A study of the effects of consanguinity at the genomic level in two Pakistani Bradaris

The purpose of the project was to assess the effects of inbreeding on the genetic constitution of two Pakistani bradaris (literally defined as brotherhoods). Both bradaris contain children born to consanguineous (first cousin) and nonconsanguineous marriages. DNA samples have been supplied by Dr Subaib Ahmed of the Armed Forces Institute of Pathology in Rawalpindi, for a total of 91 individuals. The specific allele frequencies, and levels of homozygosity of each bradari, were determined using twenty fluorescence-labelled microsatellite markers for chromosomes 13 and 15. Amplification of the DNA was performed using the polymerase chain reaction (PCR). The PCR products were separated electrophoretically on an ABI Prism 310 Genetic Analyzer, with GeneScan software employed to identify the alleles of each individual. Comparisons were made between the two bradaris, and between the bradaris and previously published data available from the GDB (Genome Data Base) and CEPH (Centre d\u27Etudes du Polymorphisme Hurnain). The level of homozygosity in each bradari was also compared to expected levels, calculated assuming random mating and with a correction for the inbreeding coefficient for each pedigree. The observed allele frequencies differed significantly between the bradaris for thirteen of the twenty markers. Allele frequencies in each bradari were also compared to the GDB and CEPH data and were found to be significantly different for all loci. The observed levels of homozygosity at each locus varied from 4% to 55% in the Khattar, and 3% to 40% in the Rajpoot. Observed homozygosity in each bradari was not statistically different from the GDB or CEPH data. Both the basic and corrected values for expected homozygosity were significantly greater than observed homozygosity in each bradari. An increase in homozygosity in the children of first cousin marriages was observed, however it was less than the predicted 6.25%. Lower than expected levels of homozygosity in the Pakistani families could indicate that there is preferential early selection against homozygotes in these families. There also appear to be reduced homozygosity levels in some regions of the two chromosomes, which may indicate that the resistance to homozygosity is specific to certain loci

Homozygosity, inbreeding and health in European populations

Inbreeding results in increased levels of homozygosity for deleterious recessive alleles, leading to increased incidence of monogenic disease in inbred families. It has also been suggested that inbreeding increases the risk of diseases such as cancer and heart disease, implying a role for the combined effects of many recessive alleles distributed across the genome. A better understanding of the links between inbreeding, homozygosity and disease is therefore of interest to those concerned with understanding the genetic architecture of complex disease. A homozygous genotype is defined as autozygous if both alleles originate from the same ancestor. Quantifying inbreeding involves quantifying autozygosity. A new, observational method of quantifying autozygosity using genomic data is developed here. Based on runs of homozygosity (ROH), this approach has a sound theoretical basis in the biological processes involved in inbreeding. It is also backed by strong empirical evidence, correlating strongly with pedigree-derived estimates of inbreeding and discriminating well between populations with different demographic histories. ROH are a signature of autozygosity, but not necessarily autozygosity of recent origin. Short ROH are shown to be abundant in demonstrably outbred individuals and it is suggested that this is a source of individual genetic variation which merits investigation as a disease risk factor, although denser genotype scans than those used in the present study are required for the reliable detection of very short ROH. In the absence of such dense scans, it is suggested that ROH longer than 1 or 1.5 Mb be used to estimate the effects of inbreeding on disease or quantitative physiological traits (QT), and that a simple measure of homozygosity be used to investigate overall recessive effects. Evidence for recessive effects on 13 QT important in cardiovascular and metabolic disease was investigated in 5 European isolate populations, characterised by heightened levels of inbreeding. A significant decrease in height was associated both with increased homozygosity and (to a lesser extent) with increased ROH longer than 5 Mb (i.e. inbreeding) estimated using a 300,000 SNP panel. No evidence was found for recessive effects on any of the other QTs. Evidence for recessive effects on colorectal cancer risk were investigated in two outbred case control samples typed with a 500,000 SNP panel. Cases were significantly more homozygous and had more of their genome in short ROH than did controls. Cases were significantly more homozygous than controls even when inbred individuals were removed from the sample. There was also some evidence of an inbreeding effect, with inbred subjects having slightly significantly higher odds of colorectal cancer than outbred subjects. This study provides evidence of recessive effects on a common, complex disease in outbred populations and on height in both inbred and outbred populations and shows that such effects are not solely attributable to increased levels of homozygosity resulting from recent inbreeding. Individual variation among outbred individuals in the proportion of the genome that is homozygous may be important in disease risk. The development of denser genotype scans will facilitate better enumeration of short ROH in outbred individuals so that these can be properly enumerated and investigated as a disease risk factor

Genetic admixture, inbreeding and heritability estimates in captive African cheetahs (Acinonyx jubatus) including linkage analysis for the King cheetah phenotype

