed for the genetic improvement of commercial breeds of turkey for economically important traits. A linkage map of turkey is essential not only for the mapping of quantitative trait loci, but also as a framework to enable the assignment of sequence contigs to specific chromosomes. Comparative genomics with chicken provides insight into mechanisms of genome evolution and helps in identifying rare genomic events such as genomic rearrangements and duplications/deletions.</p> <p>Results</p> <p>Eighteen full sib families, comprising 1008 (35 F1 and 973 F2) birds, were genotyped for 775 single nucleotide polymorphisms (SNPs). Of the 775 SNPs, 570 were informative and used to construct a linkage map in turkey. The final map contains 531 markers in 28 linkage groups. The total genetic distance covered by these linkage groups is 2,324 centimorgans (cM) with the largest linkage group (81 loci) measuring 326 cM. Average marker interval for all markers across the 28 linkage groups is 4.6 cM. Comparative mapping of turkey and chicken revealed two inter-, and 57 intrachromosomal rearrangements between these two species.</p> <p>Conclusion</p> <p>Our turkey genetic map of 531 markers reveals a genome length of 2,324 cM. Our linkage map provides an improvement of previously published maps because of the more even distribution of the markers and because the map is completely based on SNP markers enabling easier and faster genotyping assays than the microsatellitemarkers used in previous linkage maps. Turkey and chicken are shown to have a highly conserved genomic structure with a relatively low number of inter-, and intrachromosomal rearrangements.</p

Evolutionary algorithms for the selection of single nucleotide polymorphisms

BACKGROUND: Large databases of single nucleotide polymorphisms (SNPs) are available for use in genomics studies. Typically, investigators must choose a subset of SNPs from these databases to employ in their studies. The choice of subset is influenced by many factors, including estimated or known reliability of the SNP, biochemical factors, intellectual property, cost, and effectiveness of the subset for mapping genes or identifying disease loci. We present an evolutionary algorithm for multiobjective SNP selection. RESULTS: We implemented a modified version of the Strength-Pareto Evolutionary Algorithm (SPEA2) in Java. Our implementation, Multiobjective Analyzer for Genetic Marker Acquisition (MAGMA), approximates the set of optimal trade-off solutions for large problems in minutes. This set is very useful for the design of large studies, including those oriented towards disease identification, genetic mapping, population studies, and haplotype-block elucidation. CONCLUSION: Evolutionary algorithms are particularly suited for optimization problems that involve multiple objectives and a complex search space on which exact methods such as exhaustive enumeration cannot be applied. They provide flexibility with respect to the problem formulation if a problem description evolves or changes. Results are produced as a trade-off front, allowing the user to make informed decisions when prioritizing factors. MAGMA is open source and available at . Evolutionary algorithms are well suited for many other applications in genomics

