Reconstructing pedigrees using probabilistic analysis of ISSR amplification

Data obtained from ISSR amplification may readily be extracted but only allows us to know, for each gene, if a specific allele is present or not. From this partial information we provide a probabilistic method to reconstruct the pedigree corresponding to some families of diploid cultivars. This method consists in determining for each individual what is the most likely couple of parent pair amongst all older individuals, according to some probability measure. The construction of this measure bears on the fact that the probability to observe the specific alleles in the child, given the status of the parents does not depend on the generation and is the same for each gene. This assumption is then justified from a convergence result of gene frequencies which is proved here. Our reconstruction method is applied to a family of 85 living accessions representing the common broom {\it Cytisus scoparius}.Comment: 5 figure

Estimating genealogies from linked marker data: a Bayesian approach

<p>Abstract</p> <p>Background</p> <p>Answers to several fundamental questions in statistical genetics would ideally require knowledge of the ancestral pedigree and of the gene flow therein. A few examples of such questions are haplotype estimation, relatedness and relationship estimation, gene mapping by combining pedigree and linkage disequilibrium information, and estimation of population structure.</p> <p>Results</p> <p>We present a probabilistic method for genealogy reconstruction. Starting with a group of genotyped individuals from some population isolate, we explore the state space of their possible ancestral histories under our Bayesian model by using Markov chain Monte Carlo (MCMC) sampling techniques. The main contribution of our work is the development of sampling algorithms in the resulting vast state space with highly dependent variables. The main drawback is the computational complexity that limits the time horizon within which explicit reconstructions can be carried out in practice.</p> <p>Conclusion</p> <p>The estimates for IBD (identity-by-descent) and haplotype distributions are tested in several settings using simulated data. The results appear to be promising for a further development of the method.</p

Wolf outside, dog inside? The genomic make-up of the Czechoslovakian Wolfdog

Background Genomic methods can provide extraordinary tools to explore the genetic background of wild species and domestic breeds, optimize breeding practices, monitor and limit the spread of recessive diseases, and discourage illegal crossings. In this study we analysed a panel of 170k Single Nucleotide Polymorphisms with a combination of multivariate, Bayesian and outlier gene approaches to examine the genome-wide diversity and inbreeding levels in a recent wolf x dog cross-breed, the Czechoslovakian Wolfdog, which is becoming increasingly popular across Europe. Results Pairwise FST values, multivariate and assignment procedures indicated that the Czechoslovakian Wolfdog was significantly differentiated from all the other analysed breeds and also well-distinguished from both parental populations (Carpathian wolves and German Shepherds). Coherently with the low number of founders involved in the breed selection, the individual inbreeding levels calculated from homozygosity regions were relatively high and comparable with those derived from the pedigree data. In contrast, the coefficient of relatedness between individuals estimated from the pedigrees often underestimated the identity-by-descent scores determined using genetic profiles. The timing of the admixture and the effective population size trends estimated from the LD patterns reflected the documented history of the breed. Ancestry reconstruction methods identified more than 300 genes with excess of wolf ancestry compared to random expectations, mainly related to key morphological features, and more than 2000 genes with excess of dog ancestry, playing important roles in lipid metabolism, in the regulation of circadian rhythms, in learning and memory processes, and in sociability, such as the COMT gene, which has been described as a candidate gene for the latter trait in dogs. Conclusions In this study we successfully applied genome-wide procedures to reconstruct the history of the Czechoslovakian Wolfdog, assess individual wolf ancestry proportions and, thanks to the availability of a well-annotated reference genome, identify possible candidate genes for wolf-like and dog-like phenotypic traits typical of this breed, including commonly inherited disorders. Moreover, through the identification of ancestry-informative markers, these genomic approaches could provide tools for forensic applications to unmask illegal crossings with wolves and uncontrolled trades of recent and undeclared wolfdog hybrids