This multifaceted study primarily aimed at understanding the genetic make-up of captive versus wild cheetah (Acinonyx jubatus) populations in South Africa, with a specific emphasis on a valuable gene pool of a recessive phenotype that is increasingly being maintained in captive population country-wide. The current literature on cheetah genetics has very little information on diversity levels of wild South African cheetahs, and no information on founder dynamics and genetic make-up of South African captive populations. Decisions on cheetah relocations are being made, implementing current conservation policy, from assumptions on origin and relatedness. This research compared population genetic parameters within the largest South African captive cheetah population to free-ranging Namibian and South African conspecifics. The study addressed concerns regarding excessive Namibian genetic introgression into the native captive population and established the extent of genetic variability and Namibian ancestry within the captive population. The study has attempted to address the rising concern among conservation officials with respect to illegal trade of wild-captured cheetahs, wild caught cheetahs that are sold as captive-bred after implanting a microchip. In addition to establishing routine parentage verification using genetic markers that are polymorphic in this species, this study established a technique powerful enough to estimate ancestry in cheetahs of unknown antecedents. The potential of spatial Bayesian clustering to differentiate the point of origin of unknown cheetahs was exploited and in addition, a database for future forensic efforts to address the problem of illegal trade was established. The captive population that was part of this dataset proved to be quite admixed, excepting for the King lineage which was distinct. The second aspect of this study investigated complex conditions such as development of gastritis, renal conditions and/or susceptibility to infections and its relation to pedigree and marker based inbreeding levels. Heritability values for important breeding traits were estimated from pedigree records of 532 cheetahs and are reported for the first time. Gastritis was weakly correlated to the expression of the King trait. Finally, a smaller cohort of the captive pedigree that segregates for a recessive colour variant called the King phenotype was tested for the assumption that the variation is a mutation of the tabby locus described in domestic cats. Genetic linkage analysis was done by testing microsatellite markers detected linked to Tabby for linkage to a conserved region in the cheetah that potentially codes for the King coat colour. Genetic linkage analysis was not detected between the King locus and the domestic cat microsatellite markers used for this study, with LOD scores remaining non-significant for all the markers.Thesis (PhD)--University of Pretoria, 2011.Production Animal Studiesunrestricte

Strategies to Eliminate Inherited Pigmentation in Australian Merino Sheep

The viability of eliminating inherited pigmentation from the Australian Merino flock by DNA technology was investigated as a means of reducing dark fibre contamination of white wool. Two genetically distinct forms of inherited pigmentation are known. Symmetrical patterns follow simple recessive inheritance. Meanwhile the inheritance of piebald spots is uncertain. Inheritance models for piebald were assessed against new and prior field records to resolve this point, but a clear-cut conclusion was not possible at this time - further field experimentation is required. Gene discovery for Mendelian characters by homozygosity mapping was reviewed and applied in simulation to livestock situations. The method was found to be efficient, powerful, robust, and readily adaptable to a wide range of gene discovery problems. In particular, modifications to the design of HM to suit livestock had a relatively small effect on experimental power in many cases. For a ram-breeding flock, paternal culling in addition to phenotypic culling was found to be a highly effective strategy to reduce the frequency of undesirable pigmentation alleles as well as being cost-effective through reduction in the incidence of pigmented phenotypes. Taking steps to minimise allele frequency prior to the commencement of DNA gene testing also gave large benefits. When DNA gene testing becomes available, early adoption and rapid elimination of pigmentation alleles were found to be preferable in most situations for ram breeding flocks. The costs of eliminating pigmentation alleles and the concomitant loss of selection intensity were found to be inversely proportional to the initial allele frequency. Across a spectrum of inheritance models (excluding simple dominance) the particular inheritance model had little additional effect. An efficient testing strategy could significantly reduce costs. Economic analysis at the industry level has revealed the key costs and sources of revenue which would be affected by eliminating inherited pigmentation. While many factors were difficult to specify, the cost of DNA testing emerged as the most critical factor. This study has demonstrated the technical potential of DNA technology to reveal many of the missing pieces of the puzzle of inherited pigmentation and its elimination from Merino flocks. DNA technology is vital to both gene discovery and gene testing for the presence of undesirable pigmentation alleles, and no practical alternatives exist. The economic viability of widespread DNA gene testing is subject to many uncertainties at this time. However many industry players are keen to adopt gene testing even at quite a high test cost and the trend for the cost of a new technology to decline over time would improve the financial outcome. Meanwhile, indirect benefits through enhancing the reputation of Australian apparel wool could be substantial. While the uncertainty over the eventual returns from investments in research should prompt some caution, continuation of research in this field is encouraged

Characterization of the genetic structure of the azorean population

Tese de doutoramento em Bioquímica (Genética Molecular), apresentada à Universidade de Lisboa através da Faculdade de Ciências, 200

Analyses of Genetic Diversity in the Endangered “Berrenda” Spanish Cattle Breeds Using Pedigree Data

Pedigree analyses of two endangered cattle breeds were performed in order to study the structure and the genetic variability in their populations. Pedigree data were analyzed from 12,057 individuals belonging to the “Berrenda en Negro” cattle breed (BN) and 20,389 individuals belonging to the “Berrenda en Colorado” cattle breed (BC) that were born between 1983 and 2020. BN and BC reference populations (RP) were set up by 2300 and 3988 animals, respectively. The generation interval in BN and BC reference populations was equal to 6.50 and 6.92 years, respectively. The pedigree completeness level was 82.76% in BN and 79.57% in BC. The inbreeding rates were 4.5% in BN and 3.4% in BC, respectively. The relationship among animals when they were born in different herds was 1.8% in BN and 5% in BC; these values increased to 8.5% and 7.7%, respectively when comparing animals that were born in the same herd. The effective number of founding herds was 23.9 in BN and 60.9 in BC. Number of ancestors needed to explain 50% of genes pool in the whole population was 50 and 101, in BN and in BC, respectively. The effective population size based on co-ancestries was 92.28 in BN and 169.92 in BC. The genetic variability has been maintained in both populations over time and the results of this study suggest that measures to promote the conservation of the genetic variability in these two breeds would go through for the exchange of breeding animals among farms and for monitoring the genetic contributions before implementing any selective action