Genetic control and variation in turkey: molecular insights in selection

The turkey (Meleagris gallopavo) is an important agricultural species that is largely used as a meat type bird as egg production of this species is very low. Turkey is the second largest contributor to the world’s poultry meat production after chicken. Understanding the etiology and biology underlying production and health traits is very important for the genetic improvement of these traits in the desired direction and to avoid undesired side-effects. The aim of the research described in this thesis was to interrogate the genetics of turkey traits related to meat production and to investigate the genetic diversity of commercial and heritage turkey populations. Different analyses were performed that included the estimation of genetic and (common) environmental variances for growth (body weight as well as growth curve traits), breast meat yield and meat quality traits in turkeys. I describe the construction of a single nucleotide polymorphism (SNP) based linkage map of turkey and its comparison with the physical map of chicken to investigate genome structural differences between these highly important poultry production species. Two inter-, and 57 intra-chromosomal rearrangements between these two species were confirmed or discovered which is a low number in comparison to mammals and lead to the conclusion that turkey and chicken have highly conserved genomic structure. I used the linkage map of turkey together with individual phenotypes to map quantitative trait loci (QTL) in the same population for the traits described above. Results showed quantitative trait loci on 21 of the 27 turkey chromosomes covered by the linkage map. Forty-five quantitative trait loci were detected across all traits and these were found in 29 different regions on the 21 chromosomes. The next step, after the analyses on the reference population was to investigate the genomic variation in turkeys Next generation sequencing was used to investigate genome variation and the discovery of genome-wide signatures of selection in the turkey respectively. Sequencing was performed on 32 individuals from eleven different turkey populations (seven commercial, three heritage and a South Mexican wild population). Analysis of next generation sequencing data resulted in the detection of 5.49 million putative SNPs compared to the reference genome. The average frequency of heterozygous nucleotide positions in individual turkeys was 1.07 Kb-1 which is substantially lower than in chicken and pigs. The SNPs were subsequently used for the analysis of genetic diversity between the different populations. Genetic diversity analysis using pairwise Nei’s genetic distance among all the individuals from the 11 turkey populations showed that all of the commercial lines branched from a single node relative to the heritage varieties and the ancestral turkey population, indicating that commercial lines appear to share a common origin. After assessing genome wide variation and diversity between breeds, the SNP data from ten of the turkey populations (29 individuals) was used to detect selective sweep regions. Across the turkey populations, 54 genomic regions with significant evidence for a selective sweep were detected. These sweeps were distributed over 14 different chromosomes. This study has investigated the genetics i.e. analysis of variances and QTL mapping related to economically important traits in turkey production and the genomic variation of turkey. Furthermore, this study has also created resources e.g. millions of discovered SNPs for subsequent genomic work in the turkey such as to discover variant (s) for both minor and major effects on traits of economic importance, and a high-resolution linkage map can be developed. </p

