Summary
A computerized procedure to construct integrated genetic maps is presented. The computer program (Join Map) can handle raw data from F2s, backcrosses and recombinant inbred lines, as well as listed pair-wise recombination frequencies. The procedure is useful for combining linkage data that have been collected in different experiments; the result is a mathematical alignment of the distinct genetic maps. Data from single experiments can be dealt with as well. In view of the fast growing amount of linkage information for molecular markers, which is often being generated by different research groups, integrated maps provide useful information on the map position of genes and DNA markers.

The procedure performs a sequential build-up of the map and, at each step, a numerical search for the best fitting order of markers. Weighted least squares is used for the estimation of map distances.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-313X.1993.00739.x

Construction of integrated genetic linkage maps by means of a new computer package: JOINMAP.

Publisher Summary In this chapter linkage and centromere data from neurospora crassa have been compiled from all published material, as well as unpublished sources Tetrad data from gene–centromere and gene–gene intervals have been placed on a uniform basis for mapping by computing map lengths from second-division segregation frequencies and tetratype segregation frequencies, respectively Maps of the seven linkage groups have been constructed from tetrad data Seventy-five loci are shown Confidence limits are indicated for the position of each locus Two sets of maps are presented, the first is completely uncorrected for multiple crossovers and the second is corrected by means of the mapping function A few additional genes have been assigned to specific linkage groups on the basis of random isolates The use of random isolates for mapping is also discussed

Map construction in Neurospora crassa.

In analyzing genetic linkage data it is common to assume that the locations of crossovers along a chromosome follow a Poisson process, whereas it has long been known that this assumption does not fit the data. In many organisms it appears that the presence of a crossover inhibits the formation of another nearby, a phenomenon known as "interference." We discuss several point process models for recombination that incorporate position interference but assume no chromatid interference. Using stochastic simulation, we are able to fit the models to a multilocus Drosophila dataset by the method of maximum likelihood. We find that some biologically inspired point process models incorporating one or two additional parameters provide a dramatically better fit to the data than the usual "no-interference" Poisson model.

/pdf/modeling-interference-in-genetic-recombination-2ba5w1cyrl.pdf

Modeling interference in genetic recombination.

Disease-susceptibility loci are now being mapped via genomewide scans in which a linkage statistic is computed at each of a large number of markers. Such disease-susceptibility loci may be identified via a peak in the test statistic when the latter is plotted against the genetic map. In this paper we establish, by appealing to renewal theory, that true positive peaks are expected to be longer than false positive peaks. These results are verified by a realistic simulation of a genomewide linkage study based on the affected-sib-pair design. Since longer peaks are more likely to contain a gene of interest than are shorter peaks, these differences may aid in linkage mapping, justifying assignment of lower priority to shorter peaks. However, since these differences are generally small, statistics based on both peak length and height may not be much more powerful than those based on height alone. The results presented here also provide a theoretical framework for methods that use the length of shared haplotypes in populations to map disease genes.

True and False Positive Peaks in Genomewide Scans: Applications of Length-Biased Sampling to Linkage Mapping

U NDER the title “Fifty Years Ago: The Neurospora Revolution,” HOROWITZ (1 99 1) has celebrated an anniversary of the epochal 1941 paper of BEADLE and TATUM, which reported the first mutants with biochemically defined nutritional requirements. HOROWITZ’S account and others (HOROWITZ 1973, 1985, 1990; LEDERBERC 1990) have focused on the people who were involved, the genesis of their ideas, and the role of the 1941 results in transforming biology. The present essay will be concerned mainly with the research organism that was so important to the success of the initial experiments. Neurospora possesses a combination of features that made it an ideal choice not only for accomplishing the original objectives set by BEADLE and TATUM but also for a continuing succession of contributions, including many in areas that transgress the bounds of biochemical genetics and molecular biology. 1 shall begin by outlining the story of Neurospora prior to BEADLE and TATUM and then go on to sketch its subsequent history. The previous accounts have stressed biochemical genetics and molecular biology. I shall consider other aspects as well, focusing first on genetics, continuing with a summary of research accomplishments of all sorts, and concluding with a consideration of the potential usefulness of Neurospora for population studies. The vegetative phase of Neurospora was described and used for experiments by French microbiologists nearly 100 years before BEADLE and TATUM (PAYEN 1843; MONTAGNE 1843). In the warm, humid summer of 1842, bread from bakeries in Paris was spoiled by massive growth of an orange mold. A commission was set up by the minister of war to investigate the cause of the infestation and to make recommendations. The commission’s report (PAYEN 1843) includes a colored plate which shows colonies, mycelia, conidiophores and conidia of the “champignons rouges du pain.” An experiment in photobiology is described. Colonies

https://www.genetics.org/content/genetics/130/4/687.full.pdf

Neurospora: The Organism behind the Molecular Revolution

Publisher Summary The aim of genetical research is to determine the topography of the genetical material in various organisms and to represent the mutable genes on each chromosome as occupying positions on a linear map. The order and spacing of the genes in the main has to be inferred from the amounts of recombination exhibited by sets of genes when appropriately designed backcross experiments are carried out, though this process is, occasionally, aided by cytological studies and the artificial production of rearrangements. This chapter highlights the recent mathematical developments and the cytological evidence on which its main ideas are founded, and to give a survey, arranged partly in historical and partly in logical order, of the development of the theoretical concepts involved in the study of linkage. The focus is on the normal situations in diploids, as the theory of linkage in polysomic inheritance is relatively far less advanced. The whole subject of estimation of recombination values is omitted; all though it is of extreme practical importance it is not directly relevant.

The theory of genetical recombination.

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The theory of genetical recombination.