Estudio de factores genéticos de los sistemas relacionados con estrés oxidativo

RESUMEN El riesgo de desarrollar una enfermedad cardiovascular en pacientes con hipertensión (HTA) se incrementa en más de 3 veces con respecto a otras enfermedades de elevado riesgo cardiovascular (diabetes, hipercolesterolemias, etc.), siendo además la HTA la mayor causa de mortalidad y morbilidad cardiovascular. La HTA se representa como una patología compleja que a menudo se asocia a otras alteraciones como microalbuminuria, disfunción endotelial, etc. Bajo estas condiciones fisiopatológicas se ha demostrado que se produce un aumento en la generación de especies oxidantes en el organismo, superando la capacidad de protección de los sistemas celulares de defensas antioxidantes, lo que provoca estrés oxidativo (EO). En la presente tesis doctoral se ha caracterizado el EO a nivel bioquímico y genético, mediante el análisis de los productos finales de EO, niveles de ARN mensajero y polimorfismos de genes implicados en la producción y defensa de EO y que pudieran afectar a la presión arterial y el daño orgánico. En este estudio se han analizado parámetros de EO como los glutatión reducido y oxidado, malondialdehido y 8-hidroxi 2-desoxiguanosina tanto en células mononucleares circulantes como en plasma de pacientes hipertensos (con y sin tratamientos) y en normotensos. Además, se han cuantificado los niveles de ARNm de los principales genes de estos sistemas, en linfocitos de hipertensos y controles (NADPHoxidasa, catalasa, superóxidos dismutasas y enzimas del sistema glutatión y tiorredoxina). Por otra parte, se ha realizado el estudio de variantes genéticas de genes de los sistemas implicados en EO, localizados en regiones que podrían afectar en la homeostasis oxidativa, lo que da lugar a alterarse la función de las proteínas y promotor región polimorfismos que alteran los niveles de EO como consecuencia de la regulación de genes. Esta parte del estudio se ha llevado a cabo en una población de hipertensos, controles y una población general. Los resultados obtenidos nos muestran que en la HTA esencial: 1. Exite un aumento en los niveles de estrés oxidativo tanto en plasma como en células monolinfocitarias y a su vez este aumento se ve correlacionado con los niveles de presión arterial (PA) de los sujetos. Además, el EO se relaciona con el aumento los niveles de excreción urinaria de albúmina (EUA) independientemente de los valores de PA. 2. Se produce un aumento de los niveles de ARNm de genes que codifican las distintas subunidades de NAD(P)H oxidasa y una disminución de los niveles de ARNm de las enzimas antioxidantes en monolinfocitos. Además, estos cambios se relacionan con el estado crónico de EO presente en la HTA, a pesar de la activación del sistema tiorredoxina y la enzima Manganeso Superóxido Dismutasa. Por tanto, los pacientes hipertensos tanto en presencia o en ausencia de microalbuminuria se encuentran peor protegidos frente a EO que los sujetos control. 3. Independientemente del tratamiento antihipertensivo utilizado, los niveles de los marcadores bioquímicos de EO se reducen, y también los niveles de ARNm de todas las enzimas implicadas. 4. Los análisis de asociación han mostrado que ciertas variantes, y sus haplotipos, se encuentran asociadas a niveles de EO, PA, EUA y riesgo de microalbuminuria en sujetos hipertensos. Hay que destacar que estos datos se han replicado en otra población de hipertensos y en la población general, donde se han mantenido dos de estas asociaciones. 5. En el análisis de asociación entre los polimorfismos de distintos genes observamos la interacción entre el gen de la XDH y GPX1 en la población hipertensa. Estas interacciones nos confirman la naturaleza compleja de esta patología y de la necesidad de enfocar las nuevas investigaciones hacia el estudio de las interacciones entre distintos genes y estos con los factores ambientales. __________________________________________________________________________________________________Hypertension is a complex disease that is often associated with other disorders such as microalbuminuria, endothelial dysfunction, etc. Under this pathophysiological condition has been shown that there is an increase in the generation of oxidizing species in the body, without being able to avoid the protection capacity of cellular antioxidant defense systems, leading to oxidative stress (OS). In this thesis OS status has been characterized by biochemical and genetic level of OS byproducts, messenger RNA levels and polymorphisms of oxidant and antioxidant system genes. The results have shown increased levels of oxidative stress in blood and peripheral mononuclear cells and this increase is correlated with levels of blood pressure (BP) in essential hypertension. Furthermore OS seems to be a determinant of urinary albumin excretion (UAE) independent of BP levels even in hypertensive subjects. The increase in mRNA levels of genes encoding different subunits of NAD(P)H oxidase complex and decreased mRNA levels of antioxidant enzymes in peripheral mononuclear cells, has been related to the chronic state of OS in the hypertension, despite the action of thioredoxin system and manganese superoxide dismutase enzyme. Thus, hypertensive patients in presence or absence of microalbuminuria are less protected from OS compared to control subjects. Furthermore, any type of antihypertensive treatment reduced the levels of OS, and therefore also the mRNA levels of all enzymes involved. The association analysis have confirmed that certain genetic variants, their haplotypes and their interactions, are associated with levels of OS, BP, UAE and microalbuminuria risk in hypertensive subjects. It should be noted that these results have been replicated in another hypertensive population and in spanish general population some associations have remained

Information management applied to bioinformatics

Bioinformatics, the discipline concerned with biological information management is essential in the post-genome era, where the complexity of data processing allows for contemporaneous multi level research including that at the genome level, transcriptome level, proteome level, the metabolome level, and the integration of these -omic studies towards gaining an understanding of biology at the systems level. This research is also having a major impact on disease research and drug discovery, particularly through pharmacogenomics studies. In this study innovative resources have been generated via the use of two case studies. One was of the Research & Development Genetics (RDG) department at AstraZeneca, Alderley Park and the other was of the Pharmacogenomics Group at the Sanger Institute in Cambridge UK. In the AstraZeneca case study senior scientists were interviewed using semi-structured interviews to determine information behaviour through the study scientific workflows. Document analysis was used to generate an understanding of the underpinning concepts and fonned one of the sources of context-dependent information on which the interview questions were based. The objectives of the Sanger Institute case study were slightly different as interviews were carried out with eight scientists together with the use of participation observation, to collect data to develop a database standard for one process of their Pharmacogenomics workflow. The results indicated that AstraZeneca would benefit through upgrading their data management solutions in the laboratory and by development of resources for the storage of data from larger scale projects such as whole genome scans. These studies will also generate very large amounts of data and the analysis of these will require more sophisticated statistical methods. At the Sanger Institute a minimum information standard was reported for the manual design of primers and included in a decision making tree developed for Polymerase Chain Reactions (PCRs). This tree also illustrates problems that can be encountered when designing primers along with procedures that can be taken to address such issues.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Investigation into the use of Single Nucleotide Polymorphisms for forensic identification purposes

Major limitations of the short tandem repeat (STR) loci that form the basis of criminal DNA databases are the 'partial' profiles that result from degradation of the longer repeat sequences. In contrast, Single Nucleotide Polymorphisms (SNPs) can be encompassed in smaller amplicons increasing the chance of amplification in degraded and limited samples. To aid SNP analysis a range of studies were performed including creation of the ASGOTH (Automated SNP Genotype Handler) software for rapid and accurate sample genotyping on microarrays. A multiplex assay for simultaneous detection of 20 SNPs plus a sex-determining locus by single-tube PCR amplification and electrophoretic detection was also developed. All loci conformed to Hardy- Weinberg equilibrium and showed independent inheritance. Computer simulations characterised the effects of inbreeding and supported the use of current STR Fst correction factors. Both paternity testing and kinship analysis were compared to STR DNA profiling results. Interpretation criteria were formulated for correct genotyping of the 21-SNP multiplex to control for stochastic variation at low DNA inputs. Each locus was individually characterised for allele dropout, homozygous thresholds and heterozygous balance. The performance of the 21-SNP multiplex on degraded samples was compared with the AMPF/STR SGMplus (SGM+) STR method currently used for the UK National DNA Database and other DNA profiling techniques used across Europe. Applying the 21-SNP multiplex to casework samples previously profiled using low copy number (LCN) SGM+ amplification indicated that partial SNP profiles could be generated in samples that had given partial LCN SGM+ profiles, but samples failing to amplify using LCN PCR parameters would also fail with SNPs. This study demonstrated the use of SNPs for human forensic identification purposes as an adjunct to current STR methods and has formed the basis of further work on degraded DNA and the design of the next generation of DNA profiling systems.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Investigation into the use of Single Nucleotide Polymorphisms for forensic identification purposes

Major limitations of the short tandem repeat (STR) loci that form the basis of criminal DNA databases are the 'partial' profiles that result from degradation of the longer repeat sequences. In contrast, Single Nucleotide Polymorphisms (SNPs) can be encompassed in smaller amplicons increasing the chance of amplification in degraded and limited samples. To aid SNP analysis a range of studies were performed including creation of the ASGOTH (Automated SNP Genotype Handler) software for rapid and accurate sample genotyping on microarrays. A multiplex assay for simultaneous detection of 20 SNPs plus a sex-determining locus by single-tube PCR amplification and electrophoretic detection was also developed. All loci conformed to Hardy- Weinberg equilibrium and showed independent inheritance. Computer simulations characterised the effects of inbreeding and supported the use of current STR Fst correction factors. Both paternity testing and kinship analysis were compared to STR DNA profiling results. Interpretation criteria were formulated for correct genotyping of the 21-SNP multiplex to control for stochastic variation at low DNA inputs. Each locus was individually characterised for allele dropout, homozygous thresholds and heterozygous balance. The performance of the 21-SNP multiplex on degraded samples was compared with the AMPF/STR SGMplus (SGM+) STR method currently used for the UK National DNA Database and other DNA profiling techniques used across Europe. Applying the 21-SNP multiplex to casework samples previously profiled using low copy number (LCN) SGM+ amplification indicated that partial SNP profiles could be generated in samples that had given partial LCN SGM+ profiles, but samples failing to amplify using LCN PCR parameters would also fail with SNPs. This study demonstrated the use of SNPs for human forensic identification purposes as an adjunct to current STR methods and has formed the basis of further work on degraded DNA and the design of the next generation of DNA profiling systems